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User Guide: Imaging

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1. Front Battery Holder Front Rear 6 rlrr ae 3 lo 4 Jo Front Rear Front Rear q4 Bottom 5 O 6 lo Top Retaining Screws Figure 103 Battery Replacement Procedure 1 Locate and remove the two retaining screws that hold the black plastic flange around the rear panel of the preamplifier 2 Remove the black plastic flange using a small Phillips screw driver 3 Slide the lower cover of the unit to reveal the battery holder 4 Lift the edge of the battery holder closest to the front panel upwards and slide the old battery out of the holder 5 Insert the fresh battery into the battery holder Make sure that the metallic terminals of the battery face the side of the holder that is wired to the internal circuit board 6 Replace the black plastic flange 212 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 9 2 Hardware Description Before reassembling the unit check the function of the new battery by turning on the power to the unit The LED in the optical fiber jack should light and the low battery indicator should remain dim If this test is successful power off the unit If the new battery does not cause the LED in the optical fiber jack to light during power up then the unit has failed the battery is incorrectly inserted into the internal holder or the battery itself is exhausted Try another battery Persistent failure of the optical fiber LED to light d
2. Figure 133 Interactive Image Planning Interface Select Tilt and rotate the stack to the desired orientation with the left mouse button Add slices to the stack by clicking near the in the Slice box or remove slices by clicking near the 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 253 Chapter 11 Interactive Image Planning 254 Table 23 iplan Controls Thickness Stretch Tilt Position Slice Spacing Exit Adjust the slice thickness The current value is displayed on the graphics area Adjust the width of the set of slices The width is the dimension orthogonal to the number of slices Therefore the size of a slice is defined by its width and thickness The width is also the width of the field of view Rotate the stack of slices about their center Adjust the position of the center of the stack of slices Add or subtract a slice to the stack Adjust the spacing between slices Therefore the number of slices their thickness and spacing determine the height of the field of view Exit the planning mode and show a list of experiments to be used as targets The menu above the display region also reflects the possible targets When you click one of these buttons the planning parameters are transferred to the target experiment ready for use Other planning operations include setting the width of the slices thickness of each slice and interslice spacing 6 W
3. User Guide Imaging Horizontal and Micro NMR Imaging With VNMR 6 1C Software Pub No 01 999163 00 Rev A0800 ave TAN VA AJ IAN User Guide Imaging Horizontal and Micro NMR Imaging With VNMR 6 1C Software Pub No 01 999163 00 Rev A0800 Revision history A0800 Initial release for VNMR 6 1C Applicability of manual Imaging modules on Varian NMR superconducting spectrometer systems with VnmrIMAGE version 4 4 software installed Technical contributors Simon Chu Matt Howitt Chris Price Alan Rath Subramaniam Sukumar Evan Williams Technical writers Michael Carlisle Dan Steele Technical editor Dan Steele Copyright 2000 by Varian Inc 3120 Hansen Way Palo Alto California 94304 http www varianinc com All rights reserved Printed in the United States The information in this document has been carefully checked and is believed to be entirely reliable However no responsibility is assumed for inaccuracies Statements in this document are not intended to create any warranty expressed or implied Specifications and performance characteristics of the software described in this manual may be changed at any time without notice Varian reserves the right to make changes in any products herein to improve reliability function or design Varian does not assume any liability arising out of the application or use of any product or circuit described herein neither does it convey any license under its
4. nocheck is a keyword to override checking if there is not enough free disk space for the complete 1D or 2D FID data set to be acquired nosafe is a keyword to disable probe protection during the experiment next is a keyword to put the experiment started with go next at the head of the queue of experiments to be submitted to acquisition 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 291 Appendix A Commands Macros and Parameters wait isa keyword to stop submission of experiments to acquisition until wexp processing of the experiment started with go wait is finished Examples go go nosafe Alternate Go button in the Acquire Menu Related acqi Interactive acquisition display process C au Submit experiment to acquisition and process data change Submit a change sample experiment to acquisition M gain Receiver gain P ga Submit experiment to acquisition and FT the result C gf Prepare parameters for FID spectrum display in acqi M go_ Pulse sequence setup macro called by go ga and au M load Load status of displayed shims P loc Location of sample in tray P lock Submit an Autolock experiment to acquisition C method Autoshim method P probe_protection Probe protection control P sample Submit change sample Autoshim exp to acquisition M seqfil Pulse sequence name P shim Submit an Autoshim experiment to acquisition C spin Submit a spin setup experiment to acquisition C spin Sample
5. A gradient power cable 00 967702 02 is cabled into the standard system gradient coil and rf shield during installation to provide quick disconnect capability for this coil The probe and bore equipment kit is designed to augment the standard system bore equipment to provide experimental capability for the HPAG gradient coil Auxiliary Gradient Coil The function of the 183 mm auxiliary gradient coil is to provide the static and switched magnetic field gradients required for imaging and spectroscopy experiments Figure 82 is a diagram of the coil The gradient coil is fitted with an internal rf shield spacing rings gradient power cable shim connector port thermocouple connector water connectors and hoses and a locking mechanism The following sections describe each part Internal RF Shield The rf shield prevents interference from external rf sources and leakage of rf power from the system during transmission The rf shield is completed by a pair of doors that fit on to both ends of the gradient coil Spacing Rings The spacing rings are used to adjust the position of the gradient coil inside the magnet bore These rings are adjusted during installation of the HPAG accessory to provide proper positioning of the gradient coil If the spacing rings become misaligned for any reason contact Varian Service to have them realigned Figure 83 shows a number of important connectors located on the rear housing of the coil The functions of th
6. Figure 32 Curve Control Point Note that if a 1 this reduces to a power function which is the case if the control point has x 0 5 If the control point is in region 2 the curve is reflected through the x y line This family of curves includes power functions of the form y xllb Eq 25 which applies if the control point is on the y 0 5 line If the control point is in region 3 or 4 the curves for regions 2 or 1 respectively are reflected through the x y 1 line Linear Mode The linear mode allows the user to specify a piecewise linear function that passes through all of the control points Any additional number of control points can be added by clicking the eft mouse button anywhere on the canvas away from an existing control point Control points can be deleted by clicking on them with the middle mouse button It is best to avoid large discontinuities in the slope of this function at the control points Due to the characteristics of human vision these discontinuities can make a surface that increases smoothly in intensity across a picture appear to be non monotonic in intensity For this reason the third mode might be more useful Spline Mode The spline mode is like linear mode except that a spline curve is drawn through the control points instead of straight lines It is also coupled to the linear mode in that the two modes VNMR 6 1C User Guide Imaging 01 999163 00 A0800 4 3 Graphics Tools share the same co
7. Slice Extraction Orientation First xy front on Maximum Intensity Projections MIPs can also be extracted by selecting the Extract MIPs button in the Slice Extraction window This option extracts up to three MIPs one for each orientation A MIP slice is created by assigning each pixel in a MIP the highest intensity of that pixel in any of the slices that would be extracted by the Extract Slices button To delete a data set from Image Browser memory select the data set in the File menu and press Unload however the file will not be deleted from the disk The separate program disp3d can be used to look at a 3D data set more directly and determine which slices are of interest See the manual VNMR Command and Parameter Reference for more information on disp3d If the Slice Extraction tool has been closed it can be opened again by selecting Slice Extractor from the Tools button menu Saving Files Select the Save menu item from the File option on the control panel to open a File Browser for saving files To save an image a graphics frame a ROI or a filter to a file make sure the desired item is selected then type or select an existing file name into the top line and click the Save button That item is saved in the current directory under the file name given 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 105 Chapter 4 Image Browser 106 Storing Images If more than one frame is selected all the images a
8. image 0 go epiph df2d 60 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 3 5 Echo Planar Imaging and Phase Correction Map Files epiph creates the phasemap file in the current experiment directory from the reference scan The first data array must correspond to the reference scan which is collected with the phase encode gradient turned off image 0 5 Acquire and display an EPI image a Enter the epirun macro epirun collects calculates and displays the EPI image epirun is used to obtain a single EPI image epirun is equivalent to executing the following commands go epift epift processes and displays EPI data in array number index it is used for EPI processing The first data array must contain the reference scan epift uses the command epirs which reverses spectral data b To display the image use the dconi command Other Ways to Collect Store and Process EPI Data EPI data processing requires a reference scan for calculating the phase map So you should collect and store the reference scan as part of the EPI dataset for later processing The following methods are other ways for collecting storing and processing EPI data Collecting Images You can use the image parameter to specify single or multiple images 1 To collect images set image to either of the following values image 0 1 One EPI image is obtained image 0 1 1 1 1 Four images are obtained as in a time course experiment image 0 refers to t
9. If the Show Saturation button at the top of the Gamma Correction window is selected pixels that are mapped to the maximum grayscale value are displayed yellow This button should normally be left off the Overflow button in the Vertical Scaling window essentially performs the same function VNMR 6 1C User Guide Imaging 01 999163 00 A0800 4 3 Graphics Tools VsProp Menu Unbind or Bind The last choice in the Vertical Scaling Properties menu is Bind or Unbind e If Unbind is displayed the current mode is bound and the images in all selected Gframes are rescaled the same as the one you click on e IfBind is displayed it means that the current mode is unbound Clicking the left button on an image affects only that image Math Tool The Math tool is used in conjunction with the Image Math processing window to enter Gframe numbers in mathematical expressions Position the mouse inside a Gframe and press the eft mouse button to insert the Gframe number in the math text window The Math Properties menu has no choices in it Chapter 5 Image Browser Math Processing has more information about this tool ROI Tools The following sections describe the tools that draw and modify regions of interest ROIs ROI Selector The ROI Selector tool is used to select and adjust any of the ROIs It is the aa default mode of the graphics tools After any ROI has been drawn a graphics aS tool reverts to the Selector tool In this mode both
10. Opening Image Browser Math this page e 5 2 Image Browser Math Expressions page 112 e 5 3 Image Browser Math Functions page 113 e 5 4 The Fit Program page 120 e 5 5 Problems with Image Browser Math page 127 Image Browser Math is used in conjunction with the Math Tool described previously in Chapter 4 Image Browser Image Browser Math provides a way to do more complex processing than image arithmetic but requires more processing overhead Instead of being limited to simple four function operations any function that can be expressed in the C language can be specified Operations in Image Browser Math are defined as either expressions or functions e Expressions are specified by typing any legal C expression into the Image Browser Math Panel using symbols such as 5 to specify images The expression is applied to each data pixel and each output data pixel value is a function of the values of the corresponding data pixels in the input images Operations can involve an arbitrary number of input images as well as the X and Y coordinates of the data pixel within the image e Functions are used for operations that cannot be specified in a single expression You write a C subroutine that performs the desired operations 5 1 Opening Image Browser Math Image Browser Math works on either 2D or 3D data sets For operations with expressions the image operands must all be the same size The following steps
11. The phase encode time t pe is set to 2 t rise and the phase encode increment is then computed in G cm to satisfy the expression y tpe lpe gpe 1 Some imaging sequences might internally alter the value of tpe with a corresponding change in gpe where timing of the sequence events allows set gpe performs these computations for each phase encode gradient A 2D sequence generally has one readout dimension and one phase encode dimension described by the parameters gpe sw1 and tpe A second or third phase encode dimension is described by the triad of parameters gpe sw2 tpe2 and gpe3 sw3 tpe3 respectively The spectral width associated with each phase encode dimension is computed as 1 tpe or 1 tpe2 etc and has no physical significance sw1 is present to provide compatibility with analytical 2D NMR data processing and display routines in VNMR The comprehensive setup macro imprep incorporates the functions of set gpe so that set gpe is not normally directly executed by the operator gpe Phase encoding gradient increment in DAC units P imprep Set up rf pulses imaging and pulse power levels M nv Number of phase encode steps forlst indirectly detected dim P setgro Set readout gradient strength and spectral width M setgss Set slice selection gradient strength M swl Spectral width in first indirectly detected dimension P tpe Duration of the phase encoding gradient pulse P Set readout gradient strength and spectra
12. stats Syntax Description 300 Examples VNMR 6 1C User Guide Imaging dimensions and header information against the processed data file and if there are differences rtphf fails For example any phasefile stored in phase sensitive mode cannot be successfully loaded into an experiment where the data has been processed in absolute value mode because the headers for absolute value and phase sensitive phasefiles differ see imcalc for hints Regarding errors an rt phf failure is not catastrophic that is it will not crash VNMR and will not harm the resident raw or processed data in any way But it will result in display of the previous phasefile found in datdir phasefile is the name of a stored phase file This file must have been saved previously with svphf or by some other process such as imcalc imfit or a user written program The named phasefile should be in the planes directory in the current experiment e g vnmrsys exp4 planes rtphf fleming imcalc Interactive prompt for imcalc M imconn Display 2D data without erasing the screen M svphf Save currently displayed phasefile to planes directory M Automatically set receiver gain M setgn Automatically determines the receiver gain based on the input signal gain Receiver gain P Load default single pulse sequence imaging parameters M spuls Loads s2pul pulse sequence parameters The parameters are initialized for imaging experiments For exam
13. t performs an inverse Fourier transform of the entire spectrum VNMR does not currently support inverse Fourier transformation of arrayed 1D or 2D data sets options can be any of the following all string arguments must precede the numeric arguments e acq isakeyword to check if any elements of a multi FID experiment have already been transformed If so these previously transformed elements will not be retransformed e nodc is a keyword to not perform the usual FID drift correction e nods is a keyword to prevent an automatic spectral display ds from occurring This outcome is useful for various plotting macros e noft is a keyword to skip the Fourier transform thereby allowing use of all spectral manipulation and plotting commands on FIDs e zero is a keyword to zero the imaginary channel of the FID prior to the Fourier transform This zeroing occurs after any FID phasing Its use is generally limited to wideline solids applications nf is a keyword that makes a single FID element containing nf traces to be transformed as if it were nf separate FID elements If nf precedes the list of numeric arguments the rules for interpreting the numeric arguments change slightly Passing no numeric arguments results in the transformation of all nf traces in the first FID element Passing a single numeric argument results in the transformation of all nf traces in the requested FID element e g ft nf 3 transforms all nf t
14. 1 x width 2 i y height 2 4 exp x x y y 2500 Note that in this example unlike the previous example 2500 is written as an integer because temporary variables x and y are floats that force the division to be done in floating point Using temporary variables like this often makes expressions more readable 5 3 Image Browser Math Functions Sometimes you might need to perform an operation that cannot be put into a single C expression such cases require user functions An Image Browser Math function is distinguished from an expression simply by whether the first field to the right of the equals sign is the name of an existing function The following example shows how user function foo is activated 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 113 Chapter 5 Image Browser Math Processing 114 11 foo 1 8 bar 7 Here the expression calls foo passes it images 1 through 8 the string bar and the number 7 as input and puts the output of foo in frame 11 Image Browser Math Function specifications are not parsed as C expressions so the syntax format is not strictly defined However for the sake of consistency and to be compatible with future versions use the style in the last example Note that double quotation marks s are required around every string argument to be passed Specifying Images in Functions Image Browser Math Functions allow lists or vectors of images to be specified The following form
15. 2 8 Image Reconstruction The imaging data is collected as a 2D arrayed time domain signal S t t2 in which t 1 and t 2 respectively refer to the phase encoding and readout dimensions For historic reasons in conventional 2D NMR the subscript numerals 1 and 2 respectively refer to the phase encoding and detection dimensions When the signals are viewed along either the phase encode or readout dimension the time domain signals take the form of an echo signal Fourier transformation with respect to t 1 and t 2 using the ft 2d routine yields the spatial frequency data S F1 F2 The symmetry properties of the echo signal yields only absorption mode components in the dataset S F1 F2 without any undesirable dispersion mode components The yield of only absorption mode components is a significant advantage in imaging because the final image can be obtained by simply taking the absolute value spectrum IS F1 F2 I without the need for any phase correction The appearance of the image can be improved or modified by digital filtering Filter functions can either be applied in the time domain or the spatial domain In the case of time domain data t 0 point is in the center of the time axis Therefore an apodization function symmetrical to t 0 should be applied For example a gaussian shifted function has the effect of improving the SNR of the resulting image at the expense of loss of resolution blurring of the image Anoth
16. Chapter 3 Imaging Pulse Sequences 10 11 12 13 Gradient calibration values are saved in a file in the vnmr imaging gradtables directory The gcoil parameter must be set to the correct gradient coil entry On systems with a single gradient coil assembly gcoil is usually set to main If the parameter gcoil does not exist in a parameter set and must be created you must set the protection bit that causes the macro _gcoil to be executed when the value for gcoil is changed There are two ways to create gcoil e Use the macro updtgcoil which will create the gcoil parameter if it does not exist and set the protection bits e Enter the following commands create gcoil string setprotect gcoil set 9 Set the imaging parameters Check and if necessary initialize all imaging parameters Table 5 on page 62 lists the parameters used in imaging Prepare the imaging parameters If any of the imaging parameters are altered the gradient strengths and or rf amplitude need to be re evaluated The imprep macro evaluates the new gradient and rf power levels Execute imprep before running an imaging sequence Optimize the rf power or flip angle imprep calculates the rf power level needed to generate a flip angle specified by the fliplist parameter the default is 30 For GEMS the power is usually set to correspond to about 10 to 30 To reduce the flip angle by a factor of two reduce the tpwr1 value by 6 dB Usin
17. Generating a Playlist Once a Movie Control panel appears a playlist can be started by selecting the Load Frames button which opens an empty Playlist window and a Movie Frame Loader window Now files can be browsed and images can be loaded into the playlist Put entries into the playlist by selecting the Load button or Load All button from the Movie Frame Loader menu When an image is loaded into the playlist it is also displayed in the currently selected Gframe Entries are always inserted in front of the currently selected line in the playlist To delete entries from the playlist choose an image name then select Delete When a playlist has been completed it can be saved as an FDF file so that it can be retrieved at a later time A playlist file consists of the fully qualified names of all the image files used in the movie Because there is no data associated with an FDF playlist file the file is in standard ASCII format and can be edited if desired Be aware that the files are specified as fully qualified names Therefore if the image files are moved or if they are found on different mount points on different workstations they might not be found when the playlist is later loaded However using the fully qualified name does allow more user flexibility with a personal directory structure when storing images Playing the Movie After the playlist has been constructed play the movie by selecting either Forward or Reverse in the Movie C
18. On systems with solids high power amplifiers never operate the amplifiers with a liquids probe The high power available from these amplifiers will destroy liquids probes Use the appropriate high power probe with the high power amplifier Take electrostatic discharge ESD precautions to avoid damage to sensitive electronic components Wear a grounded antistatic wristband or equivalent before touching any parts inside the doors and covers of the spectrometer system Also take ESD precautions when working near the exposed cable connectors on the back of the console Radio Frequency Emission Regulations The covers on the instrument form a barrier to radio frequency rf energy Removing any of the covers or modifying the instrument may lead to increased susceptibility to rf interference within the instrument and may increase the rf energy transmitted by the instrument in violation of regulations covering rf emissions It is the operator s responsibility to maintain the instrument in a condition that does not violate rf emission requirements 14 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Introduction This manual describes the parameters macros pulse sequences and general operating procedures used for imaging and localized spectroscopy experiments on Varian NMR spectrometers using VNMR version 6 1C The primary purpose of this manual is to document the Varian VnmrIMAGE advanced applications interface The manual contains
19. St Ingbert 1992 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 11 1 Introduction Chapter 11 Interactive Image Planning 11 1 Introduction You can perform interactive image planning on an image When you enter the command iplan the interactive image planning program opens The ip1lan macro also executes the transverse slice specification tool t box By choosing a button in the iplan graphics area you can stretch tilt and move the t box tool You can also adjust the number of slices and the area that they cover Clicking the Exit button executes the rsliceplan macro to load these settings for the next images 11 2 Starting the Planning Session To start planning 1 Open the scout image preferably more to the right of the display area Enter the command iplan A vertical column of boxes appears on the left side of the display area as shown in Figure 133 The cursor has also changed to a pointing hand The boxes are active controls that you can select with the cursor and a left mouse click Table 23 describes the controls Select Position Press and hold down the left mouse button and move the center of the current stack to the desired place on the image Release the mouse button Seq sems Exp 7 Index 35 CURSOR iplan o Abort Acq Box Trace Proj Full Redraw Plot Mark Return Cancel Cmd Menu On Main Menu Help Flip Resize Exit Vnmr
20. Using Baseline Correction Baseline correction can be performed by using sampled peaks or baselines The SINC correction method works with peaks and the Spline and Polynomial fitting methods work with baseline points To start sampling for the baseline correction 1 Define the selection parameters then click the Sampling Go option 2 After the initial sampling points have been placed on the spectrum use the Picking tool to augment baseline or peak points that have been missed 3 After the display points are satisfactory select Edit OK to save the displayed points for performing the correction 4 If the correction is satisfactory select the Correction OK option to save the correction values to be used with the Write all global correction mode To globally remove peaks on all the voxels or the selected voxels by using the Box ROD 1 Select the Correction OK option 2 Select the rm Peak item the Write all mode and the Apply to All option The following list describes the functions of the baseline correction processing attributes Sampling Item Selects Baseline or Peak Baseline sampling usually needs to be augmented by using the Picking tool Sampling Points Sets number It must be in the range of 10 to 20 Prior Knowledge Used with the Peak File PK File for peak sampling PK File List Prior Knowledge peak files stored in the SCSIDIR PEAK directory Sampling Phase Indicates which part of the complex data to sample R
21. c Maximum diameter of probe mm Imagine a sphere in the magnet center that completely contains the probe under investigation Take the diameter of the sphere increase it by roughly 20 and take the resulting value as the diameter of the field of view FOV of your BP image or volume d Number of points in profile np The number np refers to the number of points during acquisition real plus imaginary values Therefore np is twice the number of points in the reconstructed image For setting np use a power of 2 64 128 256 or 512 Table 21 lists the estimated acquisition and reconstruction times in the table TE is the spin echo time TR includes the recovery time and preparation time required and np 4 projections are assumed Note that measurement and reconstruction time does not increase linearly with the increasing np for 3D data sets Expected pixel resolution Hz The pixel resolution in Hz refers to linewidth of the probe For discrimination between two adjacent pixels having a Lorentzian lineshape on at least the 50 amplitude level the pixel resolution has to be greater than or equal to the linewidth This requirement can easily be met in biological samples In polymers usually only equality can be achieved In rigid materials the maximum gradient results in a limitation The macro bp_setup checks your value against the technical limitations internally 01 999163 00 A0800 VNMR 6 1C User Guide Imaging
22. m_center parameters 251 m_size parameter keyword 250 maclib directory 255 imaging subdirectory 17 255 macros 98 capabilities 99 directory 68 134 imaging 17 parameters as 99 recording 98 startup 103 storage See maclib user created running 290 01 999163 00 A0800 Index MAGICAL II macro programming language 67 98 magnet quench warning 12 magnetic resonance spectroscopy 26 magnetic media caution 13 magnetization recovery 315 magnitude calculation on profiles 249 main magnetic field strength 307 makephf macro 297 manipulating graphic frames 70 mapping function 83 149 markers creating 130 markvs macro 297 math command 103 Math tool 87 maximum gradient DAC value 309 maximum gradient strength for each axis 309 maximum intensity projection 98 mchelp command 249 mean filtering 96 measurement setup 227 median filtering 96 memory warnings threshold level setting 102 mems macro 260 MENU button 70 135 menus displaying 70 message area 131 meta_image filter 251 metabolic map 132 calculation 144 processing function 131 metal objects warning 11 microimaging gradient calibration constant 266 gradients 175 hardware 190 phase encoding 310 311 MIFF file format 107 mixing time constant definitions 197 modifying the instrument 12 modulation causes of 246 circular or spherical 246 mouse buttons 134 movepro macro 21 24 260 movetof macro 42 62 movie mode
23. necessary The Gamma Correction window has a plot at the bottom that graphs the pixel value between 0 and 255 against the index into the grayscale portion of Image Browser s colormap Pixel value is actually a color that has a red green and blue value but the grayscale always uses the same value for each color The graph background is painted with several rows of gray steps to demonstrate the current gamma correction The top row shows every step in the grayscale ramp the second row every other step the third row every fourth step and so on It appears to the eye that each ramp step is shaded from a lighter gray on the left to a darker gray on the right This is an optical illusion which can be seen by masking out the surroundings of one of the steps with a paper frame Ideally no steps should be visible anywhere in the top row but if the Image Browser colormap is fairly small like the 64 step default for 8 bit color machines they can be easily seen The goal of gamma correction then becomes to make each intensity step equally apparent to the eye For a short grayscale ramp this process can involve looking only at the top row of steps For a larger ramp the second or third row might need to be 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 85 Chapter 4 Image Browser 86 examined The size of the grayscale ramp is set in the colormap init file in the SBROWSERDIR directory See Initialization Directory pag
24. t4 In this equation is the phase in radians For a square pulse Figure 14 reduces to the following expression gt Y y gpe tpe Eq 15 In Equation 15 tpe is the phase encode time in sec VNMR 6 1C User Guide Imaging 01 999163 00 A0800 2 6 Image Resolution From Equation 15 it is clear that either t pe or gpe can influence the phase of the resulting NMR signal In the spin warp experiment the phase encode gradient is varied rather than the phase encode time from scan to scan in a stepwise manner Therefore the phase of the spins at location y are phase modulated in a predictable linear fashion The modulation frequency is directly proportional to the spatial location y Fourier transformation along the phase encoding direction converts the time domain and phase modulation into spatial frequency domain The field of view along the phase encode dimension is related to the gradient step size Therefore it is convenient to define the parameter pest ep which is equal to the incremental area of the phase encode gradient pulse defined by the following equation t7 Eq 16 pestep spe dt t4 The number of 2D phase encode steps to be acquired is determined by the parameter nv nv experiments are run when the phase encode gradients are set to the values defined by the following equation pestep n nv 1 2 Eq 17 In Equation 17 n 1 2 3 nv Equation 17 ensures an equal number of positive and ne
25. 241 242 duration 240 242 320 flip angle list 63 number control 238 242 pattern control 240 power level parameter list 341 power output 63 power calibrating 42 sequence execution controlling 338 01 999163 00 A0800 Index sequence parameters 233 setting power 43 shape 42 shape parameter list 340 specifying power for excitation pulse 64 specifying power output 63 width 285 pulse width of first pulse 340 specifying 63 pulsecal command 18 creating modifying deleting entry in rf calibration file 285 database 42 44 file 18 263 macro 62 updating database 62 285 pulses gradient setting limits for 204 pw parameter 42 63 234 240 pwpat parameter 42 240 244 Q QRS complex 208 QT interval 209 R r_center parameters 251 r_size parameter 251 radio frequency emission regulations 14 read button 195 readout compensation gradient 312 dimension resolution 36 field of view 324 gradient 33 gradient strength 311 position 326 specifying dimension length 63 receiver gain 42 50 63 reconstructed volume size 251 reconstruction backprojection process 225 macros 249 selecting filter type process 251 recovery time 240 recycle time adjusting 43 specifyiing 64 reference images reconstructing 132 parameters 233 reflect images 77 103 refocusing gradient for slice selection 313 parameters 20 refresh graphics frames 108 regions of interest See ROIs relief valv
26. 258 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 isis Related Syntax A 2 Macros for Setting Up Experiments dimension present The gradient t ime integral for the increment between phase encode levels is governed by the requirement that the spins at the edges of the field of view undergo a phase shift of 180 The phase encode time t pe is set to 2 t rise and the phase encode increment is then computed in G cm to satisfy the expression y tpe lpe gpe 1 Some imaging sequences might internally alter the value of tpe with a corresponding change in gpe where timing of the sequence events allows imprep performs these computations for each phase encode gradient found in the sequence A 2D sequence generally has one readout dimension and one phase encode dimension described by the parameters gpe swl and tpe A second or third phase encode dimension is described by the triad of parameters gpe2 sw2 tpe2 and sw3 gpe3 and tpe3 respectively The spectral width associated with each phase encode dimension is computed as 1 tpe or 1 tpe2 etc and has no physical significance sw1 is present to provide compatibility with analytical 2D NMR data processing and display routines in VNMR Slice and voxel selection gradients are computed by imprep based on the pulse lengths and shapes of all relevant pulses in the sequence imprep uses the gradient names found in sslist to determine which spatially selective gradients correspond to
27. Description Related slicemark Syntax Description Arguments See also Related sliceorder Syntax A 3 Macros for Planning Experiments Compute new imaging plane orientation and position From UNIX plane_decode psi phi theta xl yl zl x2 y2 z2 Computes the orientation and position for a new imaging plane using the coordinates of two points on a scout image plane_decode takes the coordinates of a pair of points in the logical imaging reference frame and the Euler angles that define the logical frame orientation and returns the orientation and position of an imaging slice that contains those points and is perpendicular to the scout image plane pl ane_decode is an executable macro command in vomr bin phi is the angular rotation of the image plane about a line normal to the image plane psi is formed by the projection of a line normal to the imaging plane onto the magnet XY plane and the magnet Y axis theta is formed by the line normal to the imaging plane and the magnet Z axis x1 y1 z1 x2 y2 z2 are the orientation and position of the new imaging plane returned from plane_decode orient Slice plane orientation P phi Euler angle for defining imaging plane orientation P psi Euler angle for defining imaging plane orientation P pss Slice position P theta Euler angle for defining imaging plane orientation P Interactive slice and voxel selection plan Displays a menu of interactive plann
28. PGM receiver 213 parameters 306 345 experiment control 333 flag 337 frequency 330 getting 47 image field of view 323 library 49 power level 341 pulse and gradient list 340 pulse length 341 pulse shape 340 retrieve from file 264 saving 63 302 special purpose orientation 329 spectral width 331 standard two pulse sequence setting up 264 354 VNMR 6 1C User Guide Imaging 285 300 target 341 voxel dimension 327 parameters setting 62 parlib directory 49 saving parameters in 47 PCD file format 107 pemap commands 56 63 298 299 pcemapgen command 56 63 298 PCX file format 107 PEAK file 134 pestep parameter 35 petable parameter 344 PFG calibration constant 266 PGM cardiac signal conditioning 223 component functions 210 file format 107 gating 223 hardware description 209 indicators 223 input 223 outputs 223 performance specifications 223 power 223 preamplifier battery replacement 209 receiver 213 signal detection 223 signal modulation 223 signal transfer 223 pH maps 131 132 166 phantom for gradient calibration constant 266 setup 248 phase adjustment 142 phase correction 131 159 EPI 58 map 63 298 299 map commands 56 map files 51 56 window 141 phase encoding 34 49 310 311 318 323 336 dimension resolution 36 steps 21 time 34 phasefiles 171 296 phi parameter 24 243 phi_ parameters 252 physical gradient set specifying 63 physiologica
29. Related trise Description Related System gradient coil Specially reserved configurational parameter that specifies which physical gradient set is currently installed and allows convenient updating of important gradient characteristics when one gradient set is interchanged for another The value to sysgcoil is assigned to the parameter gcoil when joining experiments or retrieving parameter sets VNMR and Solaris Software Installation boresize Magnet bore size P creategtable Generate new gradient calibration file M gcoill Current gradient coil P gmax Maximum gradient strength P setgcoil Assign sysgcoil configuration parameter M trise Gradient rise time P Gradient rise time The rise time to maximum gradient strength measured from 0 to 100 assuming a constant rise rate t rise is one of the calibration entries required ina gradtables file Its value should have been set and recorded at time of installation for gradient sets supplied by Varian boresize Magnet bore size P creategtable Generate new gradient calibration file M qcoil Current gradient coil P gmax Maximum gradient strength P sysgcoil System gradient coil P Imaging Gradient Parameters gpe Description Related gpe2 Description 310 Phase encode gradient increment Value of the change in phase encode gradient level from one phase encode step to the next More precisely the product of the parameters gpe and t pe is u
30. but the grayscale always uses the same value for each color The graph background is painted with several rows of gray steps to demonstrate the current gamma correction The top row shows every step in the grayscale ramp the second row every other step the third row every fourth step and so on It appears to the eye that each ramp step is shaded from a lighter gray on the left to a darker gray on the right This is an optical illusion which can be seen by masking out the surroundings of one of the steps with a paper frame 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 151 Chapter 6 CSI Data Processing 152 Ideally no steps should be visible anywhere in the top row but if the ImageBrowser colormap is fairly small like the 64 step default for 8 bit color machines they can be easily seen The goal of gamma correction then becomes to make each intensity step equally apparent to the eye For a short grayscale ramp this process can involve looking only at the top row of steps For a larger ramp the second or third row might need to be examined The size of the grayscale ramp is set in the colormap init file in the CSIDIR directory See Initialization Directory page 133 for details about CSI initialization Adjusting the Monitor Before adjusting the gamma correction adjust the monitor Some monitors have no easily accessible brightness control therefore monitor adjustment should be performed by a service person T
31. cardiac anatomy 207 electrode leads 215 PGM signal conditioning 223 preamplifier 210 trigger 218 cautions defined 11 cf parameter 24 change bar 16 changing color of ROI tool 88 directories 73 104 135 168 channel gain 191 checking gradient strength 236 chemical shift artifacts EPI 55 image See CSI circular or spherical modulation 246 clearing graphic frames 72 81 137 collecting EPI data 61 284 colormap init file 68 133 definition 68 133 commands Image Browser not in VNMR 100 compensation amplitudes 197 setting gain on 205 compressed data 2D converting 285 acquisition 333 348 VNMR 6 1C User Guide Imaging changing to standard 45 process 62 compressed GEMS data process 50 dataset convert 62 Compute Target button 23 contrast agent studies 47 image adjusting 51 controls cardiac preamplifier 210 PGM receiver 213 conventions used in manual 16 converting compressed 2D data to standard format 285 data in table order to linear order 303 convolution filters 69 coronal image orientation 20 63 cos_low_pass filter 251 counters 333 create command 99 creategtable macro 19 43 256 createpfgtable macro 256 creating animated images 67 backprojection images 226 gradient calibration file 43 graphic frames Gframes 70 markers 130 metabolic maps 132 credit cards caution 13 CSI command panel 130 135 csi command 134 Metabolic Map Display window
32. currently selected file on the top line image0011 fdf Just below that is the current directory The number of files in the directory is listed at the bottom There is a scrolling window that contains the names of all the files in the directory Subdirectories are indicated with a at the end of their name To select a name in the scrolling list position the cursor over the desired name and click the left mouse button 12 files Figure 77 FileBrowser Window Changing Directories Change directories by either double clicking on the directory name with the left mouse button by selecting the name so it appears in the top line and pressing the Return key or by entering the name directly in the top line and pressing the Return key Note that the UNIX prefix works in the FileBrowser The entry opens the parent directory Loading Files Select File from the command panel then select Load to open a FileBrowser for loading files To load a file into Image Browser select the desired file and press the Load option The file is loaded into the next available graphics frame To select a particular frame to load an image into immediately click on that frame before clicking the Load option To load all the files in the current directory click the Load All option Select the FDF file and click the Load option to load FDF files For VNMR phasefiles the directory that contains the phasefile must be selected when t
33. dsww Display spectra in whitewash mode C ftid Fourier transform along f dimension C ho Horizontal offset P intmod Integral display mode P pl Plot spectra C plww Plot spectra in whitewash mode C sc Start of chart P sc2 Start of chart in second direction P trace Mode for 2D data display P vo Vertical offset P vp Vertical position of spectrum P we Width of chart P wc2 Width of chart in second direction P 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 281 Appendix A Commands Macros and Parameters dssl Syntax Description Arguments Examples Related ecctool Applicability Label stacked spectra display M dssl lt options gt Displays a label for each spectrum in a set of stacked spectra Note that with wysiwyg n labels can appear at incorrect vertical positions scale is used in dss1 to compensate for a bug in write positioning Positions were empirically determined for a large screen and are not guaranteed to be correct for all displays The default label is an integer value starting with 1 and extending up to the number of spectra in the display Several options are available to control the position of the displayed index relative to each spectrum More than one nonconflicting option can be entered Positional options are e above displays a label just above the baseline of each spectrum e below displays a label just below the baseline of each spectrum
34. i_size i_size large Specifying i_size gt m_size results in an enlargement or in a reduction i_size lt m_size inthe number of pixels used This feature allows achieving a reconstruction for a fast inspection of large data set using reduction If i_size is not set bp_3d tries to obtain its value from the profile file and sets i_size m_size np 2 Number of projections used for the phi loop usually the same as ni n_phi has to be specified by the user and cannot be derived from the information given in the profile file The phi loop is the inner loop during acquisition Number of projections used for the theta loop usually the same as ni2 n_theta has to be specified by the user and cannot be derived from the information given in the profile file The theta loop is the outer loop during acquisition Controls the storage of profile data in memory in order to save overhead for disk I O thus accelerating the reconstruction process Generally in_memory_prof can be set to 1 if i_size lt 256 Otherwise setting in_memory_prof 0 is recommended to avoid keeping too much data in memory and causing unnecessary swapping to the hard disk Selects filter to be used in the reconstruction process Four different filters are implemented 1 band_pass is a purely magnitude like filter 2 si_low_pass is a magnitude filter modulated with a si sin x x function 3 cos_low_pass is a cosine modulated magnitude filter and 4 hamming is a Hamming
35. of the decctool window before actually performing the eddy current corrections Note Perform these tests with whatever gradient power supplies are in the system turned off or to standby mode We also recommend setting both the pulse width pw and the transmitter power t pwr to zero A good test sequence to use is GDACtest c although any sequence with a gradient pulse in it will work Use the front panel test points on the DECC board to monitor the compensation waveforms VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Chapter 9 Physiological Gating Module Sections in this chapter e 9 1 Cardiac Anatomy and Electrocardiography this page e 9 2 Hardware Description page 209 e 9 3 Experimental Setup page 216 e 9 4 Performance Specifications page 223 NMR is sensitive to motion Images from the thorax that contain moving objects such as the heart flowing blood and chest wall are often degraded by artifacts along the phase encoding or F1 direction of the image Referred to as motion artifacts they degrade image quality both close to the moving object blurring and away from the object ghosting With organs such as the heart image quality is often so badly degraded that details of the structure are completely obscured Such effects of motion upon image quality can be improved using a technique called prospective gating Prospective gating synchronizes the repetition of the imaging sequence with periodi
36. or an Other button enables you to type in an experiment number if the number you want is not displayed Because we previously moved parameters from experiment 2 to 6 the target experiment is the same in this case as the scout except that we are changing the slice position and orientation We could just as well have transferred the new slice parameters to a completely different imaging experiment as long as it uses the same parameters to define slice position and orientation At this point you are ready to start the new experiment Because we have not changed the field of view slice thickness or rf pulses there is no need to execute imprep again If you decide to change any of these settings just make sure you enter imprep again when everything is adjusted the way you want it Checking the FOV and Entering the go Command Before running the complete target image it is generally a good idea to make sure that the image is reasonably centered in the readout direction 1 Set nv 0 and then enter ga to get a projection and if necessary adjust the cursor and enter movepro 2 Set nv back to the proper number of phase encode steps and enter go 3 When complete t2d shows you the new target image If you planned a multislice image you have to set the c f parameter to select the slice you want remember unlike old imaging sequences the slices are in the order specified by the pss array and cf determines the array index The m
37. sw and at are related by the expression sw y lro gro but a change in 1 ro does not automatically update gro and sw Related at Acquisition time P gmax Maximum gradient strength P gror Read out dephasing gradient P imprep Set up rf pulses imaging and voxel selection gradients M 1o Field of view size for readout axis P setgro Set readout gradient M sw Spectral width in directly directed dimension P groa Readout gradient adjuster in EPI experiment P Applicability Systems with echo planar imaging EPI capabilities 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 311 Appendix A Commands Macros and Parameters Description Related gror Description Values Related grora Applicability Description Related gss Description Values Related gssf Description Corrects readout gradient imperfections in EPI experiment by adding an offset G cm to the odd readgradient episet Set up parameters for EPI experiment M grora Readout refocusing gradient adjuster in EPI experiment P tep Post acquisition delay in EPI experiment P Read out dephasing gradient Controls the level of the readout refocusing gradient when pilot n When pilot y gror is ignored by the pulse sequence and computed internally In this case the internal value is printed in the window used to start VNMR gror is opposite in sign to gro for gradient echo experiments e g FLASH and have the s
38. that will kill Image Browser 2 1 float 0 CAUTION Be careful when programming and testing new user functions Run time error messages can be found in the window from which Image Browser was started and a core dump file can be in the directory from which it was started Compilation Errors If an illegal expression is entered Image Browser does not generate a legal C program and the Error Messages window displays Math Program did not compile Compiler errors are also written into the window from which Image Browser was started Unfortunately these messages might be of limited use because the C program source is not available for inspection 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 127 Chapter 5 Image Browser Math Processing 128 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Chapter 6 CSI Data Processing Sections in this chapter e 6 1 Overview of CSI this page e 6 2 Getting Started page 133 e 6 3 Tools page 147 e 6 4 Processing Functions page 156 e 6 5 Files and Other Items page 167 CSI Data Processing is a tool based on the X Window System designed for the easy processing of chemical shift image CSI data It uses mouse oriented point and click methods to execute selection and processing requests The CSI tool was designed to process CSI data to obtain metabolic maps but other outputs can be obtained localized FID data multivoxel spectra individual spectrum
39. the next step to the target experiment You should see the target Euler angle values printed in the message window along with the slice position for the line you marked If you have defined a multislice target you also see the slice positions displayed in the text window at the bottom of the screen The newly defined slice position s are drawn over the scout image allowing you to visually verify that the target image s are properly aligned to pass through the desired sample features If the new slice position is unsatisfactory clear it and again perform the procedure to erase the old slice positions select Redraw before Compute Target Transferring the Target Parameters The new slice orientation and position parameters can now be communicated to the target experiment The parameters are the three Euler angles psi phi theta the slice position parameter pss and slice thickness parameter thk The parameter rfcoil is also transferred as well as resto if both experiments have the same tn 1 Select the Transfer menu button This button displays a new menu of possible experiment choices and a descriptive listing of each experiment in the text window this same list can be created at any time with the command exp1lib2 2 Select the experiment to transfer to in this case Exp 6 If there is not enough space to show a menu button for each experiment you might not see a Current button transfers internally to the current experiment
40. three major orientations specified by these combinations of phi psi and theta ir ns 0 0 0 Orientation theta psi phi Entering orient trans cor 90 0 0 automatically sets these sig 90 90 0 parameters to the proper values In all three cases phi is zero and its function is to rotate the imaging plane about the orientation vector Thus to reverse the readout and phase encode axes in an image set phi to 90 instead of 0 The three major imaging plane orientations are unique in their combinations of psi phi and theta and so can be easily represented with the designations transverse coronal and sagittal Orientations that do not lie in one of these major planes are oblique and have at least one of the Euler angle parameters set to a value other than 0 or 90 Since there are a nearly limitless number of oblique orientations any nonmajor orientation has have orient set to oblique indicating only that the Euler angle parameters describe a nonmajor plane Setting orient oblique does not determine a unique orientation so instead there are two mechanisms for specifying oblique planes The first is to enter a value of psi phi or theta that does not specify one of the major imaging planes for example t het a 45 The second is to follow the interactive planning procedure that allows graphical setup of imaging orientation from an existing scout image Either of these procedures automatically set orient to oblique
41. trans sag cor oblique dorient Diffusion gradient orientation P orient2 Other orientation P phi Euler angle for defining imaging plane orientation P plan Display menu for planning a target scan M pei Euler angle for defining imaging plane orientation P pss Slice position P sorient Saturation band gradient orientation P theta Euler angle for defining imaging plane orientation P vorient Voxel orientation P Euler angle for defining imaging plane orientation One of the three Euler angles used to define imaging plane orientation phi determines the angular rotation of the image plane about a line normal to the image plane phi is generally not set directly by the user but instead either by entering a string value into the orient parameter or through interactive graphical planning of a new imaging plane from an existing scout image phi can be used to rotate the readout axis into the phase encode axis and vice versa To do this add or subtract 90 to the current value of phi 180 to 180 in degrees rient Slice plane orientation P 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 325 Appendix A Commands Macros and Parameters pro psi pss 326 Description Values Related Description Values Related Description psi Euler angle for defining imaging plane orientation P theta Euler angle for defining imaging plane orientation P Position of image center on the re
42. 00 A0800 VNMR 6 1C User Guide Imaging 317 Appendix A Commands Macros and Parameters Related tm Description tpe Description Related tpe2 tpe3 Description Related tr Description 318 depends on the T relaxation time of the sample in different regions of the image if Inversion recovery mode P pi Width of an inversion pulse P pipat Shape of an inversion pulse P tpwri Inversion pulse power P Stimulated echo mixing time Time period in stimulated echo sequences between the second and third rf pulses tm is also used in the ISIS pulse sequence to specify the time between the last selective inversion pulse and the excitation pulse Duration of the phase encoding gradient pulse The length of the phase encoding gradient period in imaging and CSI experiments sw1 the spectral width in the indirect dimension is determined from tpe as sw1 1 tpe tpe can be recomputed within the pulse sequence to provide optimum performance such as minimum echo time or scaled to match the required timing for slice refocusing and readout dephasing gpe Phase encoding gradient increment in DAC units P nv Number of phase encode steps for 1st indirectly detected dim P swl Spectral width in 1st indirectly detected dimension P tpe2 tpe3 Duration of 2nd and 3rd phase encoding gradient periods P Duration of 2nd and 3rd phase encoding gradient periods Lengths of the phase encoding gradient periods that control second spati
43. 111 Chapter 6 CSI Data Processing ccsseeeeeeesseeeeeeeseseeeeeenseneeeeeseneeeeenees 129 Chapter 7 High Performance Auxiliary and Microimaging Gradients 175 Chapter 8 Digital Eddy Current Compensation c cccessseeeeesesseeeeeees 199 Chapter 9 Physiological Gating Module ccsssccccseseectssseeeeeseeeeeeeeees 207 Chapter 10 2D and 3D Backprojection ccsssscccsssseeeesesseneeeeseseeeeeenees 225 Chapter 11 Interactive Image Planning cssssscccssseeeeeeseeeeeeseeeeeeeenees 253 Appendix A Commands Macros and Parameters cccccssseeeeeeeeeeeeeeees 255 VON E E E E E E E ecient 347 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 3 4 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Table of Contents SAFETY PRECAUTIONS sisctisesnsinnnessnnatecisvastanssasarsdieainisarsdeteassdatennisasnidinssiianc 11 taldgels 101e 11o a MAE T E E E 15 Chapter 1 First Steps Making an Image ccsssseccessseeeeeeseeeeeeeeeseeeeeenseees 17 1 1 Making an Initial Scout Image o00 eee ceeeseceeceseceeeeseeeeeeeeeeeeseseaseaeeeaecaeeaeenaes 17 1 2 Using the Scout Image to Plan a New Target Image eee eeeeeeeceeceseeeeeeeeeeeees 22 Chapter 2 Imaging Experiments cccssseeccceseeeeeeessseeeeeesseeeeeeenseneeeenseees 25 2 1 Basic Imaging PHM ples ics ccseessscinaseiees Wisi ionces shsdt eueschevoawteastbesdhaveetienas a a EEE a 25 2 2 Time Domain to Spatial Domain
44. 1D transform of every data line which we don t want and go doesn t 2 When the image is complete enter t2d to see the result Uncommonly Used Parameters Although there is nearly a complete overlap in software between Varian s horizontal imaging vertical microimaging and standard analytical NMR systems there are a few parameters that are not normally used on a horizontal bore system If set incorrectly these parameters can lead to artifacts or positional errors in images It is therefore useful to check the following parameters on horizontal bore imaging machines Users with previous experience with the SISCO 93 1 version of VNMR software are particularly advised to learn about these parameters because they did not exist in version 93 1 load Determines how shim values are updated i e if they are obtained from the software settings in the current experiment or from the actual existing hardware settings Most Varian users are familiar with this but SISCO users new to Varian software should refer to the VNMR Command and Parameter Reference for more information solvent Used to fine tune the spectrometer frequency to compensate for the small reference field shifts caused by deuterium locking to different solvents Because most imaging experiments are performed without deuterium lock it is a good idea to set solvent none in all experiments including S2PUL for consistent frequency settings Failure to do this results in an
45. 21 31 specifies a vector with an arbitrary list of images Defining an Image Browser Math Function Defining the maxof function involves defining a function called mathfunc ina file named maxof c The process is similar to defining a user pulse sequence by defining the pulsesequence function in a file named after the sequence Function files are kept in the directory SBROWSERDIR math functions strc The following procedure is an example of how you would define the file maxof c in that directory File Header First enter the following line at the beginning of the file include header imagemath h VNMR 6 1C User Guide Imaging 01 999163 00 A0800 5 3 Image Browser Math Functions imagemath h declares the global variables and functions needed to access the input and output images imagemath h also includes the most commonly needed standard UNIX headers including math h mathfunc Definition Next define the mathfunc function mathfunc first checks to see if the input being passed is valid If the input is not valid mathfunc returns a FALSE value to the caller if the function encounters no errors mathfunc should return TRUE Be aware that nbr_infiles and input_sizes_differ are global variables declared in imagemath h and get set before the mathfunc subroutine is called The maxof math function also calls the want_output routine to ensure that there is someplace to put the first output image want__output n returns
46. 252 data management 228 data measuring 228 distorted images 245 dynamic range limitations 244 first image obtaining 248 image acquisition phase 236 image creating 226 imaging 234 imaging artifacts 244 imaging phantom setup 248 measurement starting 231 236 object size and field of view 244 preparation phase 236 programs 249 pulse sequences 229 reconstruction 225 228 references 252 requirements 225 routine usage 229 bandpass filter adjustment 219 type 251 baseline correction 159 battery replacement PGM preamplifier 209 bind unbind function 81 87 bins setting the number of 103 bitmap files 68 blood flow studies 48 BMP file format 107 bore size of magnet 307 Box ROI tool 89 147 154 bp_2d program 225 249 reconstruction 240 VNMR 6 1C User Guide Imaging 347 Index bp_3d program 226 249 bp_cmd file 249 bp_image c parameters 233 par directory 233 macro 225 pulse sequence 230 bp_mc program 226 249 bp_reco macro 225 228 bp_setup macro 225 234 236 250 bp_sort program 226 249 bp2d scheme 235 macro 225 measurement setup 230 parameters 227 pulse sequence 229 bp2ds excitation scheme 235 pulse program 240 bp3d macro 225 bp3d scheme 235 measurement setup 230 bphelp file 249 bptype parameter 244 brightness adjusting image 51 C calculating slice gradient 300 statistics 66 calibrating pulse powers 42 calibration file for gradient set 19
47. 2D data to standard 2D format C flashce lt nf gt ms mi rare ns traces echoes Converts 2D FID data files from compressed formats seqcon nncsn segcon nccnn seqcon nnccn to standard format seqcon ncsnn or from standard format to compressed format Compressed data is taken by using the nf parameter that is compressed data is acquired as one large uninterrupted multiFID acquisition Fh lashc reads the file fid in the acqfil subdirectory of the current experiment f lashc can convert a compressed compressed multislice multiecho or multi image sequence It can also convert a rare type sequence with a compressed phase encode echo train Fh lashc changes the values of the following VNMR parameters 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 285 Appendix A Commands Macros and Parameters Compressed compressed or Standard Format to Compressed Format e ni is set to 1 if no argument is provided e nf is set to the value of nf divided by the multislice ms or multi image mi value e arraydimis set to the product of its original value and the value of the traces argument e arrayelemts is set to 1 if no parameters were arrayed during data acquisition or to 2 if any parameter was arrayed during data acquisition Compressed Format to Standard Format e nf is set to the value of the traces argument or to if no argument is provided e ni is set to the value of nf divid
48. 2D imaging data and fit to T4 or T map M mark Determine intensity of spectrum at a point C vs Vertical scale P Execute expr C math expr 297 VNMR 6 1C User Guide Imaging Appendix A Commands Macros and Parameters Description pcmapapply Applicability Syntax Description Arguments Examples Related pemapclose Applicability Syntax Description Examples Related pcmapgen Applicability Syntax Description Executes the expression expr in the same way as if it had been typed into the Image Math panel Apply Phase Correction Map to Data C Systems with echo planar imaging capabilities pemapapply lt file gt lt index gt Applies a pixel by pixel phase shift to the current data file using the complex phase correction values from the phase correction map file Svnmruser expN datdir lt file gt file must reside in your Svnmruser expN dat dir directory where N is the current experiment number Phase correction values are generated by pcmapgen pcmapapply opens and closes a phase map file unless it has been explicitly opened with pcmapopen file specifies the phase correction map file name that resides in your Svnmruser expN datdir directory The default file is Svnmruser expN datdir pcmap If you do not provide file pcmapapp1y defaults to the pcmap file index specifies which phase correction map to us in the file This value will usually be 1 This argume
49. 3D dataset can also be viewed slice by slice by using ImageBrowser VNMR 6 1C User Guide Imaging 01 999163 00 A0800 10 4 Routine Usage disp Program The disp program displays a 3D FDF file or a raw 8 bit 3D data file with no header After data has been loaded a 3D volume appears in the display window The initial appearance of the 3D volume is as if it was viewed from the front To change the size position orientation and slice of the 3D volume do the following procedures e Adjust the size of the displayed image by using the left button of the mouse to increase or decrease the value on the Zoom slider For FDF format data the image is initially scaled to actual size or if that would be impractical itis scaled up or down by a power of two The zoom field gives the displayed scale as a percentage of actual size e Adjust the brightness and contrast of the display with the Contrast slider and the Vscale type in field The contrast adjusts the colormap to optimize the display of the 8 bit data The Vscale value is used only for FDF data with a word size greater than 8 bits The data are multiplied by the factor 255 vscale before being truncated to 8 bits If vscale 1 a data value of 1 0 scales to maximum intensity e Adjust the position of the 3D volume by using the middle button of the mouse and dragging it to the desired position inside the display panel e Adjust the orientation of the 3D image by holding down the left bu
50. 65 Chapter 4 Image Browser 66 Control Panel Graphics Region Message Area Date and Time Figure 25 Default Layout of Main Image Browser Screen Graphics Region The graphics region occupies the largest portion of the screen All graphical drawings and images are shown inside the graphics region which can have a number of graphics frames Gframes where images are displayed Before an image is displayed a Gframe at a specific location with the desired frame size must be created An image is automatically resized to fill the Gframe without losing the aspect ratio of the image Besides images regions of interest ROIs can be created lines can be drawn and text can be placed in the graphics region Message Area Date and Time Below the graphics region informative messages are displayed in the lower left corner of the window frame This is the standard way in an Open Look user interface to display messages Error messages are displayed in a separate window In the lower right corner the date and time are displayed Processing Functions Image Browser provides a number of processing functions Statistics Mean intensity standard deviation maximum minimum median area and volume can be calculated on one ROI or a number of selected ROIs Statistics are plotted when more than one ROI has been selected For example mean intensity might be plotted against the Z coordinate of the slice An intensity histogram is generated
51. 7 Weighting Preparation Phase se ms ije us pi tix trise BACKPROJECTION TRANSIENTS TIMING bptype noslice nt di 0 ACQUISITION ct te 0 402 175 np tr 0 05000 ni trise 0 00200 il ni2 tramp in GRADIENTS PROCESSING cp orient gcal Iro gro grof gss gssf SPECIAL gain tem 10000 02000 sb sbs phfid xyz 0 002000 1 00 3405 fn date Mar 30 94 file home1 pe ter BP AR_2 Schlau chi none 1 450 5000 0 500 proc math CONTRAST prep sw solvent DERIVED 25591 8 Figure 120 T Weighting aps Sequence 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 239 Chapter 10 2D and 3D Backprojection AG 240 rof2 tix trise pi dx pw dy seq ms aie us BACKPROJECTION TRANSIENTS TIMING SPECIAL bptype noslice nt d1 0 10000 gain 16 ACQUISITION ct 1 te 0 02000 temp not used sfrq 402 175 np 256 tr 0 05000 FLAGS tn H1 ni 64 trise 0 00200 il y tof 223800 0 ni2 64 tramp 0 in n tofe 0 GRADIENTS PROCESSING cp y RF_PULSES orient xyz sb 0 002 SAMPLE pi 00 gcal 0 002000 sbs 0 000 date Mar 30 94 tpwri 53 Iro 1 00 phfid 0 1 file f home1 pe pi 2 00 gro 3405 fn not used ter BP AR_2 Schlau tpwri 53 grof 1 450 proc ft chi pw 4 00 gss 5000 math f solvent none tpwr 53 gssf 0 500 CONTRAST DERIYED tpwrf 4095 prep tir sw 25591 8 pj 1000 0 tpwrj 30 Figure 121 Tiho Weighting Slice based BP Acquisition In slice based acquisition bp2ds soft pulses are used for imaging
52. 999163 00 A0800 sw3 cf ne A 5 Parameters Spectral width in 3rd indirectly detected dimension Description Spectral width for the third indirectly detected dimension of a multidimensional data set used in 3D CSI three spatial dimensions one spectral dimension for the third spatial dimension See sw1 for description except that number of phase encode steps is controlled by the parameter nv3 Refer to the VNMR Command and Parameter Reference for information about the additional use of sw3 in nonimaging applications Related imprep Set up rf pulses imaging and voxel selection gradients M nv3 Number of phase encode steps for 3rd indirectly detected dim P sw Spectral width in directly detected dimension P swl Spectral width in 1st indirectly detected dimension P sw2 Spectral width in 2nd indirectly detected dimension P tpe2 tpe3 Duration of 2nd and 3rd phase encoding gradient periods P Experiment Control Parameters Experiment control parameters can be divided into two classes e Counters are integer parameters used to specify the number of elements in different acquisition loops such as the number of phase encode steps in a 2D image or the number of slices in a multislice imaging sequence e Flags are string parameters used in many pulse sequences to turn on or turn off various optional functions such as a presaturation pulse or inversion recovery preparation Compressed vs Arrayed Data Acquisition Mu
53. Action format Similar to VNMR format command but with the following extension format number length precision interprets a string length with a leading 0 to mean pad the output string to specified length with leading zeros e g format 17 05 0 strsets str 00017 format 17 5 0 strsets str 17 groupcopy Copy parameters of a group from one tree to another length Determine length of a string rm Delete file string Create a string variable shell Similar to VNMR she11 command but at least one argument is required Cannot be used to open an interactive shell window substr Select a substring from a string Image Browser Commands Not In VNMR The following Image Browser commands by type are not in VNMR General Commands tool Shows the Tools panel ROI Commands roi_bind on off j Turns on off ROI binding roi_delete Deletes all selected ROIs roi_load file Loads an ROI stored in a named file into all selected Gframes If fi 1e does not begin with a itis searched relative to the SBROWSERDIR roi directory roi_save file Saves all selected ROIs in a named file If fi 1e does not begin with a it is presumed to be relative to the SBROWSERDIR roi directory zoom_factor Sets the factor by which zooming keyboard accelerators enlarge or reduce an image see page 79 Frame Commands frame_split nrows ncols Splits all selected Gframes into number of rows and number of co
54. EE Ee EEES 125 JACOBIAN Definition sstsisseeg onnee conose ena eee ene a aaa rE Ea erete S 126 GUESS Signature smene eanna o E EEA EE E EOE Ea T 126 Default Layout of Main CSI Windows sssssseseseeeseeseesesesteressrertrrersrrestssesreretrreererersree 130 Processing Functions Data FlOW ssssessesesssseeeserereessreesesresesrssesresreresrenresrnsesresesreneners 131 CST Command Panel sorserien roon er EREE EE A EEE 135 Graphics Tools Window cc csesisiA saves antes aeee EEE an E EER EE NEEE EEEE 136 Frame Props Window ais itsicrhessiisd adntiiecsnevisbiedsthealheeteadesstisarbentermvad caeasiys 136 CSI Data Basic Processing Steps 2 0 essesscssecrceesneesoeessesseessesssessensscnsosssensesetones 139 Filtenmg Display avait ieee ate icine EE E AEE EE eateiins 140 Phase Correction Window o eececceceeseesecssessecseessecseceaecescseeeceseseeeeeeeeeeeseseaesaaeeaeenee 141 Baseline Correction Window oo ceceeeeseesessecssessececesecesceseeeceseeeeseeeeeeseaeeenecaeeeaeenee 142 Metabolic Map Calculation oo ieee ee eceeeeceeeeeeceseeeseeseecsecaecsecaeseeseseeeeeeeeeeeeeeeee 144 Selected Voxels and Curve Fitted Data oo eee ceeeeceeeeeseeseecaeeseecaessaeceesneeaees 145 Detailed Data Flow for Metabolic Map Processing escecssessssecseeeeeseeeeeeeeecaeneees 145 Image Calctool Window cc cs ccascsscesssestessscasesdiscosesceszadveascebsseusesecpaseaategubestaasscabesana sees 146 Save Check Window sssissiscosesteaiscsbencasusevousc
55. FALSE only the header values are copied otherwise the data are also copied Example FDFptr clone_ddl FDFptr old_ddl int dataflag Creates an image data structure of the given width height and depth and returns a pointer to the structure Example FDFptr create_ddl int width int height int depth VNMR 6 1C User Guide Imaging 117 Chapter 5 Image Browser Math Processing int create_output_files void getmem int want_output get_header_int get_header_double get_header_string 118 VNMR 6 1C User Guide Imaging Creates up to n output files actually just data structures in memory File sizes are given by out_width out_height out_depth arrays This function loads out_ob ject and out_data with pointers to the data structures and data arrays respectively Example int create_output_files int n FDFptr cloner Equivalent to system malloc function except that any memory allocated this way is freed when the user function is done Example void getmem size_t size CAUTION Do not use free to release memory allocated by getmem Returns TRUE if output image number n is requested If three images are specified for output in the Image Browser Math command line want_output n returns TRUE if 0 lt n lt 2 otherwise this function returns FALSE Example int want_output int n Gets the value of an integer type header variable The variable name is read from the image referre
56. FDF files can be generated by VNMR from FID files produced by standard SISCO imaging sequences using the svib or svsis macro svsis can be modified for special user defined sequences If standard SISCO parameters have been used the modification can be as simple as adding a line to define the sequence The svib and svsis macros are described in the manual VVMR Command and Parameter Reference For 3D images the ft 3d macro can produce FDF files Another way to create FDF files is to edit or create a header defining a set of data with no headers and attach it to the data file using fdfgluer which has the syntax fdfgluer header_file lt data_file lt output_file gt gt This UNIX executable takes aheader_file anda data_file and joins them to form an FDF file It also calculates a checksum and inserts it into the header If there is no data_file argument fdfgluer assumes the data is input from the standard input and if there is no out put_file it puts the FDF file to the standard output Splitting FDF files The UNIX command fdfsplit takes an FDF file and splits it into its data and header parts The syntaxis fdfsplit fdf_file data_file header_file The header can still have a checksum value in it which should be removed 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 109 Chapter 4 Image Browser 110 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Chapter 5 Image Browser Math Processing Sections in this chapter e 5 1
57. FM 3 kHz 10 for voltage less than 4 V High pass filter 0 5 1 5 5 0 and 10 Hz Low pass filter 20 40 80 and 160 Hz Gain select x1 x10 Polarity select positive or negative Single fiber optic cable Threshold manual or automatic half of cardiac signal Inhibit time 0 05 s to 2 5 s adjustable Receiver power on off Link on preamp operational Preamp battery low on preamp and receiver ECG analog signal filtered and unfiltered 12 V range ECG trigger 1 ms active low pulse Inhibit time active low Threshold 0 V to 12 V External inhibit signal Preamplifier 6 V 1 4 mA typical battery operated Battery life 150 h with Polaroid P100 1000 h with Power dex VP 6 1400 Receiver 115 Vac 50 60 Hz switchable to 220 Vac on circuit board 01 999163 00 A0800 223 VNMR 6 1C User Guide Imaging Chapter 9 Physiological Gating Module 224 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Chapter 10 2D and 3D Backprojection Sections in this chapter e 10 1 Installation this page e 10 2 Backprojection Image Generation page 226 e 10 3 Getting Started page 227 e 10 4 Routine Usage page 229 e 10 5 Artifacts in BP Imaging page 244 e 10 6 BP Macros and Programs Details page 249 e 10 7 References page 252 This chapter shows how to acquire and reconstruct 2D and 3D NMR images based on the backprojection BP or projection reconstruction The acquisition
58. M plan Interactive slice and voxel selection M Draw outline of a planned target voxel on scout image drawvox Displays the outline of a newly planned voxel or multiple voxels on the scout image drawvox is called by the Compute Target button in the voxel planning 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 273 Appendix A Commands Macros and Parameters See also Related location Syntax Description Related log_mag Syntax Description Arguments Related 274 VNMR 6 1C User Guide Imaging menu and is not normally executed from the command line However because it is a macro it is possible to change the color used to draw the voxel position drawvox uses the box coordinates found in the parameter t_mark which must have previously been selected using the Mark button in the voxel planning menu Target Parameters page 341 drawslice Draw a set of planned target imaging slices on scout image M plan Interactive slice and voxel selection M Display spatial coordinates at a point in an image location Computes and displays the position of a point in an image defined by the intersection of the horizontal and vertical cursors Two sets of coordinates are computed e Logical reference frame coordinates corresponding to the readout phase encode e Slice select axes and the absolute magnet frame coordinates corresponding to the laboratory X Y and Z axes log_mag Conve
59. Macros for Planning Experiments Use the macros in this section when planning experiments addpss Syntax Description Arguments Related drawslice Syntax Description See also Related drawvox Syntax Description Examples Shift a set of multislice positions addpss lt shift gt Shifts a set of multislice positions by adding a constant value to all elements of the pss array addpss adds a constant value to each element of the pss array to shift a set of multislice positions a fixed distance shift specifies the amount of shift in cm The default is the macro prompts for a value addpss addpss 2 plan Interactive slice and voxel selection M pss Slice position P Draw a set of planned target imaging slices on scout image drawslice Displays the positions of a newly planned set of multislice planes on the scout image drawslice is called by the Compute Target button in the slice planning menu and is not normally executed from the command line However because it is a macro it is possible to change the color used to draw the slice positions drawslice uses the coordinates of a pair of points found in the parameter t_mark which must have previously been selected using the Mark button in the slice planning menu These two points define the orientation of the new target imaging plane Target Parameters page 341 drawvox Draw outline of a planned target voxel on scout image
60. Max Median Mean Stdy chris ib HEARTDATA ms001 fdf 815 0 9551 0 00102 0 01603 0 009656 0 009251 0 002674 01 737 0 01091 0 01048 0 003134 chris 1b HEARTDATA ms020 fdf 857 1 004 0 0005962 Figure 37 Statistics Output Generated by Print Stats Button Data Output Once the statistics have been output to the Info Messages window there are several ways you can save the data in a file e Use standard cut and paste methods to select a part of the data and paste it into another document e Select the Messages Info Messages Save choice in the control panel to display the File Browser This method allows you to save all of the current contents in a file e Press the right mouse button when the cursor is in the Info Messages text area and select File Save As which opens the OpenWindows file browser Raw data values can also be dumped into a file Selecting the Dump Data button writes the values of all the data pixels in all the selected ROIs into the file named in the File field If the file name is not an absolute path it is taken to be relative to the directory from which Image Browser was started If the file name is blank the data is written to the Info Messages window Currently a hard copy of the histogram plot and the statistics graph can only be produced by capturing the screen output OpenWindows has a utility program Snapshot that takes a picture of screen output other documentation software such as FrameMake
61. P seqcon Acquisition loop control P setloop Set values for ni and nf to control arrayed and real time looping M Number of trigger pulses for external gating Specifies the number of trigger pulses the system waits before proceeding with pulse sequence execution Most imaging pulse sequences include the pulse sequence function xgate ticks to synchronize the timing of pulse sequence execution with an external trigger event Although any parameter name may be chosen by the pulse sequence programmer t icks is predefined and available for this use hold Post trigger delay P xgate Load time counter P Flag Parameters ticks Description Related ir Description Values Related mt Description Values Related pilot Description Inversion recovery mode A flag used to turn on or off execution of an inversion recovery pre pulse in sequences that include this capability Generally used to control an inversion recovery block that uses the parameters pi pipat ti and tpwri y specifies inversion recovery mode n specifies the mode is not used jenn Inversion pulse length P pipat Inversion pulse shape P ti Inversion recovery time P tpwri Inversion pulse power level P Magnetization transfer on off A flag used to turn on or off magnetization transfer preparation in sequences that include this capability This parameter is generally used to control a magnetization transfer block that uses the parameters p
62. Peak Width Factor Min Peak Intensity Factor Delay Curve Check Peak Registration Mmap No Set Auto Curve Fit Fitting OK Quit Assigns a number to a peak Used with the Prior Knowledge file specified in the Mmap calculation window shown in Figure 61 Zero means unused Assigns a name a character string to a peak Assigns a map number Specifies the maximum frequency shift difference that a peak can have from its defined frequency when generating a Mmap Specifies the maximum width a peak can have from its defined value when generating a Mmap Specifies the minimum peak intensity that a peak can have from its defined value when generating a Mmap Assigns a delay when performing spectral reconstruction Redisplays the fitted curve Registers all peaks as confirmed information Done for all peaks not just the displayed peak Registers all metabolic map numbers with their peaks Done for all peaks not just the displayed one Curve fits all peaks Overlays curve fit on selected spectrum Assigns local fitting parameters to global ones to help the global curve fit routines and closes the Interactive Fitting Tool Exits from the Interactive Fitting Tool window Metabolic Map Display After performing peak picking and curve fitting select the desired peaks and click on Display Mmap to open the Metabolic Map Display window shown in Figure 74 Figure 74 Metabolic Map Display Window VNMR 6 1C User Guide I
63. ROIs and Gframes can be selected or deselected in the graphics region The left button selects an object while deselecting all other objects of the same type The middle button toggles the state of an object The object selected is chosen according to a priority hierarchy 1 Ifthe mouse pointer is inside an ROI near a line or point ROI or near text the corresponding object is selected If there is more than one qualifying object only the most recently created object is selected 2 Ifthe mouse pointer is outside any ROI but inside a Gframe the frame is selected Table 6 lists the ROI properties of the ROI Selector tool ROI Drawing Tools The following tools are used for drawing various types of ROIs Normally after an ROI is drawn a graphics tool reverts to the ROI Selector To prevent this reversion when you are drawing a series of similar ROIs hold down the Shift key while drawing each ROI Before you draw the last ROI release the Shift key to allow the graphic tool to revert to the Selector Line ROI Tool The Line ROI tool draws a straight line segment ROI Line ROIs are used in the Line Data processing function It is also possible to obtain statistics from a line ROI The points included in the statistics are the points along the line To draw a line after the tool is selected position the cursor at one of the desired endpoints press the left mouse button and drag the cursor to the other end point As 01 999163 00
64. Related mvfov Syntax Description Arguments Examples Related offset Syntax Description A 2 Macros for Setting Up Experiments movepro has no effect on the value of tof which is normally not used to define any positional information in imaging Unlike movetof the image or projection display is unchanged and no redisplay in full mode should be necessary To accurately center an image or projection move the box cursors to the edges of the imaged object use the macro split to place the cursor at the exact midpoint of the box then type movepro Iro Field of view size for readout axis P movetof Move transmitter offset M pro Position of image center on the readout axis P resto NMR resonance offset frequency P split Split difference between two cursors M Move the field of view from one experiment to another mvfov lt from_exp gt to_exp Copies the field of view parameters which describe the imaging orientation and position in the current experiment to another experiment The destination experiment can be any type of imaging application as long as it uses the same set of field of view parameters For example the imaging position and orientation used to acquire a SEMS image can be copied with mvfov to a second experiment set up to acquire a FLASH image The following parameters are copied by mvfov Ipe phi psi resto theta lro pro pss rfcoil thk If mv fov is used with only one a
65. TRUE if you have asked for the nth output image Image Dimensions If the input images are all the same size input_sizes_differ is FALSE their common dimensions are in the global variables img_width img_height and img_depth and the product of the three variables is in img_size Some functions can deal with input images of different sizes In such cases you must use the arrays in_width in_height in_depth and in_size These arrays determine the width height depth and size for each individual image unless otherwise mentioned all arrays start indexing from 0 in typical C fashion Memory Allocation The create_output_files function allocates memory for all the requested outputs making them all the same size as the input files maxo f limits the number of output files to two and gives files header characteristics like those of the first input image Pixel Looping The maxof function then loops over all the pixels in the input images e img_size has the number of pixels per input image e nbr_infiles has the number of images The nbr_infiles variable has the total number of images in all input image vectors To access individual image vectors use the variable nbr_image_vecs which provides the number of image vectors and the array in_vec_len which provides the number of images in each vector e in_data J i has the ith pixel in the jth input image The maximum value in the ith pixel is written to the first o
66. Up to three phase encode gradient levels e Slice and or voxel selection gradient levels imprep requires that the rfcoil parameter be set to the name of a valid entry inthe pulsecal database file previously created with the pulsecal macro The information found in pul secal is used to compute the pulse power levels for each rf pulse required to give the flip angles found in fliplist imprep uses the names found in pwrlist to determine which power level corresponds to which rf pulse The rf pattern parameter names found in pat list are used by imprep to obtain the names of the pulse shapes that correspond to each rf pulse in the sequence The pulse integral relative to a square pulse found in the header of each rf shape file is used with the pulse calibration found in pulsecal to calculate the value for each power level The readout gradient gro is determined with an algorithm that attempts to balance possible chemical shift errors from too low a gradient strength against excessive bandwidth spectral width sw which can result in reduced signal to noise Once a value for the readout gradient is selected spectral width is determined through the relationship sw y 1ro gro If the values of gro or sw selected by imprep are unsatisfactory for any reason use the macro setgro to explicitly set gro imprep computes and sets the phase encode increment and timing and the indirect dimension spectral width associated with each phase encode
67. and bottom caps are half as tall as the slice thicknesses 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 93 Chapter 4 Image Browser 94 Each axis of the graph can be chosen by selecting an item from the Y coord list and the X coord list using the right mouse button The following items can be selected from each list Y coord Area volume integrated intensity mean intensity median intensity minimum intensity maximum intensity and standard deviation SDV of intensity X coord ROI number slice location user parameter area volume integrated intensity mean intensity median intensity minimum intensity maximum intensity and standard deviation SDV of intensity The user parameter can be time information for T T data or any other information However the field must be put into the FDF file header Normally it is a VNMR parameter dumped out into the FDF file by the svib macro If the Y coord or X coord selection is changed the display is updated automatically However any change in the limits or changes to the ROIs themselves are not reflected until the Update button is pressed Statistics Output If desired statistics values can be written to a file for further processing by using the Print Stats button Print Stats writes the formatted statistics in the Info Messages window Figure 37 shows the output from two selected ROIs generated by Print Stats Info Messages ROI Statistics Name Pixels Area Min
68. and pH maps Input to the CSI tool is expected to be 2D CSI or image for reference images data in the Varian VNMR raw data FID format CSI or image data can be imported and processed as long as the data is formatted to the specifications of the Flexible Data Format FDF 6 1 Overview of CSI This section describes the system requirements for operating the CSI tool the CSI screen layout processing and graphics functions used by CSI display controls and data formats System Requirements CSI operates on platforms with the following configuration e Sun SPARC computer e OpenWindows and higher e 8 bit 24 bit frame buffer e Solaris 2 3 or higher The minimum memory requirement is 12 MB however more that 16 MB is recommended to enhance performance CSI does not take advantage of 24 bit color Swap space is also a factor because CSI data sets can be very large Three times the memory size in swap space is recommended Screen Layout The overall layout of the CSI screen is shown in Figure 52 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 129 Chapter 6 CSI Data Processing 130 gt Command Panel aA A ha a a re ie ee A a daf ad da dal Graphics region Sampling DONE Tuesday 08 03 93 17 26 12 Message Area Date and Time Figure 52 Default Layout of Main CSI Windows Command Panel The command panel contains command menus where specific operations can be invoked such as process data or display an image or
69. another window Graphics Region The graphics region occupies the largest portion of the screen and can be directly interacted with the mouse All graphical drawings and images are shown inside the graphics region The region can have a number of graphics frames where CSI data spectra and images are displayed Before data can be displayed a graphics frame must be created somewhere in the graphic region Data is automatically resized to fill the graphics frame CSI and image data keep their aspect ratio Besides displaying data region of interest ROI tools and markers can be created lines can be drawn and text written in the graphics frame VNMR 6 1C User Guide Imaging 01 999163 00 A0800 6 1 Overview of CSI Message Area Date and Time Below the graphics region informative messages are displayed on the bottom bar of the window frame This is the standard way of displaying messages in the OPENLOOK user interface Error messages are displayed in a separate window The date and time are displayed in the lower right corner Processing Functions When using the CSI tool it is best to think of it as a series of processing steps used to process and manipulate CSI data to obtain multivoxel spectra MVS data metabolic maps and pH maps or frequency difference maps Supporting these processing steps are interactive tools input output tools and viewing tools that make these steps easier Figure 53 shows the data flow through the m
70. be updated to reflect the hardware status 1 Enter the command setgcoil file where file is the appropriate gradtables file name for example setgcoil asg33 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 19 Chapter 1 First Steps Making an Image 20 This has the effect of setting sysgcoil to the same file name but in this special case it also updates the configuration file as well 2 As new parameter sets are retrieved and as other experiments are joined the system updates gradient calibration parameters to new values To verify this enter gmax and trise to see that they have the correct values for your gradient hardware Note that gmax and t rise are updated when a new parameter set is loaded or when you join a different experiment One exception is joining an experiment that has gcoil parameter set to the value of sysgcoil If you update the gradient calibration parameters of an already existing entry in gradt able you must manually update gmax and trise in the current experiment and others that have gcoil set to the sysgcoil value or run the macro _gcoil in each case Setting the pilot Parameter Some SEMS parameter sets might have not set the pilot parameter To ensure that all of the refocusing parameters are properly computed within the pulse sequence e Set pilot y Setting the resto Parameter The value of the resto parameter is used to make sure all positions are properly referenced to the center o
71. board apinterface 1 homo y also causes the decoupler signal to be combined with the observe signal before being sent to the probe Related apinterface AP Interface board type P dn Nucleus for first decoupler P homo2 Homodecoupling control for second decoupler P homo3 Homodecoupling control for third decoupler P tn Nucleus for observe transmitter P nD Application dimension Description Sets the number of spatial dimensions nD is used in automated setup to specify the number of phase encode dimensions that must be computed Values 1 2 3 or 4 nD is 2 in 2D imaging and 3 in 3D imaging Related imprep Set up rf pulses imaging and voxel selection gradients M seqcon Acquisition loop control P petable Table name in tablib Description Specifies the name of a table in tablib The table named by pet able is normally used to control the phase encode k space order during data acquisition in sequences that offer this capability Sequences written to support external phase encode tables generally allow pet able n in which case the phase encode order is computed internally in the conventional monotonic order tabc the routine that reorders data acquired in table order also uses pet able to obtain the name of the table to be used in the reordering process Related tabc Convert data in table order to linear order M presig Preamplifier signal level selection Applicability NTYZ OVA and UNITYplus imaging sys
72. button The purpose of the Enable button is to let you select or deselect values without losing track of their numeric values as an aid in installation or troubleshooting Upon deselection values of zero for that particular ECC term are sent to the system Another installation and troubleshooting aid is a feature that lets you graph enabled values See the section Graphing Values page 205 for a description of this feature Setting Rise Time and Duty Cycle The Limits panel is used to set Rise time and Duty cycle These settings occur on the SDAC board Rise time is alternatively known as slew rate Duty cycle sets a limit for the gradient pulses if their duration exceeds this value an error signal is generated Setting Gains The Scale panel is used to set various gains on the SDAC board The ECC gain setting affects the ECC signal coming into the summing junction on the SDAC board where the ECC is combined with the main gradient signal Note that the value VNMR 6 1C User Guide Imaging 01 999163 00 A0800 8 3 Using the decctool Interface in the X Y and Z parameter entry values is what you see is what you get meaning that if an amplitude of 2 is entered as an ECC parameter then no matter what value the ECC scale factor is in the Scale window the 2 correction is applied to the gradient This correction occurs because the software makes the adjustment For the most part you can set the ECC scale to a value and forge
73. by computer iterative procedures to give slice profiles that are closer to rectangular shape Such pulses minimize contamination of the image from regions outside the slice region of interest The optimization procedures can also produce pulses that are closer to ideal in terms of flip angle and phase response across the slice profile So far we have assumed the transmitter frequency is on resonance which corresponds to a slice plane at z 0 It is also possible to excite a slice at any f location along the slice direction by changing the rf transmitter frequency during the excitation phase of the experiment as shown in Figure 8 For offset slice selection the transmitter offset frequency depends on the amplitude of the slice gradient that Slice 1 is applied and is defined by the T following equation J Slice 2 fs fo Yd gss Eq 7 q In this equation fs is the transmitter Slice 3 frequency in Hz that is needed to 0 i excite a slice at distance d in cm from the origin fgis the resonance frequency in Hz of water and Gss is the slice select gradient in gauss cm Figure 8 Multislice Excitation Note You must return the transmitter reference frequency to the original position during the detection stage of the experiment for proper referencing of the resulting profile Slice thickness is directly related to the bandwidth of the excitation pulse For a sinc pulse the
74. by using the FileBrowser However in this case simulated data is used Select the Gen Data Cont entry in the File menu with the right mouse button An 8 voxel by 8 voxel phosphorus data set is generated Note that nothing is displayed Only a message in the bottom left corner indicates the data has been generated Spatial Reconstruction Select the Process option in the command panel to open the Spatial Reconstruction window It can also always be opened from the submenus with the right mouse button The menu appears with default values specified in all the fields Select the Apply option in the Spatial Reconstruction window to process the raw data and display the localized FID data in the currently selected Gframe The processing parameters associated with spatial reconstruction are zero filling filtering voxel shifting and rotation To use a parameter change the desired field or fields and select 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 139 Chapter 6 CSI Data Processing 140 the Apply option The data set is reprocessed and the localized FID is redisplayed in the currently selected frame The default graphics tool is the frame tool To select another Gframe for displaying position the cursor in another frame and click the left mouse button Filtering or Weighting The Filtering or Weighting tool described on page 156 is available but its use is limited with spatial reconstruction The reconstruction of one line o
75. calibrating the rf pulse power e Setting the receiver gain e Checking the signal to noise ratio e Optimizing the pulse sequence parameters such as te and tr Readout gradient strength determines the frequency spread of image components in a profile Therefore the spectral width must be sufficiently wide to resolve all the spatial frequency components along the readout direction Otherwise frequency components outside the spectral window cause fold over artifacts The readout gradient and spectral width determine the field of view along the readout dimension defined by the following equation sw Y gro lro Eq 12 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 33 Chapter 2 Imaging Experiments In Equation 12 gro in gauss cm is the readout gradient 1 ro is the field of view along the readout dimension in cm and sw is the spectral width or bandwidth in Hz The spectral width is related to the acquisition parameters defined by the following equation sw np 2 at Eq 13 In Equation 13 np is the total number of real plus imaginary points digitized and at is the acquisition time in sec The maximum bandwidth sw is determined by the digitizer used on the system A typical 16 bit digitizer used on most imaging systems allows a spectral bandwidth limit of 500 KHz whereas some 12 bit digitizers used in solids NMR systems allow a maximum bandwidth of 5 MHz The parameter np is usually set to approxima
76. changes happening in the sample must be slower than the scan time of an image otherwise the image will show artifacts Contrast Agent Studies The short recycle time used in GEMS can cause spins with a long T to be selectively saturated while the spins with a shorter T are enhanced For example in contrast agent studies the signals from normal tissues can be suppressed while those containing contrast agents are enhanced 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 47 Chapter 3 Imaging Pulse Sequences 48 Angiography In the case of blood flow studies stationary spins in the slice plane can be selectively saturated by the rf pulses whereas spins that are flowing into the imaging plane remain in an equilibrium state and therefore contribute to the signal intensity Functional Imaging Gradient echo sequences such as GEMS particularly at high fields tend to enhance the signal loss caused by susceptibility effects In functional imaging brain activation is measured by the susceptibility changes caused by the increased deoxygenated blood in the activated regions Hardware Requirements Hardware requirements for GEMS are not as rigid as some of the other fast scan techniques such as EPI Therefore GEMS can be readily implemented on standard imaging systems Limitations The followings sections describe the limitations of GEMS Inhomogeneity Effects During the te delay spins are influenced by T gt inhomogenei
77. compressed Format or Rare Format to Standard Format flashc simple compressed phase encode flashc ms ns compressed phase encode and multi slice flashc mi ns compressed multi image and phase encode flashc rare ns etl Related arraydim Dimension of experiment P fiz Fourier transform 2D data C tad Fourier transform 3D data C nf Number of FIDs P 286 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 ft Syntax Description Arguments A 4 Commands and Macros for Processing and Display ni Number of increments in 1st indirectly detected dimension P segcon Acquisition loop control P Fourier transform 1D data C 1 ft lt lt options gt lt nf gt lt start gt lt finish gt lt step gt gt 2 ft inverse exp_number expansion_factor In syntax 1 performs a Fourier transform on one or more 1D FIDs without weighting applied to the FID ft executes a left shift zero order phase rotation and a frequency shift first order phase rotation according to the parameters lsfid phfid and 1sfrq respectively on the time domain data prior to Fourier transformation The type of Fourier transform to be performed is determined by the parameter proc Solvent suppression is turned on or off with the parameters ssfilter and ssorder For arrayed data sets ft Fourier transforms all of the array elements To Fourier transform selected array elements ft can be passed numeric arguments In syntax 2
78. course experiments The gradient hardware must be capable of handling the higher duty cycle that is commonly encountered in EPI Water and air cooling are typically used to remove the excess heat generated by the gradient coils The hardware is typically equipped with protection devices to detect unusual temperature increase and shut down the amplifiers Special precautions are necessary to avoid exceeding the duty cycle limits recommended for a given gradient set Eddy Current Effects Eddy currents create undesirable fields in the magnet region These fields cause severe artifacts in images Actively shielded gradients along with eddy current compensation preemphasis hardware can be used to minimize eddy currents effects Slewing the gradients increasing t rise can also minimize eddy currents but the acquisition times are increased accordingly In EPI on vertical bore high field microimaging systems the high spatial resolution and small field of view requirement for microscopy requires very high gradient strengths of the order of 25 to 100 gauss cm Fortunately the smaller diameter gradient coils used in microscopy are also more efficient Therefore the high gradient strengths and shorter rise fall times needed for magnetic resonance microscopy are easily achieved Note however that the residual eddy current fields can also be quite high because of the relatively high gradient strengths used in microscopy experiments For that reason act
79. created by overwriting the current default file roi Directory where any created ROIs for loading onto a set of images can be saved PEAK Directory containing peak information files for peak picking and curve fitting using prior knowledge Personal prior knowledge files can be inserted here macro Directory containing user macros and in particular the macro startup which is executed when ImageBrowser starts startup might load a set of Gframes and set various options such as the gamma correction settings Starting CSI CSI is started with the command csi which actually starts two processes One process runs the CSI command panel and is named csi The other process controls everything else including the processing and graphics and is named P_csi When CSI starts it reads the colormap init and window init files to initialize the colormap and the window locations and sizes on the screen It also executes startup in the file SCSIDIR macro startup Before manipulating frames and loading images you need to know how the mouse buttons and the command panel menus function because CSI is a point and click based tool Using Mouse Buttons Details about mouse buttons use can be found in the OpenWindows Version 2 User s Guide In general mouse button use can be summarized as follows Left button SELECT Inside the command panel the left mouse button is used to invoke commands Inside the graphics region the left button is
80. d1 delay With this placement of the gating statement the sequence acts directly after the desired number of gating pulses have been counted off by the acquisition system An auxiliary delay parameter hold is provided to adjust the timing after the sequence triggers This delay can be used obtain images at different phases of motion The value of hold can be varied from zero to the value of the heart period Experiments that operate in the multislice mode trigger at the beginning of the sequence used to obtain the first slice Subsequent slices are then run at a constant rate The result is that all images are synchronized to the physiological trigger but different slices are obtained at different points of the cardiac cycle A second auxiliary delay rcvry is provided before the gating statement for use in the multislice mode where the d1 delay controls sequence to sequence repetition The revry delay is executed once before the sequence used to collect the first slice The value of rcvry is chosen to allow the ECG to recover from the disturbance caused by the multislice sequence cascade The quality of gated images improves at short values of the echo time te and for higher numbers of averages nt Simple Gated Spin Echo Imaging To perform simple gated spin echo imaging select the shorter sequence which provides a spin echo imaging sequence compatible with short TE values Select a TE value of 15 ms Obtain an initial scout image
81. data by moving fid orig back to fid To gain more disk space explicitly delete id orig after you are satisfied that conversion is successful Use tabc on either saved data that has been loaded into a VNMR experiment or on data in an experiment that has just been acquired but not yet saved In the first case converted data must be saved again for the saved data set to reflect conversion tabc supports all 2D data types recognized by VNMR arrayed compressed multislice and arrayed compressed multislice tabc requires that data must have the same number of traces as the table elements It does not support any of the advanced features of table expansion e g the entire table must be explicitly listed in the table file and expects to find only one table in a file whether the table is t1 or t60 is unimportant dimension specifies the type of data which has been acquired with an external table to be converted The default is standard 2D data tabc tabc 1 converts the order of compressed 2D data nf specifies the second dimension tabc 2 converts the order of standard 2D data ni specifies the second dimension tabc 3 converts the order of imaging 3D data nf specifies the second dimension and ni specifies the third dimension Flashe Convert compressed 2D data to standard 2D format C Et2d Fourier transform 2D data C nf Number of FIDs P ni Number of increments in 1st indirectly detected dimension P Ap
82. decctool decctool Open decctool window Parameter deccgo Action to perform for decctool Opening decctool 1 To start decctool enter decctool in the VNMR command window The window shown in Figure 97 opens decctool Gradient coil None X Z Limits Scale Allowed X compensation xx X gt X Y gt X Z gt X X gt B0 Enable Tau ms 004 Workspace 001 001 Text fields 001 004 LU ih 14 dh dm b d ai zi al zi al z aj zi a z a zi am a a a m a KV Compensation terms ECC File R z Unmodified Version j Figure 97 decctool Window 2 Click in the ECC File field to activate it Type a name of your choice then click on the Save button Do this step now before proceeding 202 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 8 3 Using the decctool Interface Loading and Saving Files At the top of the decctool window there is a reference to the name of the magnet gradient coil which is the value of the sysgcoil parameter None in Figure 97 The master file name internally used to hold the ECC values is named after the coil used because the compensation parameters are associated with the coil magnet combination in use When the decctool window opens the values for the parameters are those in the master file and there is no name in the ECC File field In the ECC File field you can enter a filename of your choice which becomes the scratchp
83. derivative is forced to zero the defining condition for the so called natural cubic spline Underflow and Overflow The Underflow and Overflow menus control how data values outside of the domain of the mapping function are displayed The default is Off meaning that data values less than the minimum data value x lt d are displayed the same as x d and that data values x gt D are displayed the same as if x D The menus offer a number of alternative color choices for such values Vs Prop Menu Gamma Correction The Gamma choice in the Vertical Scaling Properties window opens the Gamma Show Saturation _ Correction window shown in Figure 70 Gamma Correction The primary purpose of gamma correction is to make optimal use of the limited number of grayscale steps in ImageBrowser s colormap A secondary purpose is to compensate for any unusual nonlinearities in the monitor s displayed intensities Compensation allows images to appear Figure 70 Gamma Correction Window the same with identical scaling on any monitor once gamma correction has been done For a properly adjusted monitor minimal gamma correction should be necessary Gamma Correction Window The Gamma Correction window has a plot at the bottom that graphs the pixel value between 0 and 255 against the index into the grayscale portion of ImageBrowser s colormap Pixel value is actually a color that has a red green and blue value
84. display 2D data in upper left corner M uright Set chart parameters to display 2D data in upper right corner M Transform arrayed imaging data and save as phasefiles M makephf basefile lt upper_limit gt Performs a 2D Fourier transform on each element of an arrayed imaging data set and saves the resulting images as sequentially numbered phasefiles basefile isa phasefile name An incremented numerical extension starting with 1 is added to this basename to form a set of numbered phasefiles in the planes directory of the current experiment upper_limit specifies an upper limit to the number of arrayed elements to be processed The default is that all images are transformed and saved makephf phantom makephf fleming 10 svphf Save currently displayed phasefile to planes directory M Display data value at cursor position in a 2D display M markvs Displays the data value at the cursor position in a 2D display markvs runs the VNMR mark command divides the obtained height by the vertical scale parameter vs and displays the resulting true data value mark displays the height of the data at the point designated by the intersection of the two cursors in a 2D display In actuality this height is the true data value multiplied by vs For example it is useful to know the true data value to determine the T value from a T map computed by imfit or the phase angle in a phase map image imfit Process arrayed
85. distance from last point 4 804 cm The projected distance is only 3D distance from last point 7 228 cm meaningful between slices with the same orientation and X Y position Distance is determined by drawing both pictures at the same scale and lining up the upper left corners The 3D distance is correct between any two images Figure 42 Cursor Data Window Line Data Line Data uses line or polyline gt A DEER ROIs when obtaining Coordinates 37 6 130 5 to 252 7 127 6 Reset Scale information The popup Length of line 5 38 cm window is blank until an Max 0 029252 Display On Line Projection appropriate ROI is drawn or selected The Line Data window provides coordinates lengths traces of intensities on the line and projections of intensities across the line Figure 43 shows a window with an intensity trace displayed Figure 43 Line Data Window 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 97 Chapter 4 Image Browser On Line in the Display field displays a trace over the currently selected line ROI Projection displays the maximum intensity projection across the line the projection function is not available for polylines The on line plot is updated in real time as you move the line around but the projection plot is not updated until you stop moving the line and release the left mouse button 4 5 Macros 98 Image Browser incorporates the MAGICAL II macro programming language which
86. domain image Most of the other commonly used imaging sequences can be regarded as variations of this basic sequence GEMS uses a single excitation pulse therefore the pulse flip angle can be reduced at the expense of signal to noise ratio The main advantage of using a smaller flip angle is that the sequence can be rapidly repeated using a shorter repetition time t r This advantage enables you to obtain images in about one second Imaging Sequence The initial excitation pulse is a slice selection pulse designed to excite a specific slice in an object The slice offset is specified by the parameter pss in cm and its thickness by the parameter thk in mm The flip angle of the excitation pulse is usually set to about 5 to 30 so that each scan can be rapidly repeated with a short recycle time t r Because rapidly repeated scanning is an important feature of the GEMS sequence it is commonly used in situations in which rapid image acquisition is the primary goal For a gradient echo to be generated by the read gradient the signal must first be dephased and then rephased as shown in Figure 17 The Fourier transform ft of the echo signal yields a profile along the readout direction During the initial setup process you can view the echo and its profile by setting the number of phase encode steps nv to 0 The profile VNMR 6 1C User Guide Imaging 01 999163 00 A0800 3 3 GEMS Multislice Imaging can be used to position the sampl
87. dorient Diffusion gradient orientation Description Orientation of a diffusion gradient with respect to the magnet coordinate system Description and definition is equivalent to vorient Related dphi dpsi dtheta Euler angles for diffusion gradient orientation P vorient Voxel orientation P dphi dpsi dtheta Euler angles for diffusion gradient orientation Description Euler angle parameters used to define diffusion gradient orientation Descriptions and definitions are equivalent to vphi vpsi and vtheta Related dorient Diffusion gradient orientation P vphi vpsi vtheta Euler angles for voxel orientation P orient2 Other orientation Description Spare orientation parameter for use in defining the orientation of any gradient other than for diffusion saturation slice or voxel with respect to the magnet coordinate system Description and definition are equivalent to vorient Related vorient Voxel orientation P phi2 psiz2 thetaz Euler angles for other orientations P phi2 psi2 theta2 Euler angles for other orientations Description Spare Euler angle parameters Descriptions and definitions are equivalent to vphi vpsi and vtheta Related orient2 Other orientation P vphi vpsi vtheta Euler angles for voxel orientation P sorient Saturation band orientation Description Orientation of a saturation band with respect to the magnet coordinate system Description and definition is equivalent to vorient Related sph
88. draws a point or cursor ROI Cursor ROIs are used in the Cursor Data processing function and can also be used by the Statistics processing function To draw a point after the tool is selected position the cursor at the desired point and click the left mouse button A point ROI appears and is selected This tool has the same ROI Properties menu choices as the ROI Selector tool VNMR 6 1C User Guide Imaging 01 999163 00 A0800 4 3 Graphics Tools Box ROI Tool The Box ROI tool draws a rectangular ROL It is used in the Statistics processing function To draw a rectangular ROI after the tool is selected do the following steps 1 Position the cursor at one of the desired corner coordinates 2 Press the eft mouse button and drag the cursor over the desired region of interest area As the cursor is being dragged a rectangle is drawn in the active ROI color 3 Release the left button The completed rectangle appears in the selected ROI color This tool has the same ROI Properties menu choices as the ROI Selector tool Polygon ROI Tool The Polygon ROI tool draws a freehand or polygon ROI It is used in the Statistics processing function The Polygon ROI tool has the same ROI Properties menu choices as the ROI Selector tool To draw a freehand ROI after the tool is selected do the following procedure 1 Position the cursor at the starting location along the boundary of the desired region of interest 2 Press the eft
89. e center displays start of a label horizontally at the center of each spectrum left displays start of a label horizontally at the left edge of each spectrum e right displays start of a label horizontally at the right edge of each spectrum e top displays a label at the top of the graphics screen e bottom displays a label at the bottom of the graphics screen list displays values stored in an arrayed processing parameter such as intensity integral time frequency etc An arrayed processing parameter can be created with the set group and setprotect commands from any acquisition parameter and used to store a list of values entered on the command line or with any data analysis macro list xyz produces a display of the values contained in the arrayed parameter xyz This can be used to force dss1 to display the arrayed values of one of the parameters in a multiple arrayed parameter experiment e format abc uses the format abc to control the display of each label For example dss1 value format 2f forces each label to be displayed with two figures to the right of the decimal e value can be used in addition to any positional arguments to produce a display of the values of each array element instead of an integer index only a single arrayed parameter is supported dss1 value fails if multiple arrayed parameters are present e dssl value format 3 1 sec results in labels of the form 8 3
90. excitation bandwidth w in Hz is defined by the following equation w 2 A Eq 8 In Equation 8 refers to the wavelength in sec of the sinc pulse The slice thickness parameter is dependent on the slice gradient because the slice gradient affects the frequency spread or the profile along the slice direction Equation 9 represents the relationship between the band width of the rf pulse w in Hz slice gradient Gss in gauss cm and slice thickness st in cm w y Gss st Eq 9 The presence of a slice gradient during the slice selection pulse has an undesirable effect on the signal The signals lose phase coherence which results in a rapid signal loss This signal loss can be restored by applying a gradient of opposite sign as shown in Figure 9 The amplitude of the slice rephasing gradient Gsd can be obtained by the following equation by to Eq 10 k gss dt gss dt t7 t4 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 31 Chapter 2 Imaging Experiments Slice refocusing gradient rf Gss Figure 9 Signal Loss Restoration In Equation 10 the factor k is approximately equal to 1 Equation 10 simply means that the shaded areas in Figure 9 must be approximately equal for maximum refocusing of the spins after the slice selection pulse Some experimental macros and parameters in VNMR related to slice selection are listed in Table 1 For more information on VNMR macros parameters and commands refer
91. following procedure 1 Select a point with the ROI Select tool 2 Hold down the left mouse button and move the cursor marker to the desired location on the spectrum Delete Points To delete a point do the following procedure 1 Select the point 2 Select Delete from the Picking tool Marker Properties menu Make the Correction When you are satisfied with the points do the following procedure to apply the edits 1 Select Edit OK 2 Make sure the correction method is either Spline or Polynomial then select Correction Go Peak Sampling Peak Sampling can be performed by selecting Not Use or Use in the Prior Knowledge field Prior Knowledge is usually desirable If it is used the correct Prior Knowledge PK File file must be selected In this case it is the 31P in vivo standard The PK files can be viewed and selected by using the right mouse button Select Prior Knowledge Use and PK File 31P in vivo standard and then select Sampling Go A marker should appear on each peak If no markers appear they can be added using the picture tool If the markers are properly positioned make sure the SINC correction method is specified and then select Correction Go Metabolic Map Calculation To calculate the metabolic map information the CSI spectral peaks must be defined and if desired for more accurate information curve fit This is the last standard processing step Select the Metabolic Map option from the Process menu to ope
92. following procedures outline all of the steps you need to take to begin using SEMS for the first time Some of the steps such as pulse calibration may not be necessary once you have done them once It is likely that in a real experimental session you may go through two or more stages in defining the image orientation and position for the area of interest We call this final image the target image But first you will probably need to acquire an initial scout image that can be used to accurately locate the target image 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 17 Chapter 1 First Steps Making an Image 18 Calibrating the Pulse Length The first step is to calibrate the 90 pulse performance of the particular combination of probe and sample and to enter that information into the pulsecal database file e Use a simple pulse acquire sequence e g S2PUL set the power level to intermediate range on newer UN TYINOVA or UNITYplus systems set t pwr to about 50 on UNITY or VXR S systems set tpwr closer to 90 e Determine either the 90 or 180 pulse length either value works for this procedure but a 180 is easier to determine and is generally not distorted by T relaxation Now make an entry in the pulsecal file as follows 1 Enter the command pulsecal If you have an entry in pul secal a table appears in the text window and the following syntax message appears Usage pulsecal name pattern length flip p
93. for specifying a hold time between an external trigger and the start of the actual pulse sequence events For example in cardiac triggered imaging hold provides a mechanism for offsetting the start of the sequence by a variable amount to obtain images at different times in the cardiac cycle See also VNMR Pulse Sequences Related ticks Number of trigger pulse P xgate Load time counter P 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 315 Appendix A Commands Macros and Parameters pad Description Values Related tau tau2 Description tcrush Description Related tdelta Description Related tDELTA Description Preacquisition delay Each NMR experiment starts with a single delay time equal to pad over and above the delay d1 that occurs before each transient Normally pad is set to a small nominal time 0 5 seconds to allow any hardware changes that may be required at the start of the acquisition to settle in During experiments in which the temperature is changed the acquisition starts pad seconds after the temperature regulation system comes to regulation Since the sample temperature does not actually come to equilibrium for some time after that it is generally desirable to increase pad to perhaps 300 seconds This is especially true when running experiments involving arrays of temperatures The pad parameter is most useful for running kinetics experiments For example pad 0
94. g 64 63 62 1 0 1 62 63 The ft 2d program assumes this structure in its operation Data from table driven 2D pulse sequences is used by entering t abc only once before normal 2D processing and or parameter storage t abc takes no arguments and is executed by entering t abc in the VNMR command window A simple check is done by t abc to prevent it from being executed more than once on the same data set tabc expects to find 2D data in the standard VNMR format i e using the ni parameter see the third example You must specify the compressed form of data i e use the nf parameter and enter a value of 1 in the dimension argument see the second example 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 303 Appendix A Commands Macros and Parameters Arguments Examples Related tcapply Syntax Description tabc 3 reorders 3D data acquired with an external table 3D data is expected to be in the compressed standard format in which there are ni standard 2D planes of data the third dimension each consisting of nf compressed FIDs the second dimension see the fourth example tabc reads the file fid in the acqfi1 subdirectory of the current experiment Before the data is reordered this file is written to another file named fid orig inthe same acqfil directory If for any reason t abc fails or results in an unpredictable or undesired transformation you can salvage the original raw
95. generate stimulated echoes or other spurious signals that can severely distort the resulting images Gradient and rf spoiler pulses as discussed by Zur Y Magnetic VNMR 6 1C User Guide Imaging 01 999163 00 A0800 3 4 Obtaining a GEMS Image Resonance in Medicine 21 251 1991 are usually employed in the pulse sequence to minimize such artifacts 3 4 Obtaining a GEMS Image WARNING GEMS sequences are sometimes run using brief recycle and echo times Under such conditions gradient levels can exceed recommended duty cycle or temperature limits If temperature limits are exceeded protection circuitry in the gradient amplifiers automatically disables the amplifier But some amplifiers do not have such protection circuitry Pay special attention to the duty cycle limits if you are doing imaging on a system without protection circuitry Collecting Non Time Course GEMS Images To obtain a GEMS image perform the following steps Table 5 on page 62 lists the commands macros and parameters used during this procedure 1 Initially verify the following conditions before proceeding to the imaging experiment a The resonance frequency of the signal usually water has been determined and the Hloffset file has been initialized with the set of macro as described in the section Initial Setup b The rf power levels are calibrated and the entry has been included in the pulsecal database c The appropriate rf amplifier has been t
96. image is redisplayed Vertical Scale Tool The Vertical Scale tool adjusts the vertical scale of an image When the Vertical Scale tool is active frames cannot be selected or deselected with the mouse because clicking on an image changes the displayed intensity instead However a frame does not have to be selected in order to adjust its vertical scale with the mouse any image that is clicked on is rescaled Vertical scale can be adjusted two ways e Click the left mouse cursor on the image The program finds the maximum data value within a ten pixel square box centered on the cursor and the vertical scale is adjusted to put this pixel at the top of the grayscale e Use a window to enter the desired vertical scale value Figure 67 shows the Vs Prop Vertical Scale Properties menu for selecting vertical scaling Figure 67 Vertical Scale Properties Window 148 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 6 3 Tools V scale option gamma correction Gamma option and binding or unbinding images Each property is described in the following sections Vs Prop Menu Vertical Scaling The V scale option of the Vs Prop menu displays the Vertical Scaling window in which vertical scaling can be set as shown in Figure 68 The range of data values to be mapped to grayscale values and the form of the mapping function can both be changed Any changes in vertical scaling are applied to all the selected Gframes Changes to
97. images can be saved filter Directory containing the supplied convolution filters Personal filters should be saved here or in a subdirectory Starting Image Browser Image Browser is started by typing the command browser ona UNIX command line The following examples show the command line syntax for browser browser browser lt macro_name gt browser lt XView_arguments gt browser lt image path_name gt browser lt imagelist path_name gt browser arguments can appear in any order e macro_name is the file name of a macro which must be stored in SBROWSERDIR macro macro_name The macro is executed when Image Browser starts If no macro name is specified the macro startup is executed e XView_arguments are any type of standard X View arguments which can be found by typing man xview ona UNIX command line e image path_name specifies the full path of an image that should be loaded at startup It is loaded after the st art up macro is executed Multiple image arguments can be used to load multiple images e imagelist path_name specifies a file containing a list of file names of images to be loaded When Image Browser starts it reads the file colormap init to initialize the colormap and the file window init to initialize the window locations and sizes on the screen It also starts two processes ib_ui which runs the Image Browser control panel and ib_graphics which controls everything else including processing and g
98. in aps The parameter sat controls the duration between the first pulse and second pulse The parameters pi and t pwri control the pulse Figure 120 shows an example of T weighting using aperiodic saturation T1rho Weighting Ti rho Weighting is achieved by a 90 pulse that flips the magnetization in the xy plane and a subsequent spin lock pulse pj which phase is perpendicular to the 90 pulse After the spin lock duration pj the magnetization is flipped back in the z direction and the standard imaging sequence follows Between the 90 pulses and the spin lock pulse a small delay typically 4 us is necessary to allow for transmitter phase switching Note that the spin lock pulse is in the range of milliseconds Figure 121 shows an example of T weighting VNMR 6 1C User Guide Imaging 01 999163 00 A0800 10 4 Routine Usage BACKPROJECTION TRANSIENTS TIMING SPECTAL bptype noslice nt 1 di 0 10000 gain 16 ACQUISITION ct 1 te 0 02000 temp not used sfrq 402 175 np 256 tr 0 05000 FLAGS tn H1 ni 64 trise 0 00200 il tof 23800 0 ni2 64 tramp oO in n tofc 0 GRADIENTS PROCESSING cp RF_PULSES orient xyz sb 0 002 SAMPLE pi 2 00 gcal 0 002000 sbs 0 000 date Mar 30 94 tpwri 53 lro 1 00 phfid 0 1 file homei1 pe p1 2 00 gro 3405 fn not used ter BPYAR_2 Schlau tpwr1 53 grof 1 450 proc ft chi pw 4 00 gss 5000 math f solvent none tpur 53 gssf 0 500 CONTRAST DERIVED tpwrf 4095 prep sr sw 235591 8 MA Figure 119
99. indefinite acquisition set nt to a very large number such as 1e9 Number of phase encode steps for 1st indirectly detected dimension The number of phase encode steps for the first indirectly detected dimension in a multidimensional imaging or CSI experiment In a 2D or 3D image nv controls the resolution in the second spatial dimension 1pe Ina CSI experiment nv controls the first spatial dimension 1pe The lower level parameters ni and nf are automatically set each time a value of nv is entered through the macro set loop which uses the seqcon parameter to determine if the acquisition is standard or compressed in the dimension controlled by nv and appropriately sets either ni or nf Because nv is 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 335 Appendix A Commands Macros and Parameters nv2 nv3 336 Values Related Description Related Description Related explicitly used in most imaging pulse sequences to specify the number of phase encode steps the user should never directly set ni or nf but instead set nv and let the software automatically assign ni and nf Number greater than 0 usually in powers of 2 Typical values 0 64 128 256 flashc Convert compressed 2D data to standard 2D format C imprep Set up rf pulses imaging and voxel selection gradients M lpe Field of view size for phase encode axis P nf Number of FIDs P HE Number of increments in 1st indirectly detected dime
100. is the parameter holding the name of the pulse shape power is the power level parameter corresponding to the pulse flip_angle is the flip angle in degrees setflip p2 p2pat tpwr2 180 imprep Set up rf pulses imaging and pulse power levels M yfegil RF pulse calibration identity P Set the gradient calibration constant setgcal 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 265 Appendix A Commands Macros and Parameters Description Determines the gradient calibration constant gcal by using a proton phantom of known dimensions set gcal requests the linear dimension of the phantom in the readout direction It uses the value entered together with cursor separation of this dimension from the image profile and the strength of the readout gradient gro or gz1v11 if pulsed field gradients to calculate gcal in units of gauss em DAC units You are then prompted whether this value should be entered If you answer yes it is stored as a system constant in the your global file Note that a particular value of gcal is closely related to the current eddy current compensation settings If these settings are changed e g reading in a new curecc file a different value of gcal should be expected Before running set gcal use the pulse sequence set up by profile to acquire a signal from a known sized object while the gradient is on Related gcal Gradient calibration constant P gro Readout gradient strength in DAC units P
101. loaded by double clicking by selecting the file and pressing the Return key or by selecting the file and selecting Load Storing Data Data can be stored at intermediate steps while it is being processed Figure 53 on page 131 contains a data flow diagram that shows at what points during processing that data can be saved CSI data is easily stored by clicking the right mouse button on the File option in the command panel and then selecting Save The FileBrowser window opens in the data save mode or else the current FileBrowser window is changed to that mode As with Load FileBrowser opens with the directory in which CSI was started Choose a directory a file name and select Save CSI opens a menu prompting for the type of data to be saved This process is different from ImageBrowser which saves the data in the currently selected Gframe CSI keeps global data buffers that might not be currently displayed but the data is processed and saved All data is saved as FDF files See Processing Functions page 156 for more information about data processing Using Graphics Tools The graphics tools or G Tools window is opened by selecting the Tools option in the command panel The graphics tools window opens with the Frame tool as the default tool Graphics tools are mostly used to support the following processing functions e ROI manipulation e Gframe manipulation e Zooming e Vertical scaling scales the data to the pixel display value
102. module for cardiac gated experiments Familiarity with the individual hardware components and the function their controls is necessary Hardware Preparation This section describes assembly and connection of the PGM 1000 components to obtain ECG gated studies from the subject A diagram showing the interconnections between the PGM 1000 modules and the system is shown in Figure 107 1 Power up the cardiac preamplifier unit only and check the internal battery status Replace the battery if necessary Power down the preamplifier to avoid wasting the battery after testing 2 Mount the cardiac preamplifier unit in one of the front slots of the animal cradle the slots are normally used to hold rf coil tuning boxes The edge of cardiac preamplifier should slide into the slot so that the front panel of the unit is visible from the magnet entrance Connect the cardiac electrode leads to the corresponding color coded sockets on the rear panel of the cardiac preamplifier Users who have older style probe and bore equipment can mount the cardiac preamplifier on a tuning box bracket or to the animal bed Firmly secure the unit in place with tape If the preamplifier is placed in the animal bed make sure that it is at least 10 cm to 12 cm from the intended position of image slice planes 3 Connect the optical fiber cable to the front of the cardiac preamplifier and run the cable over to the PGM 1000 receiver 4 Mount the PGM 1000 receiver unit on to
103. on files press the right mouse button All files in the directory appear even if they are not compensation data Finally the contents of the eccTool Files window are updated only when the window is opened so that a new file name will not show up until the window is closed and reopened VNMR 6 1C User Guide Imaging 01 999163 00 A0800 7 4 Microimaging Hardware Advanced Use of eccTool and eccsend Programs The information in this section is most useful to those operators who want to use different gradient hardware systems that have different range requirements for the specifiers used in the eddy current compensation units The actual eddy current setup is performed any time the file eddy out is present in the VNMR system acqqueue directory and su is typed The content of eddy out is binary data If it is present in acqqueue when su is executed psg renames eddy out to exp xpan Acqproc takes this file sends it to acquisition and then deletes it The file eddy out is created by a program eccsend This program takes a compensation file that specifies the details of the eddy current controls as text The compensation file may be made or altered by hand or by eccTool although manual operation of eccsend can send information from any location The gradient compensation boards default to gain and duty cycle setting of zero when powered up The slew rate is set to zero the compensation amplitudes are zero and the time constants are m
104. one or more FDF files exist in the experiment dat dir directory Programs bp mc bp _ sort bp 2d bp 3d The BP package contains the programs bp_mc bp_sort bp_2d and bp_ 3d bp_mc Performs a magnitude calculation Used prior to bp_2d and bp_3d bp_sort Shuffles projections obtained using an arrayed parameter in a 2D acquisition in the order required by the bp_2d program 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 249 Chapter 10 2D and 3D Backprojection bp_2d Controlled by a command file that holds several lines Each line contains the bp_3d parameter name in the first position and the value of the parameter to be used in the second position separated by a blank or a tab Adding a comment to a line or a particular parameter setting is possible by using a blank or tab as a separator The value of the parameter may not be assigned by an equals symbol The command file holds two classes of parameters labeled essential and optional The essential parameters have to be specified in the command file whereas the optional parameters are derived from the essential parameters and some general assumptions if they are omitted Table 22 provides a summary about the valid parameters and their defaults Table 22 Parameters Passed to the bp_2d and bp_3d Programs Parameter Keyword Parameter Type Essential Optional Default Setting prof_file string x m_size int x VNMR np i_size int X VNMR np n_phi int x n_theta in
105. or more spectra horizontally When a single spectrum is displayed integral display is controlled by the parameter intmod which can have the following values e intmod off turns off the integral display e intmod full displays the entire integral e intmod partial displays every other integral region For arrayed 1D spectra or for 2D spectra a particular trace can be viewed by supplying the index number as an argument For 2D data sets spectra can be displayed from either the f4 or f2 domain by setting the parameter t race equal VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Arguments Examples See also Related A 4 Commands and Macros for Processing and Display to f1 or f 2 respectively After entering ft 1d interferograms can be viewed by setting trace f1 and then entering dss Multiple spectra can be displayed by supplying indexes of the first and last spectra The position of the first spectrum is governed by the parameters wc sc and vp For 1D data subsequent spectra are positioned relative to the preceding spectrum by the parameters vo vertical offset and ho horizontal offset For 2D data ho defines the total horizontal offset between the first and last spectrum Also for 2D data vo is inactive while the parameter wc2 defines the total vertical offset between the first and last spectrum To display spectra horizontally the command dssh causes vo to be set to zero and for ho sc and wc to be ad
106. parameters groa and grora and the timing parameter tep tep controls acquisition delay time in us to allow for propagation of the gradient pulse b Collect a dataset reference scan with the phase encode gradient turned off image 0 and display the echo signals on the screen by using episet or by entering the following commands image 0 go df2d The echoes might appear tilted Usually the odd and even echoes appear to line up differently as shown in Figure 22 c Change the tilt by adjusting the groa parameter in 0 01 unit steps At this stage you might see two parallel echo trains corresponding to the odd and even echoes respectively as shown in Figure 23 t2 F t2 t1 ti Figure 23 Echo Train After Figure 22 EPI Echo Train groa Adjustment d Adjust the grora parameter in 0 1 unit steps until the echoes line up as shown in Figure 24 e If the echo train is offset with respect to t2 0 adjust the tep parameter so that the echoes are centered according to t2 as shown in Figure 25 Note that tep corresponds to a delay in us Usually tep is set to about 0 us to 50 us t2 t2 esceeoeveeeeed O O eee2e00008000 t1 ti Figure 24 Aligned Echoes Figure 25 Centered Echoes f Use episet to generate the phase correction map file 7hasemap in the current experiment directory and display the 2D time domain data episet is equivalent to executing the following commands
107. parameters are related to the BP package tofc Transmitter frequency offset for slice selective excitation gro Readout gradient grof Factor for fine tuning of the readout gradient compensation gss Slice gradient gssf Factor for the fine tuning of the slice gradient compensation at Acquisition time ni Loop count for 2D imaging and inner loop count for 3D imaging ni2 Not used in 2D imaging but is used in array 2D imaging and is the outer loop count for 3D imaging phi Angular range 180 or 360 in 2D and 3D imaging theta Angular range 180 or 360 in 3D imaging trise Gradient settling time te Spin echo time tpe Duration of dephasing period of read gradient tph Time for setting the pulse phase T1 p only tr Recovery time pl tpwrl Duration and transmitter power of 90 pulse pi tpwri Duration and transmitter power of sr ir pulse pj tpwrj Duration and transmitter power of spin lock pulse Tip only 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 243 Chapter 10 2D and 3D Backprojection sat Delay between the first two saturation pulses in the aps sequence nsat Number of pulses in the aps sequence The following parameters are string type parameters related to the BP package orient String of three letters assigning the orientation for the x y and z gradients orient xyz assigns direction x to the x gradient direction y to the y gradient and direction z to the z gradient orient
108. patent rights nor the rights of others Inclusion in this document does not imply that any particular feature is standard on the instrument UNITYTNOVA MERCURY VX MERCURY Gemini GEMINI 2000 UNITYplus UNITY VXR XL VNMR VnmrS VnmrX VnmrlI VnmrV VnmrSGI MAGICAL II AutoLock AutoShim AutoPhase limNET ASM and SMS are registered trademarks or trademarks of Varian Inc Sun Solaris CDE Suninstall Ultra SPARC SPARCstation SunCD and NFS are registered trademarks or trademarks of Sun Microsystems Inc and SPARC International Oxford is a registered trademark of Oxford Instruments LTD Ethernet is a registered trademark of Xerox Corporation VxWORKS and VxWORKS POWERED are registered trademarks of WindRiver Inc Other product names in this document are registered trademarks or trademarks of their respective holders Overview of Contents SAFETY PRECAUTIONS siscvssccstinvetesatsaxseavesievesatetlatevexisassecaeelivestirtectttexecececte 11 ialis olo io MP E 15 Chapter 1 First Steps Making an Image cccsssseeeeeeeseeeeeeseeeeeeeeeseeees 17 Chapter 2 Imaging Experiments cccsseeccessseeeeeeesseneeeeessneeeeesseneeeeensneeees 25 Chapter 3 Imaging Pulse Sequences ccssseeeeesseeeeeeeeeseeeeensseneeeeeeseeeees 41 Chapter 4 Image Browser ccccssseeeceeseeeeeeenseeeeeeesenneeeeensneeeeenseneeeesesneaes 65 Chapter 5 Image Browser Math Processing cccsseeccssseeeeeeeseseeneeeeees
109. peaks and the metabolic maps by selecting the Peak Registration and Mmap No Set options Perform a curve fit of the entire spectrum by selecting Auto Curve Fit If the curve fit is satisfactory select Fitting OK to close the interactive Curve Fitting window Remember the peaks must be registered and the Mmap numbers must be set before closing the Interactive Curve Fit window Otherwise the Global Calculation does not work correctly To adjust the fitting parameters place the cursor on one of the peaks To better adjust the cross hair cursor zoom in on the selected peak After adjusting one or all of the ends of the cursor select the Edit from Marker option on the panel to update its values Select the Curve Check option to update the fit Global Calculation After the peak and metabolic map numbers have been registered select either the Integral or the Curve fitting method and then the Apply To All button in the Global Calculation field Integral Method The Integral Method is the fastest way to get Mmap information It finds the peaks in a voxel and calculates the area under the peak However if there are two peaks close together VNMR 6 1C User Guide Imaging 01 999163 00 A0800 6 2 Getting Started the integral method does not find all the area under the peak It only gets the area directly under the peak and when the second peak starts this method starts integrating the area under it When this situation occurs the Integral
110. second phase encode dimension Higher order phase encode dimensions are found in 3D volume imaging and Chemical Shift Imaging CSI experiments with two spatial dimensions Number in cm gpe2 2nd phase encoding gradient increment P imprep Set up rf pulses imaging and voxel selection gradients M lpe3 Field of view size for 3rd phase encode axis P seqcon Acquisition loop control P setgpe Set phase encode gradient levels M sw2 Spectral width in 2nd indirectly detected dimension P tpe Duration of the phase encoding gradient pulse P Field of view size for 3rd phase encode axis The size of the field of view along a third phase encode dimension Higher order phase encode dimensions are found in Chemical Shift Imaging CSI experiments with three spatial dimensions Number in cm gpe3 3rd phase encoding gradient increment P imprep Set up rf pulses imaging and voxel selection gradients M lpe2 Field of view size for 2nd phase encode axis P seqcon Acquisition loop control P setgpe Set phase encode gradient levels M sw3 Spectral width in 3rd indirectly detected dimension P tpe Duration of the phase encoding gradient pulse P 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 323 Appendix A Commands Macros and Parameters lro Field of view size for readout axis Description The size of the image field of view along the readout dimension This parameter is used by dconi and imconi to specify the read
111. selection if a spectrum does exist in the frame After data has been selected filtering functions in the Spectral Reconstruction window Matrix Filter Type Time Const Shift Const can all be interactively selected to adjust the filter applied to the data 6 4 Processing Functions 156 When an entire CSI data set is being processed the interaction is different than when a selected voxel is processed When applying an operation to the whole CSI data set the data might not necessarily be displayed The CSI tool has the following global data buffers for CSI data e CSI raw data e Localized FID data e Multivoxel spectra MVS e MVS curve fitted data e Metabolic map data The CSI tool has the following global data buffers for reference image data e Raw image data e Reconstructed image data Most processing operations on an entire data set operate on one global data buffer and process it into another global data buffer These global data buffers keep their data until another processing operation is performed that overwrites the data buffer That is even though MVS data is being processed and displayed the processing operation to transform raw data into localized FID data can be run at any time Also when performing a processing VNMR 6 1C User Guide Imaging 01 999163 00 A0800 6 4 Processing Functions operation on the entire data set one and no more than one graphics frame must be selected This selected graphics frame is the destin
112. spin rate P su Submit a setup experiment to acquisition M usergo Experiment setup macro called by go ga and au M wshim Conditions when shimming is performed P image Display noninteractive gray scale image M Applicability Systems with imaging capabilities Syntax image Description Brings up a dcon 2D display of an image using grayscale and linear scaling of the intensity that can be used for adjusting the display while using dconi Related dcon Display noninteractive color intensity map C dconi Interactive 2D data display C dconn Display color intensity map without erasing screen C imageprint Print currently displayed image on plotter C Syntax imageprint Description Produces a dithered density map of the currently displayed image and sends it to the current plot device The dithered image prints in reverse contrast black for white so that the gray tones are inverted in the plot output imageprint is not suitable for pen plotters Alternate Image button on the 2D Plotting Menu See also User Guide Liquids Related plot Automatically plot spectra M imark Label a 2D image or spectrum M Syntax mark label lt color gt 292 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Description Arguments Examples Related imcalc Syntax Description Arguments A 4 Commands and Macros for Processing and Display Writes a label to a point on an interactive 2D image or spectrum determined by t
113. switch of the PGM 1000 receiver can be used to correct the sign of the ECG signal if the leads to the forelegs are connected in the reverse sense Bring the electrode lead wires from the underside of the animal bed so that they can be taped to the bed surface to prevent the wires from moving during the experiment Securely tape the animal s limbs and electrode clips to the animal bed These precautions minimize the disturbance observed in the ECG signal due to small motions of the subjects limbs and vibrations of the electrode leads Before inserting the cradle into the magnet check the electrode placement and ECG signal by powering up the cardiac preamplifier Adjust the oscilloscope to trigger on the ECG signal on channel 1 of the oscilloscope If the ECG is weak increase the gain of the PGM receiver using the X10 gain setting If an acceptable ECG signal with a QRS complex of about 1 to 1 5 V and baseline features of less than 0 5 V can be obtained note the following features of the ECG R to R wave time interval R to T wave time interval P to R wave time interval These features are useful in choosing acquisition parameters If a poor signal is obtained check the electrodes electrode connections and power on status of the PGM modules Correct any defects in the preparation ECG signals greater than 1 5 V can be observed Try to scale the peak of the R wave so that it is less than 12 V Place the animal cradle into the magnet Tune
114. than once appears which is normal Enter make depend only after you change include directives in a file or change the makefile itself Enter make myfunc to compile the myfunc routine Variables Macros and Functions Available to User Functions This section lists global variables macros and functions for use in mat hfunc routines Global Variables Except where noted global variables are initialized before mathfunc is called int nbr_image_vecs Number of image vectors passed to the user s program int in_vec_len Array of length nbr_image_vecs giving the number of images in each input image vector int vecindx Array of length nbr_image_vecs giving the index in the in_object and in_data arrays of the first member of each image vector The rest of the members of a given vector sequentially follow in those arrays int nbr_infiles Number of input images in all the image vectors put together int input_sizes_differ Set to TRUE if the input images are not all identical in size If the images are all the same size it is set to FALSE int img_width If all input images are identical in size these arrays have img_height their dimensions The img_size is the total number of img_depth img_size data pixels int in_width If input images vary in size use these arrays to get the in_height sizes of the individual images The dimension of these in_depth in_size arrays is nbr_infiles FDFptr in_object A
115. the following chapters e Chapter 1 First Steps Making an Image introduces you to the typical steps in setting up and running a VnmrIMAGE pulse sequence e Chapter 2 Imaging Experiments describes the basic concepts necessary to understand MRI experiments e Chapter 3 Imaging Pulse Sequences describes some of the pulse sequences for imaging available in Varian NMR spectrometers e Chapter 4 Image Browser covers ImageBrowser a comprehensive image viewing and analysis program e Chapter 5 Image Browser Math Processing describes ImageBrowser which is used in conjunction with Image Browser to do more complex processing e Chapter 6 CSI Data Processing describes a tool for easy processing of chemical shift image data CSI e Chapter 7 High Performance Auxiliary and Microimaging Gradients covers the high performance auxiliary gradient HPAG accessory e Chapter 8 Digital Eddy Current Compensation describes the function of the Digital Eddy Current Compensation module and the associated software interface decctool e Chapter 9 Physiological Gating Module explains how to use the physiological gating module PGM which detects the ECG of the experimental subject and sends a trigger pulse to the spectrometer for prospective gating experiments e Chapter 10 2D and 3D Backprojection shows how to acquire and reconstruct 2D and 3D NMR images based on the backprojection B
116. the mapping function are also applied to any new images when they are loaded but the data range is scaled to match the data in the particular image The graph at the bottom of the Vertical Scaling window is a plot of gray level as a function of data value The gray level corresponds to the index into Image Browser s colormap The intensity of the screen pixel as a function of colormap index is set by the Gamma Correction window discussed in Vs Prop Menu Gamma Correction on page 151 Data Range The range of data values to map to the full Figure 68 Vertical Scaling Window range of gray values is set by the two type in fields labeled Data Range The data values are plotted linearly along the horizontal axis between the values in the Data Range fields The Return key must be pressed in at least one of the fields for the changes to take effect Mapping Function The shape of the mapping function is selected by the buttons at the upper left of the Vertical Scaling window The mapping function translates the data value in a pixel to a corresponding grey level In the following discussions normalized variables are used x and y for the data and for the grey level values d and g These variables are defined as oe SG tt Eq 27 Cage Amin and yao Eq 28 Emax Emin Therefore both x and y vary from 0 to 1 Note that with the appropriate gamma correction discussed in the next section the actual sc
117. the rf coil as usual Adjusting the PGM Receiver to Obtain a Cardiac Trigger Once the animal cradle has been inserted into the magnet check the ECG signal on channel 1 of the oscilloscope It should show slight changes after the animal cradle is placed into the magnet Typically the T wave appears with a larger amplitude and baseline noise might increase The peak of the QRS complex should be at least 0 5 V above the largest baseline feature if an acceptable cardiac trigger is to be obtained Adjusting the receiver to obtain a cardiac trigger consists of the following steps 1 Adjust the bandpass filter to obtain a stable electrocardiogram with a flat baseline 2 Set the voltage threshold used to detect the QRS complex 3 Adjust the inhibit delay to control the frequency of the trigger pulses VNMR 6 1C User Guide Imaging 01 999163 00 A0800 9 3 Experimental Setup Adjusting the Bandpass Filter The low pass filter control of the PGM receiver reduces the high frequency noise in the ECG High frequency noise is attenuated as the low pass frequency is decreased Attenuation improves the signal to noise ratio of the QRS complex although the total amplitude of the ECG will be progressively reduced as the low pass frequency is reduced It is best to initially set the low pass frequency to 160 Hz The high pass filter control removes low frequency undulations from the baseline of the ECG Low frequencies are attenuated as the hi
118. their respective parameter sets such as IMAGE and SSFP will continue to work properly when used with the proper macros but you need to take care not to mix and match old and new Notational Conventions The following notational conventions are used throughout all VNMR manuals e Typewriter like characters identify VNMR and UNIX commands parameters directories and file names in the text of the manual For example The shutdown command is in the etc directory The same type of characters show text displayed on the screen including the text echoed on the screen as you enter commands during a procedure For example Self test completed successfully e Text shown between angled brackets in a syntax entry is optional For example if the syntax is seqgen s2pul lt c gt entering the c suffix is optional and typing seqgen s2pul cor seqgen s2pul1 is functionally the same e Lines of text containing command syntax examples of statements source code and similar material are often too long to fit the width of the page To show that a line of text had to be broken to fit into the manual the line is cut at a convenient point such as at a comma near the right edge of the column a backslash is inserted at the cut and the line is continued as the next line of text This notation will be familiar to C programmers Note that the backslash is not part of the line and except for C source code should not be typed when ent
119. this manual and in the manual VWMR Command and Parameter Reference 3 1 Initial Setup This section describes the procedure for initially setting up imaging experiments using a single pulse sequence The main purpose of the initial setup procedure is to make sure that the system is properly functioning and to determine the rf calibration parameters Once the initial setup has been completed the rf calibration parameters such as transmitter frequency and power can be used for subsequent imaging experiments and therefore do not need to be repeated However if the sample or coil is changed it might be necessary to repeat the initial setup procedure Table 5 on page 62 summarizes the commands macros and parameters that are used 1 Position the sample in the magnet Because imaging coils and samples come in various sizes and shapes it is important to position the sample and the rf coil in the center of the magnet 2 Place the sample in the magnet and tune the probe Be aware that different imaging samples can influence the tuning of the probe depending on their sizes compositions or even the positioning within the rf probe 3 Use the single pulse sequence s2pu1 to check for the NMR signal Initially use a sufficiently wide spectral bandwidth to avoid aliasing of the proton signal The spuls macro can be used to load the default parameters suitable for imaging rather than for high resolution spectroscopy 01 999163 00 A0800 V
120. to a lower value It might also be necessary to further attenuate the incoming signal by manually setting a signal attenuator or by setting the parameter presig 1 topresig h The macro setgn automatically sets the receiver gain based on the input signal VNMR 6 1C User Guide Imaging 01 999163 00 A0800 3 2 Conditions for Use Recycle Time Adjusted When setting gain or measuring pulse power you must increase the predelay parameter d1 or recycle time parameter t r to greater than 4 7 to allow the spins to return to equilibrium before subsequent rf pulses Lock Spinner Decoupler Commands and Parameters Disabled If you use a spectrometer that is also used for high resolution spectroscopy make sure that the commands and parameters relevant to the lock spinner and decoupler are disabled The commands and parameters are disabled when they have the following settings homo n lock u lockpower 0 spin 0 spin n The spuls macro is convenient for loading s2pu1 pulse sequence parameters for imaging systems The s2pu1 macro is used in high resolution spectroscopy and might incorrectly initialize the parameters for imaging Pulse Power Set Low Imaging spectrometers are usually equipped with high power rf amplifiers Make sure that the pulse power is set sufficiently low to avoid any damage to the rf coil Gradient Calibration File Created Imaging systems can be equipped with either a single gradient coil or multiple
121. to by handle The value of the element is put into the location pointed to by pvalue Returns a logically true nonzero value on success and a logically false zero value on failure Example int get_header_array_int handle name index pvalue FDFptr handle char name int index int pvalue Gets the value of one element of a header variable that is an array of doubles The index member of the variable name is read from the image referred to by handle The value of the element is put into the location pointed to by pvalue Returns a logically true nonzero value on success and a logically false zero value on failure Example int get_header_array_double handle name index pvalue FDFptr handle char name int index double pvalue Gets the value of one string from a header variable that is an array of strings The index string from the variable name is read from the image referred to by handle A pointer to the character string is put into the location pointed to by pst ring Returns a logically true nonzero value on success and a logically false zero value on failure Example int get_header_array_string handle name index pvalue FDFptr handle char name int index char pstring Returns the number of pixels in the fast image dimension Example int get_image_width handle FDFptr handle Returns the number of pixels in the medium image dimension Ex
122. to specify the list of slice positions For this reason the da command does not normally display the values contained in a pss array To see this list of values enter the command da pss Number in cm da Display acquisition parameter arrays C gss Slice selection gradient strength P ns Number of slices to be acquired P seqcon Acquisition loop control P sliceorder Reorder the slice position list M thk Slice thickness P Euler angle for defining imaging plane orientation One of the three Euler angles used to define imaging plane orientation theta is the angle formed by the line normal to the imaging plane and the magnet Z axis theta is generally not directly set by the user but instead set either by entering a string value into the orient parameter or through interactive graphical planning of a new imaging plane from an existing scout image orient Slice plane orientation P phi Euler angle for defining imaging plane orientation P psi Euler angle for defining imaging plane orientation P Slice thickness Slice thickness for a 2D imaging plane or 3D slab selection To change thk enter the desired value through the VNMR command line and then run the macro imprep to update other dependent parameters thk and gss are related by the expression gss 10 BW y thk where BW is the bandwidth of the rf pulse used for slice selection Number in mm gss Slice selection gradient strength P imprep Set up rf pulses ima
123. trise Once sysgcoil is updated with the set gcoil macro gcoil in the current experiment is updated as well and new gradient calibration values are retrieved from the corresponding gradt ables file As different experiments are joined or new parameter sets retrieved gcoil and the gradient calibrations are updated in each case to match the new sysgcoil Therefore each experiment and all saved data sets retain a record of what gradient hardware was in place at the time of data acquisition Arguments file specifies the name of the gradtables calibration file Examples setgcoil asg33 Related config Display current configuration and possibly change it M creategtable Create new gradient calibration file isotropic strengths M 266 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 setloop Syntax Description A 2 Macros for Setting Up Experiments gcoil Current gradient coil P gmax Maximum gradient strength P sysqeoil System gradient coil P trise Gradient rise time P updtgcoil Update gcoil and gradient calibration parameters M Set nf and ni values to control arrayed and real time looping setloop Sets the values for the parameters nf and ni to control arrayed and real time looping Loop control in imaging experiments such as multislice multiecho and phase encoding is set through a series of parameters that the user sets directly ne ns nv nv2 and nv3 Underlying these parameters are two lower leve
124. used to select an object or to draw an ROI or to annotate text Selecting an object deselects any previously selected objects Objects that can be selected include graphics frames voxels ROIs and markers and text The object selected is chosen according to a priority hierarchy 1 Ifthe cursor is inside an ROI near a line or point ROL or near text the corresponding object is selected If there is more than one qualifying object only the most recently created object is selected 2 Ifthe cursor is inside a frame boundary the frame is selected The shape of the cursor changes when different graphics tools are selected to identify which operations the mouse is ready to perform MIDDLE button ADJUST The middle button of the mouse is not used inside the command panel VNMR 6 1C User Guide Imaging 01 999163 00 A0800 6 2 Getting Started Inside the graphics regions the middle mouse button toggles the state of an object selecting it if it is not selected and deselecting it if it is RIGHT button MENU The right mouse button is used to open menus in the command panel Using FileBrowser The FileBrowser tool for loading files is the default choice when the command panel File option is selected The initial FileBrowser directory is the directory where CSI was started A file or directory is selected when the name is highlighted in the scrolling list or when the name appears on the top line of the FileBrowser To change director
125. value of the first array element end is the value of the last array element number is the total number of array values exparray exparray d2 0 01 2 10 array Easy entry of linearly spaced array values M 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 257 Appendix A Commands Macros and Parameters flash3d Syntax Description gems Syntax Description Examples imprep Syntax Description array Parameter order and precedence P setarray Set up a parameter array M Retrieve parameters for FLASH3D imaging experiment flash3d Retrieves the standard parameters for the FLASH3D imaging experiment from vnmr parlib Load default parameters from gems par gems Loads the default parameters from the gems par file into the current experiment gems first searches for a parameter file in SHOME vnmrsys parlib and loads the file if it is present otherwise the file is loaded from the vnmr parlib directory gems SHOME vnmrsys parlib gems par H1 gems vnmr parlib H1 Set up rf pulses imaging and pulse power levels imprep A one pass macro that sets all gradient and pulse power levels in imaging and localized spectroscopy experiments All applications that use list parameters plist patlist pwrlist etc can be set up with imprep imprep sets all of the following parameters where applicable e Power levels for all pulses found in plist e Readout gradient strength together with sw e
126. window Store Saves the frequency difference in the current voxel to global map Display diff pH Selects whether or not to output diff pH values to Info Message info window when performing global mapping Mapping Apply Performs global mapping of Map Type by using Peak Define and displays map in currently selected Gframe Save Map opens a Save Check window that is the same type window as the Image Calctool save window It allows the mapped image definition to be saved into the current global buffer of mapped images The window opens with metabolic map number set to 1 plus the number of global metabolic maps ROI Spectrum ROI Spectrum is used with the ROI Line tool and the ROI Box tool on reference images e Used with the ROI line spectrum it extracts and stacked plot of all the spectra underneath the ROI e Used with the ROI Box tool it extracts and average spectrum of all the spectrum within the box It relates areas in a reference image to the voxel spectra in its CSI data set To generate a stacked plot of spectra use the ROI Line tool to draw a line across a reference image Then select ROI Spectrum from the Process menu and a series of stacked spectra appear in one of the canvas windows To generate an average of all the spectra in an ROI region use the ROI Box tool to draw a box in the desired region of a reference image Then select ROI Spectrum from the Process menu and an averaged spectrum appears in one of the canvas w
127. 0 causs em max gradient coil name tc203 for a cad 7 three axis gradient set with unequal ganaz 10 00 gaussrcmi maximum gradient strength boresize Magnet bore size P creategtable Generate new gradient calibration file M gmax Maximum gradient strength P 308 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 gmax Description Values See also Related gradstepsz Description Values See also A 5 Parameters setgcoil Assign sysgcoil configuration parameter M sysgcoil System gradient coil P trise Gradient rise time P updtgcoil Update gradient coil M Maximum gradient strength Allowed maximum gradient level absolute value It is one of the calibration entries ina gradtables file gxmax gymax and gzmax are used when the maximum gradient level is different for each axis which is the case for triple axis PFG coils Number in gauss cm VNMR and Solaris Software Installation boresize Magnet bore size P creategtable Generate new gradient calibration file M gcoil Current gradient coil P gxmax gymax gzmax Maximum gradient strength for each axis P sysgcoil System gradient coil P trise Gradient rise time P Gradient step size Maximum gradient DAC value that determines the type of gradient DAC board used in the system 12 bit or 16 bit This parameter is used internally to convert gauss cm gradient levels to the proper hardware DAC level Systems with 12 bit DACs older SISCO
128. 00 however MERCURY and GEMINI 2000 automatically use gated decoupling when tn and dn are both in the high band ie if tn and dn is H or F and dm y Enables time shared decoupling Unlike the dm dmm and hs parameters homo is not under status control On systems with type 2 or 3 interface board apinterface 2 or apinterface 3 homo does not control any signal routing the position of the relevant relays is controlled by whether homonuclear decoupling tn equals dn or heteronuclear decoupling tn not equal to dn is in effect On UN YINOVA and UNITYplus the values are n or y where e n specifies no gating e y specifies that the receiver is gated which is done by controlling the observe L O local oscillator line If dm y first decoupler rf amplifier blanked unblanked and preamplifier are gated If dm n no gating of these signals takes place When homo is set to y dmm should be set to c for continuous wave CW modulation On UNITY and VXR S the values are n or y where 343 VNMR 6 1C User Guide Imaging Appendix A Commands Macros and Parameters e n disables decoupler time sharing which is appropriate for heteronuclear decoupling or for cases in which the decoupler is off during acquisition e y selects time shared decoupling which is appropriate for homonuclear decoupling in which the receiver is gated off when the decoupler is on On systems with the type 1 interface
129. 00 958198 20 The decoded electrocardiogram filtered or unfiltered inhibit output threshold output and gate output signals can be examined using an oscilloscope connected to coax cables 00 958198 10 Cardiac Preamplifier Panels Controls and Connections The function of the cardiac preamplifier is to receive electrical signals from the three limb electrodes attached to the animal subject The signals are amplified and encoded for optical transmission to the PGM 1000 receiver module Input output jacks and the unit s controls are located on the front and back panels of the module Preamplifier Front Panel The front panel of the preamp lifier shown in Figure 101 is fitted with the following ON OFF This switch is used to activate the unit when it is fitted with an internal battery VNMR 6 1C User Guide Imaging 01 999163 00 A0800 9 2 Hardware Description e LOW BAT The low battery LED indicates when the PGM 1000 PREAMP power supplied by the internal battery is low If the low battery LED blinks when the O O module is powered up replace the battery before LOW BAT using the unit e Optical Fiber Output Jack Figure 101 Front Panel of Cardiac Preamplifier This jack is used to connect the unit to the PGM 1000 receiver via the optical fiber cable It also contains a small LED used to transmit the optical signal The LED lights on power up unless the internal battery is exhausted Pream
130. 00 A0800 VNMR 6 1C User Guide Imaging 27 Chapter 2 Imaging Experiments The frequency fy of the spins at various y locations is defined by the following equation fy By t y G Eq 3 In this equation y refers to the y location in cm and Gy refers to the applied field gradient in gauss cm Equation 3 is the most important equation in MRI because it correlates the spatial position of the spins y to the measured parameter fy That is the frequency spectrum measured is a direct reflection of spatial information along y because as shown in Equation 4 ey Eq 4 when y 0 Equation 4 is the same as Equation and Equation 2 so the frequency at the origin of our frame of reference is equal to the resonance frequency of water f It is necessary to place the rf transmitter frequency at f so that images can be spatially referenced with respect to the origin of our reference frame or the center of the magnet Under the previously described conditions a single pulse sequence yields a spectrum that contains a continuous range of frequencies as shown in Figure 3 Profile with a gradient on Spatial frequency spectrum The frequency spread is a direct reflection of the 0 0 spatial position of the spins along the y direction Signal intensity l is directly related to the J4 amount of water at various positions along y The tube f as 0 fo of water appears as a Transmitter Tra
131. 002 fdf 7 Min 0 001353 Statistics Histogram limits Span ROI intensities a window with a Max 0 03317 Soi Median 0 02411 Histogram bins 100 histogram of intensities Mean 0 02328 Image segmentation keep range Stdv 0 005166 Min infinity Max infinity similar to Figure 34 is Area 3 957 sq cm Segment images Segment ROIs elias Zhi Se Show segmented region opened A full Update Auto On ROI Change Print Stats Dump Data File complement of statistics is displayed for the ROI minimum maximum median mean and standard deviation of pixel intensities and ROI area and volume Figure 34 Statistics Window with One ROI Only pixels with intensities between the set limits are included in the histogram or in the statistics calculations So for example the calculated volume decreases as the limits are imposed The Statistics Histogram limits menu offers the following ways to set histogram limits Span ROI Intensities Sets the histogram limits to the maximum and minimum intensity values in the ROI This option is equivalent to no limits on the pixel intensities included in the statistics and volume calculations Span Image Intensities Sets the histogram limits to the maximum and minimum intensity values in the image The median value might change when using this span as opposed to Span ROI Intensities because of the finite data binning used to calculate the median The real difference is in the h
132. 0800 VNMR 6 1C User Guide Imaging 141 Chapter 6 CSI Data Processing 142 After registering the values you can wait to update the data set and apply the phase and baseline corrections at the same time To skip the previous procedure select the Automatic option in the Mode field Adjusting the Phase with the Spectrum Tool If the automatic phase adjustment is not making the desired phase adjustments the Spectrum tool il described on page 154 in the G Tools window can be used After a spectrum has been selected select the Spectrum tool The default type of phasing is constant phasing however this method can be changed by clicking on the Filter Properties option in the G Tools window After the type of phasing has been selected the phase can be manipulated by positioning the cursor over the spectrum holding down the left mouse button and moving the cursor up and down within the Gframe After the desired phasing has been reached select the Auto Go option in the Local Phase Correction field to register those phase values then select Write All Baseline Correction The same as with phasing the procedure to apply a baseline correction to the data can be skipped if desired Baseline correction is performed in a similar manner to phasing but different functions and tools are used Click on Baseline Correction in the Process menu see Figure 60 Select a spectrum and perform the correction on it before operating on the entir
133. 164 startup files 133 cubic spline interpolation 81 curecc file 266 parameter 194 current FID data block 333 current gradient coil 308 cursor 77 97 data processing 88 data window 97 functions 97 tolerance function 81 curve mode 84 150 D dl parameter 21 43 63 DAC resolution 23 data acquiring 333 acquiring points 335 collecting storing and processing EPI 61 converting to linear order 303 enhancing 77 getting and Fourier transforming 62 saving in selected frames 102 values range 83 149 data_ commands 102 datasets displaying 232 01 999163 00 A0800 date and time message 131 dconi command 46 51 deccgo macro 256 parameter 257 decctool macro 62 257 program 43 decoupler disabling 43 homodecoupling control 343 default parameters loading 62 degradation of image 245 delay first 315 preacquisition 316 deleting graphic frames Gframes 72 81 100 deselecting graphic frames 101 destroy command 99 destroygroup command 99 deuterium lock 22 dgm macro 279 diastole period 209 Digital Eddy Current Compensation DECC 43 62 199 206 dimensions application 344 spatial setting 344 voxel 328 disabling lock spinner and decoupler 43 disp3d program 232 279 display contrast setting 101 Display Control window 170 display_ commands 101 displaying 2D data interactively 278 3D FDF file 279 datasets 232 EPI data 284 GEMS images 51 Image Brow
134. 235 Chapter 10 2D and 3D Backprojection 236 f Angle phi 180 degree 360 degree This option selects between a 180 or a 360 angular span of the projections taken Usually you take the 180 span because the projections obtained at 0 is identical to the centrally mirrored from 180 degree However in slice selective excitations and cases of Bo shift caused by gradient switching the image quality can be improved by taking projections from the full 360 span g Angle theta 180 degree 360 degree This option is only valid for 3D acquisition and reconstruction It should be set to the same value as for the angle phi 2 bp_setup checks your values for validity computes sweep width and digitizer resolution checks gradient strength including an overrange test and presets the spin echo time te The values obtained are printed out similar to Figure 116 EADOUT SETTINGS field of view 15 0000 resolution 0 05859 sweep width 51200 np 2 256 acquisition time 0 00500 gro TITS readout gradient 7 9559 gauss cm Figure 116 Macro bp_setup Values Display You can accept or reject these values from the message Use these values y n 3 Enter y to accept the values or n to reject the values 4 Set the spin echo parameter te to the value you want If te is large enough the pulse sequence puts the spin echo in the middle of the acquisition time Otherwise the spin echo appears in the left sh
135. 256 4096 x TE TR 2 minutes 128 x 128 x 128 3D vol 512 16384 x TE TR 20 minutes 256 x 256 x 256 Acquisition and Reconstruction with Sequences bp2d and bp3d When setting up for an acquisition with pulse sequences bp2d and bp3d the standard imaging method should be used Setting Up for Acquisition To set up for dp2d and dp3d check the following settings and then run macro imprep 1 2 Make sure rfcoil and gcoil have been defined Set any desired pulse lengths For volume imaging using bp34d have pulse lengths as short as possible in order to irradiate as large of volume as possible Some versions of the sequence should be run with square nonselective pulses Set the transmitter offset resonance Set te and tr If te is large enough the pulse sequence puts the spin echo in the middle of the acquisition time Otherwise the spin echo will appear in the left shifted Note that reconstruction artifacts might appear if the spin echo appears too left shifted Setting t r is a compromise between total measurement time and full T4 relaxation in the case of pure T weighting as well as for sr and ir T weighting If using dp2d set 1ro image size and pss position of slice selected Set trans sag and cor orientation parameters The angles psi phi and theta can also be set for an oblique orientation Set np for the number of points to acquire np determines the size of the image Set nv for the number of projecti
136. 3 Imaging Pulse Sequences 56 Field Inhomogeneity Effects Field inhomogeneity effects are caused by either inhomogeneous fields in the main magnet or susceptibility gradients caused by the sample and other materials in the vicinity Field inhomogeneity effects are also a serious limitation in EPI because they behave like chemical shift effects These type of effects are also phase encoded and appear as frequency shifted components in the phase encode dimension often leading to severe distortions in the image as shown in Figure 21 Therefore shimming is an important part of the EPI setup procedure Shimming on the slice should give better results than the usual single pulse method A sequence such as csi2d can be used for shimming on the slice When csi2dis used the echo or FID is detected after selectively exciting the slice region Phase Correction Map Files Homogeneity at the edges of an rf coil is often poor which can lead to shimming related artifacts in EPI images Distortions caused in the edges of a sample also affect the phase correction routines used in EPI data processing Phase correction information is located in the file phasemap in the current experiment directory The commands pemapapp1ly pcmapclose pcmapgen and pcmapopen are useful for working on phase correction map files Spurious Gradient Fields Gradient echo imaging experiments are also sensitive to spurious gradient fields Therefore the FLASH sequence can be
137. 3 spectra extracting 132 obtaining information 26 phase and baseline correction 131 rearranging in 2D data set 304 rearranging in a 2D data set 304 reconstruction 131 stacked spectra display 280 Spectral Reconstruction window 158 spectral width 331 332 333 Spectrum tool 142 154 spectrum collect 268 spin echo multislice sequence 17 echo sequence EPI 58 echo time 237 240 246 frequency definition 28 lock pulse 238 242 parameter 42 43 spinner command disabling 43 splitting graphic frames into rows and columns 100 selected 80 spoiling time for gradient 319 spuls macro 41 42 43 63 spurious gradient fields 56 sr excitation 229 235 241 sr pulse 243 sslist parameter 341 stacked spectra display 280 standard 2 pulse sequence 264 285 300 340 application mode 342 deviation 91 format to compressed format 45 start and end angle values 3D backprojection 252 starting acquisition 231 startup macro 68 103 stat_ commands 103 static magnet field value 307 statistics calculating 66 function 77 getting from ROIs 77 multiple image 95 multiple ROIs window 93 one ROI window 91 output 94 processing 89 ROIs 90 91 updating 103 writting to a file 94 x coordinate setting 103 y coordinate setting 103 stats macro 300 steam macro 271 storing EPI data 61 image files 104 images 74 profile data 251 ROIs and labels 76 straight line segment drawing a 87 VNMR 6 1C Use
138. 320 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 A 5 Parameters satpwr Saturation presaturation pulse power level P ws Water suppression P wsfrq Specify water suppression frequency P Pulse Power Parameters dpwr dpwr5 Description Related mtpwr Description Related satpwr Description Related tpwr tpwr5 Description Related tpwri Description Related Power levels for second channel events General purpose rf decoupler power parameters used to specify power levels for events on a second channel Refer to the VNMR Command and Parameter Reference for information about the additional use of these parameters in nonimaging applications decpat decpat5 Pulse shape P tpwr tpwr5 Power level of obs transmitter with lin amp P Magnetization transfer pulse power level Pulse power level for magnetization transfer pulse mt Magnetization transfer on off P mtpat Magnetization transfer pulse rf shape P pmt Magnetization pulse length P Saturation presaturation pulse power level Pulse power level for saturation or presaturation pulse psat Saturation pulse length P presat Presaturation pulse execution on off P satpat Presaturation pulse rf shape P Pulse power levels General purpose rf power parameters used to specify pulse power levels where a descriptive name is not required Definitions and usages vary from sequence to sequence but generally names for p
139. 360 n degree value np echo sets 1p to 180 np 2 Also used for setting 1p for full echoes Clear erases the contents in the 1p field rp and Ip Fields that display the last applied values or the values to apply to the selected spectrum rp and Ip have the options Apply and Zero Apply assigns the values to the spectrum in the currently selected gframe Zero zeroes out the applied phases to the currently selected gframe OK Saves the phase coefficients for future use Click on the Auto Go option to initiate phasing The OK option is used to store the local rp and Ip phase coefficients into the Global rp and Ip phase correction depending on the Phase order selection e If Const is selected the rp value is stored e If Linear is selected the lp value is stored VNMR 6 1C User Guide Imaging 01 999163 00 A0800 6 4 Processing Functions e If Both is selected both values is stored Global Phase Correction corrects all voxels selected by the Voxel Pos and the Load option rp and lp Fields that display the current values for Global Phase Correction Mode Selects Write all or Automatic phasing To register the correction values for the Write all mode select the OK button after the sampled points and the correction method are satisfactory then select Apply To All Baseline Correction Local Baseline Correction performs baseline correction on a loaded spectrum Once again the spectrum can be loaded with the Voxel Select tool
140. 3600 3600 3600 3600 will run an experiment immediately when go is typed pad 0 then wait an hour 3600 seconds run the second experiment etc On GEMINI 2000 systems 0 to 4095 in seconds On systems other than GEMINI 2000 0 to 8190 in seconds d1 First delay P go Submit experiment to acquisition C Delay Predefined delays for general purpose use in imaging sequences These delays are also used in solid state experiments Crusher gradient control Delay parameter for use in controlling a crusher gradient For example tcrush is used in the MEMS sequence to control the pair of gradient events that destroy coherent magnetization from unwanted stimulated echoes gcrush Crusher gradient level P gspoil Spoiler gradient level P tspoil Gradient spoiling time P Control diffusion sensitizing gradient pulse length Timing parameter to control the length of a diffusion sensitizing gradient pulse Most diffusion weighted imaging sequences use a pair of gradient pulses to achieve contrast based on diffusion each of length t delta The separation in time between these gradient pulses is normally defined as tDELTA in an attempt to correspond to the original definitions of Stejkal and Tanner 6 and A gaitt Diffusion gradient level P tDELTA Control separation of two diffusion sensitizing gradient pulses P taiti Diffusion sensitizing gradient pulse length control P Control separation of two diffusion sensitizing gra
141. 3D experiments display 3D data file 279 3D images acquiring 237 calculating volume 93 loading 105 reconstructing 232 3rd indirectly detected dimension 336 A acqfil directory 46 304 acqqueue directory 197 acquiring data 333 number of data points 335 acquisition loop control parameters 338 number of echoes 333 number of scans 335 number of slices 334 number of transients 335 of FID with no processing 291 preparation 227 setting number of data points 335 ADC overload error message 42 adding images 67 77 90 95 addps macro 273 ADJUST button 70 135 adjusting image brightness and contrast 51 amplitude values changing 204 01 999163 00 A0800 Index angiography 48 angled brackets lt or gt notation 16 angular span of projections 236 animated image creating 67 annotating text 69 90 Annotation tool 154 aperiodic saturation aps 229 235 238 240 242 244 application mode 342 appmode parameter 17 arithmetic functions 67 array of values setting 62 arrayed data acquiring 333 arrayed spectra showing 42 showing a set of 62 artifacts EPI 53 at parameter 243 attenuating incoming signal 42 auto on ROI change and drag modes 91 automated setup providing information for 338 automatic sequence setup for gradients 337 automatic teller machine ATM cards caution 13 AVS file format 107 B BO field shift 248 backprojection 3D acquisition start and end angle values
142. 6 Commands Macros and Parameters Table 5 contains information about the commands macros and parameters that are used with imaging pulse sequences The appendix Commands Macros and Parameters contains more information about each item Table 5 Imaging Pulse Sequence Commands Macros and Parameters Command Function dconi Interactively adjusts 2D data displays dssh Displays an arrayed set of spectra stacked horizontally flashc Converts compressed GEMS data set into standard VNMR file format Needs to be executed only once on a data set TE Fourier transforms 1D data ft2d Fourier transforms 2D data Macro Function dmi Displays multiple images decctool Opens tool to set eddy current slew rate and related parameters using digital eddy current compensation DECC ecctool Opens tool to set eddy current slew rate and duty cycle using computer controlled analog eddy current compensation hardware exparray Arrays a numeric parameter findpw Measures 180 pulse length and updates pulsecal database ftnf Processes compressed data It is equivalent to the command ft nf and can be used for processing compressed data ga Acquires and Fourier transforms data gems Loads default parameters go Submits experiment to acquisition imprep Sets up rf pulses imaging and voxel selection gradients ldof Sets resto equal to transmitter offset frequency determined by setof The value of resto is changed accord
143. 77 moving graphic frames 71 137 transmitter offset 260 mp command 22 multiple images displaying 62 statistics 95 multiplying images 67 77 95 multislice spin echo imaging 222 multivoxel spectra MVS data 131 mvfov macro 261 N n_ parameters 251 ne parameter 333 nf parameter 334 VNMR 6 1C User Guide Imaging 353 Index ni parameter 243 334 ni2 parameter 243 nitrogen contact with body 12 nitrogen gas flowmeters caution 14 NMR checking for signal 41 excitation schemes 229 imaging 25 resonance offset frequency 330 noninteractive gray scale image displaying a 292 nonsteady state artifacts 48 non time course GEMS images collecting 49 notational conventions 16 np parameter 63 335 ns parameter 21 32 334 nsat parameter 238 242 244 nt parameter 63 nucleus for observe transmitter 268 number of points averages phase encoding steps 63 nv parameters 21 24 35 45 49 63 335 336 O object size and field of view backprojection 244 oblique plane setting orientation to 63 oblique slice plane 23 selection 20 324 off resonance spin echoes 247 offset frequency determining 18 macro 18 42 62 261 one scan acquiring 234 on resonance condition 234 orient parameter 20 63 244 orientation slice plane 324 to oblique plane setting 63 P pl parameter 63 240 243 plpat parameter 63 240 244 pacemaker warning 11 pad parameter 63 panels cardiac preamplifier 210
144. 9163 00 A0800 VNMR 6 1C User Guide Imaging 269 Appendix A Commands Macros and Parameters Arguments Examples Related setgss Syntax Description Arguments readout_gradient is a specific value entered in G cm as a numeric argument When this value is entered set gro can be used in manual mode to explicitly set the readout gradient level is a real number that is interpreted as a gradient level in gauss cm Provided that the number ranges from 0 to gmax set gro sets gro to the specified value and computes and sets the corresponding values of sw and at setgro setgro 3 5 at Acquisition time P gro Readout gradient strength P imprep Set up rf pulses imaging and pulse power levels M Ire Field of view size for readout axis P np Number of data points P setgpe Set phase encode gradient levels and timing M setgss Set slice selection gradient strength M sw Spectral width in directly detected dimension P Set slice selection gradient strength setgss lt gradient_parameter thickness_parameter gt In imaging experiments automatically computes and sets the value of any slice or voxel selection gradient in G cm to achieve the required slice or voxel thickness The comprehensive setup macro imprep incorporates the functions of setgss so setgss is not normally entered by the operator setgss relies on the list parameters fliplist plist patlist and sslist to provide the correspondence betwee
145. 999163 00 A0800 Chapter 4 Image Browser Sections in this chapter e 4 1 Overview this page e 4 2 Getting Started page 68 e 4 3 Graphics Tools page 80 e 4 4 Data Processing page 90 e 4 5 Macros page 98 e 4 6 Files and Other Items page 104 Image Browser is a comprehensive image viewing and analysis program that reads data saved in the Flexible Data Format FDF or in VNMR phasefiles The program uses mouse oriented point and click methods and all processing within Image Browser is performed on the data itself and not on the displayed pixel values 4 1 Overview This section explains the system requirements for operating the Image Browser program the layout of the Image Browser screen processing and graphics functions used by the program display controls and data formats System Requirements Image Browser operates on platforms with the following configuration e Sun SPARC workstation e OpenWindows version 3 or higher e 8 bit or 24 bit frame buffer e Solaris version 2 3 or higher The minimum memory requirement is 12 MB however more than 16 MB is recommended to enhance performance Screen Layout Figure 25 shows the overall layout of the Image Browser screen Control Panel The control panel consists of command menus where specific operations can be run A command might process the data display an image or open another window 01 999163 00 A0800 VNMR 6 1C User Guide Imaging
146. A0800 VNMR 6 1C User Guide Imaging 87 Chapter 4 Image Browser 88 Table 6 ROI Selector Tool Properties Property Delete Load Save Color Font Size Cursor Tolerance ROI Bind Unbind Tracking Function Deletes all selected ROIs Loads ROI tools from a file in the directory SBROWSERDIR roi Saves ROI tools to a file in the directory SBROWSERDIR roi Changes the ROI tool color The colors of all the selected ROIs and labels are changed Any new ROIs and labels are also drawn in the selected color Sets size to use for the next annotation entered 10 pt 12 pt 14 pt or 19 pt Size cannot be changed once the label has been created Adjusts the cursor sensitivity how close the mouse cursor must be to an ROI vertex to select that vertex If binding is on Unbind label shows in menu whenever a new ROI is drawn identical ROIs are drawn in all the selected Gframes All of these ROIs can be operated on as a group They are considered members of the same group solely because they are all identical Image Browser does not store any information about whether ROIs were created as a group When ROI binding is on all identical ROIs are operated on as a group If binding is turned off and one of the ROIs is modified individually it is no longer modified along with the others when binding is reactivated All identical ROIs are considered part of the group the Gframes that they are in do not have to be selected
147. ADIENTS FIELD OF VIEW rfcoil tcoil gcoil main orient sag pilot y lro 5 00 pl 4000 0 pro 0 plpat sinc gro 1 525 ACQUISITION tpwr1 24 gpe O SLICE SELECTION 32467 5 gss 1 304 ns 1 0 002 p2 4000 0 thk 2 00 128 p2pat sinc pss 0 64 tpwr2 30 1 SPECIAL y phi2 theta2 DELAYS 0 5000 0 0300 0 0010 Figure 110 Parameter Set for bp2d Setting Parameters for Acquisition The experiment setup is basically the same as for a standard imaging experiment such as SEMS Refer to Chapter 1 First Steps Making an Image for more information on setting up for an imaging experiment 1 Setthe rfcoil parameter to the correct value Check that the gcoil parameter is correctly set 2 Check that the pulse lengths p1 and pw repetition and echo times t r and te and the transmitter offset resonance resto are appropriately set 3 Set lro length of readout in cm and pss position of slice select in cm to the desired length and position BP images are square images 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 227 Chapter 10 2D and 3D Backprojection 4 Set np and nv The parameter np is the number of points in the readout projection Remember that np also determines the data size of the final image nv is the number of projections to take which determines acquisition time and image resolution 5 Enter imprep This macro uses the rfcoil and gcoil parameters to appropriately set the rf powers and gradient strengths 6 Set phi2
148. ARFIX Routine With PARFIX estimated parameters can be combined to form estimates for other parameters that were not explicitly fit There are some potential pitfalls involving the covariances between parameters For example the estimate of the sum of two parameters is E pO p1 E p0 E pl1 but the estimated value of their product is E pO p1 E p0O E pl Covar p0 pl This value is the direct result of the covariance definition Because calculating the variance of the newly synthesized parameters can be fairly complex avoid using PARFIX routines Instead directly write functions in terms of the parameters you actually want to know 5 5 Problems with Image Browser Math You should be aware of the following Image Browser Math problems Run time Errors Image Browser has no automatic run time validation of math operations so you must check data values as shown in these examples 1 2 0 270 1 2 2 sqrt fabs 1 5 1 lt 1 0e 6 log 1 0e 6 log 1 5 log 1 lt 1 0e 671 0e 6 1 If a function that you create has bugs such as using uninitialized pointers that result in memory violations the entire Image Browser program is core dumped Core dump files result because while your function is running it is actually part of Image Browser CAUTION Before performing possibly illegal operations check data values It is also possible to write Image Browser Math Expressions like the following
149. Command panel contains the following options Error Messages Option When selected the Error Messages option opens an Error Messages text window which is scrollable so that all previous error messages can be viewed If there is an error the window is automatically opened on the screen The window can remain open or it can be closed Error messages can be saved into a file or all messages can be deleted Info Messages Option When selected the Info Messages option opens an Info Messages text window which is scrollable so that all previous messages can be viewed This window is for outputting of information from a particular task such as statistics The window automatically opens when statistics or other information is output to it The desired information can be selected and output to a file The messages can be deleted and the window can either be closed or moved to a different location VNMR Files CSI reads VNMR raw data files for CSI processing and image reconstruction It does not read VNMR phasefiles The VNMR files that can be read are not files but directories These directories must contain aFID file anda procpar file These directories can be an experiment directory or any fid file saved by using the VNMR svf command Unlike ImageBrowser to read a VNMR fid file the FileBrowser must have selected the fid raw data file within the directory containing the fid file and the parameter file Select the Load option in the FileBrow
150. Conversion cceceeeseeeeceseeeeeeeeeeeeeeeeeeeeaeeeeeenee 26 2 3 Slice Selection seisein ieii ae die Har sebaesisl ven anbsl il aderabdan ns dee md EEr 29 24 FREQUENCY EN COGN D sessccseseseedesedesdvs aevecestsshecssesesshseeie ATEOA dusntesicesvsstevets EEE OE DE 32 Dev Phase Encoding seisein E E a sen tiecsnge da E A E R E SA 34 BiG Tima pe RESON sagiissaiessces setensesis setdoceostesnoencossuecksasusiscugeusnsa AEA ERE E EE NERA 35 2 7 Spatial Frame of Reference 0 0 0 eeseseessesecseeeceesseeeceeesaeseeeessecneeaeeseenecaeeeesaecaeenes 37 2 8 Image Reconstr CtON scssi coat sdeeschstecvoussnevosvachstcesdbunessdasshesnetssauh TE EEEE 38 2 9 Important Imaging Parameters ee eeeeeeceeeneeceecneecneessceseessessensesscessesaseneseeecoees 38 Chapter 3 Imaging Pulse Sequences s eccceeseeeeeeeeeeeeeeneeneeeeenseeeeeenseees 41 Soll Initial Setup gaiii ereere Eeo ar Cor EEEo resi vee di adlaebaate mommesantechtoed 41 3 2 Conditions for Use isrener sern es erran e REE Ee EEEE EEE E TEER EE E EEE EE TARE EER 42 3 3 GEMS Multislice Imaging 20 eee seesseeseeencesesensesesensosnsconsseecoecneeceesneesseessee ae 44 3 4 Obtaining a GEMS Image sii tnnc onses ai ien a Ei a eeina 49 3 5 Echo Planar Imaging and Phase Correction Map Files 00 0 cece eeeceeeseeeeeseeeeees 31 3 6 Commands Macros and Parameters ccccccccccecesssseceececeeececeeceessseseeeseseaeseeecesenaes 62 Chapter 4 Image Browser ccccssseeeeeese
151. ECC File pulldown menu If you have many old files they can be deleted by clicking on Purge When saving a file any version number in the ECC File field is ignored The version written is always one higher than the highest existing version Starting Experiments The Save amp Go button performs the same operation as the Save button but also causes VNMR to start the current experiment Until you are familiar with the operation of decctool we recommend that you use only the Save button and start an experiment by entering go in the VNMR input window The Save amp Go button sends the command deccgo to VNMR deccgo is a macro that by default performs a go command You can change the operation of deccgo by either writing your own deccgo macro or by defining a deccgo parameter which will be executed by the default deccgo macro For example to make Save amp Go execute the au command enter the following commands in the VNMR input window 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 203 Chapter 8 Digital Eddy Current Compensation 204 string deccgo deccgo au Modifying X Y and Z Compensation Parameters In the center of the window there is a series of panels this area is the workspace where you can enter parameters Across the top of the workspace are a series of tabs indicating the five main parameter entry panels Click on the tabs to familiarize yourself with each panel The following list briefly describes the functio
152. I Data Processing 136 Opening the Graphics Tools Window e Open the Graphics Tools window shown in Figure 55 by clicking on the Tools option with the left mouse button Selecting Frame Functions Select the Frame option E when performing any of the frame functions other than simply selecting a frame 1 Deleting Gframes If the setup of the Gframes on the screen is unsatisfactory select the Delete option in the Frame Props menu to remove all frames on the screen To see the Frame Properties menu position the Figure 55 Graphics cursor over the Frame Properties button and hold Tools Window down the right mouse button Frame related commands and options are displayed Hold down the right mouse button and move the cursor down the list of options shown in Figure 56 to select a command When the desired option is highlighted release the button to select it Creating Gframes Figure 56 Frame Props Window 1 Position the cursor in the graphics window and hold down the left mouse button 2 Drag the cursor across the screen A box is created 3 When the left mouse button is released the box is completed and selected Frames cannot overlap any part of another frame Selecting Gframes 1 Position the cursor within the frame and click the left mouse button The frame s corners become highlighted to show that it is selected any other selected frames are deselected Use the middle mouse button to select addi
153. I ampie TECHRON 7700 SERIES g r oor l AUUOIITOOIIIONIITOOIITNI Z QUTTA TIO TT PATTEM gradient gt PATINTTITENT TVET amplifier Figure 90 Microimaging Cabinet with Gradient Control System 190 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 7 4 Microimaging Hardware Gradient Control System The gradient system consists of the following hardware which with the exception of the gradient coils and Gradient Junction Unit are contained in a separate cabinet e Gradient waveform generators that provide 16 bit amplitude control for gradient pulse shaping e Gradient compensation preemphasis units that compensate for eddy current artifacts in the gradient pulses each with five time constants and associated amplitudes e Gradient power amplifiers three required that drive the large pulse currents through the gradient coils e Gradient coils assembly mounted in the magnet bore usually inside the shim coils e Gradient Junction Unit Eddy Current Interface Eddy currents are set by two mechanisms the macro eddysend and the window interface eccTool The next section Gradient Compensation Board describes the controls relevant to gradient compensation while the remaining sections describe the interface to those controls The gradient compensation boards become programmed only when an su command is entered after a program or macro has been run to update the boards Table 14
154. ING SPECIAL bptype slice nt 1 di 0 10000 gain 16 ACQUISITION ct 1 te 0 02000 temp not used sfrq 402 175 np 256 tr 1 50000 FLAGS tn H1 ni 64 tpe 0 00300 il y tof 23800 0 ni2 O trise 0 00200 in n tofc 0 GRADIENTS PROCESSING cp RF_PULSES orient xyz sb 0 002 SAMPLE pi 2 00 gcal 0 002000 sbs 0 000 date Mar 30 94 tpwri 50 Iro 0 80 phfid 0 1 file homeifpe pipat hrm90 gro 4000 fn not used ter BPYAR_2 Schlau pi 2000 0 grof 1 450 proc ft chi tpur i 47 gss 5000 math f solvent none pwpat hrm90 gssf 0 500 CONTRAST DERIVED pw 2000 0 prep sr sw 50000 0 tpwr 53 tpwrf 4095 Figure 124 7 Weighting Inversion or Saturation Recovery T Weighting Using Aperiodic Saturation Aperiodic saturation is achieved by a sequence of 90 pulses in the preparation phase The time period between the pulses is continuously divided by two to achieve full dephasing that corresponds to full saturation The particular advantage of the aps sequence is the short measurement time because there is no requirement on the initial state of magnetization prior to the aps sequence Therefore measurements of the points of the T relaxation curve don t need a fully relaxed state requiring 3 to 5 times T as a recovery time The parameter nsat controls the number of pulses used in aps The parameter sat controls the duration between the first pulse and second pulse The parameters pi and tpwri control the pulse Figure 125 shows an example of T weighting using aperiodic sa
155. Increasing the inhibit delay time decreases the frequency of triggering The inhibit delay can be set in a continuous fashion up to a maximum value of approximately 2 5 seconds Receiver Back Panel Figure 105 shows the back panel of the receiver CARDIAC OUT FIBER OPTIC IN INHIBIT OUT INHIBIT IN THRESHOLD OUT GATE OUT FILTERED UNFILTERED 250 A FUSE 115VAC F 50 60 Hz Figure 105 Back Panel of PGM 1000 Receiver The back panel of the PGM 1000 receiver is fitted with input output jacks as follows e FIBER OPTIC IN is used to connect the PGM 1000 receiver to the cardiac preamplifier via the fiber optic cable 214 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 9 2 Hardware Description e INHIBIT OUT can be used to view the inhibit delay signal used by the PGM 1000 receiver inhibit feature The signal available on this port is held as a 5 V signal when the unit is ready to generate trigger pulses The signal is reduced to 0 V ground during the inhibit delay e INHIBIT IN has a voltage level that is held high at 5 V to permit the PGM 1000 receiver to generate trigger pulses If an incoming signal reduces the level to 0 V ground the PGM 1000 receiver will be inhibited from producing trigger pulses This feature allows an experiment using the electrocardiogram and a signal generated by a second transducer or other external device to be double gated e THRESHOLD OUT is the threshold voltage level used to dete
156. MR 6 1C User Guide Imaging 295 Appendix A Commands Macros and Parameters Arguments Related imfit program The imfit macro requires the following information as arguments that it passes to the UNIX program e A fitting type either T for inversion recovery or T gt for decaying exponential e A base name for the collection of phasefiles that represents the arrayed set of images These phasefiles must reside in the planes directory of the current experiment and must end in consecutive integer extensions starting with 1 e A noise threshold value specifying the lower limit for the fitting program Pixels whose values in the first image are less than this threshold are not fit and are assigned values of zero in the computed T4 or T gt image Three computed images are constructed by the imfit program and placed in the planes directory of the current experiment The 7 or T gt image is named basenamet1 or basenamet 2 An error image basenamesigma represents the standard deviation of the fit at each pixel and basenamem0 the t 0 default represents the intercept of the original data at time zero Pixels in the T or T map that cannot be reliably fitted are set to zero The imfit macro automatically extracts the timing values for each array element in the data set from the parameter that it finds arrayed and passes the list of values to the imfit fitting program Only a single arrayed parameter is supported If the data c
157. Max infinity selected a graph Area 114 8 sq cm Segment images Segment ROIs Pane a elume TAZE Y coord Mean Intensity similar to Figure Update Auto On ROI Change X coord Gframe number Print Stats Dump Data File 35 is displayed ee eee with selectable items for the x and y axes The graph provides a quick look at information from processing on regions of interest Figure 35 Statistics Window with Multiple ROIs In the graphics display the histogram limits are displayed because these can still be used to segment regions when gathering statistical information from multiple ROIs The statistics displayed on the left side are for the sum of all the ROIs For example if there is no overlap the area is just the sum of the areas for all the ROIs If any of the ROIs overlap some of the pixels are counted twice in the statistics Volume calculation is a special case If a calculation is labeled simply as Volume it is just the sum of the individual ROI volumes However if a calculation is labeled 3D Volume it is calculated by accounting for the difference in ROI slice positions and interpolating the cross sectional ROI area between slices The calculation is illustrated in Figure 36 in which the cross sectional area of the volume ROI is calculated by linearly interpolating the ROI area between slices Figure 36 3D Volume Calculations The ROIs are assumed to lie at the center of the slices The top
158. Method can give misleading results However it can be useful to see which peaks are being picked up over the entire set of voxels Curve Fitting Method Global curve fitting generally takes a long time If you are only be interested in a localized region of the CSI data you can do the following 1 Select your destination Gframe which can be the last MVS data Gframe T 2 Select the Box ROI tool E described on page 154 in the G Tools window 3 Draw a box through the desired voxels Any voxel lying within or on the ROI boundaries is MJU selected 2a ine TEENETE 4 When you are satisfied EE Re e spak a with the selected Lad dt Peer hi ripe region select the Apply To All option Figure 62 shows the selected voxels with box ROI left side and the resulting curve fitted display right side Figure 62 Selected Voxels and Curve Fitted Data Metabolic Map Display Figure 63 shows the data flow for metabolic map processing Mmap amp ae sag Colormap ap Display Peak Arithmetic Figure 63 Detailed Data Flow for Metabolic Map Processing When the data is fitted and the metabolic maps based on the peaks have been registered the maps can be displayed either by using the Display Mmap option in the CSI Metabolic Map Calculation window or by clicking Colormap in the View option in the command panel 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 145 Chapter 6 CSI Data Proc
159. NMR 6 1C User Guide Imaging 41 Chapter 3 Imaging Pulse Sequences 4 Shim if necessary Unlike high resolution spectroscopy shimming is not critical for most imaging experiments Even when the linewidths are 50 Hz to a few hundred hertz good images can be obtained Typical linewidths for imaging samples such as plant and animal tissues are about 50 Hz to 150 Hz However improved field homogeneity can produce better results Good magnet homogeneity is critical for some experiments such as echo planar imaging EPI gradient echo multislice imaging GEMS and spectroscopic imaging 5 Use the s2pul sequence to set the transmitter frequency on resonance The transmitter offset frequency parameter t of is needed to define the spatial reference position the center of the magnet and gradient coils The macro setof automatically determines the spatial reference position using the tallest peak in the spectrum The offset frequency is then stored in the file SHOME vnmrsys Hloffset When running imaging sequences the macro 1dof sets the imaging reference frequency parameter resto to the value saved in the Hloffset file On vertical bore systems the ZO shim Bg field can be adjusted so that the transmitter frequency is on the peak of interest usually water in which case tof and resto parameters are usually set to 0 The of fset macro can be used to determine the frequency offset corresponding to the cursor location The movet o
160. OIs and labels are not stored with an image when an image is saved Selecting ROIs To select ROIs click on the ROI Tools button K in the Tools window This is the default mode of this window To select an individual ROI position the cursor on or very near the ROI and press the left mouse button Selection of a number of ROIs can be done two ways e Use the middle mouse button to append one ROI after another to a selection list However this is method can be time consuming e Position the cursor to one side of the group of ROIs to be selected and hold down the left button Drag the cursor so it draws a selection box around the group of ROIs Lift the left button All the ROIs in the selection box are now selected ROIs are shown to be selected when their vertices are highlighted When labels are selected they show an underscore cursor at the end of the text Adjusting ROIs To adjust the size or shape of an ROI do the following steps 1 Click on the button in the Tools window 2 Click the left mouse button near one of the ROIs vertices and hold down the button The vertex jumps to the cursor position 3 Drag the mouse then release the button at the new desired position Moving ROls To move an ROI do the following steps 1 Click on the button in the Tools window 2 Click the left mouse button on an ROI but AWAY from the vertex For box polyline and polygon ROIs click inside the area of the ROI For lines or point
161. P plan Display menu for planning a target scan M pss Slice position P seqcon Acquisition loop control P setloop Control arrayed and real time looping M Number of data points P Sets number of data points to be acquired Generally np is a dependent parameter and is calculated automatically when sw or at is changed If a particular number of data points is desired np can be entered in which case at becomes the dependent parameter and is calculated based on sw and np On GEMINI 2000 np is constrained to be a multiple of 64 Upper limit for np on broadband systems is 128 000 the limit on ty Be systems is 64 000 These limits can be doubled with the set limit command if dp n On MERCURY 64 to 128 000 in steps of 64 dp does not affect the limit because on MERCURY dp is always y On systems other than the GEMINI 2000 np is constrained to be a multiple of 2 Acquisition Controller or Pulse Sequence Controller board or a multiple of 64 Output board See the acquire statement in the manual VNMR User Programming for a description of these boards at Acquisition time P dp Double precision P setlimit Set limits of a parameter in a tree C sw Spectral width in directly detected dimension P Number of transients P Sets the number of transients to be acquired i e the number of repetitions or scans performed to make up the experiment or FID 1 to le9 for MERCURY the hardware limits nt to 16e6 For an
162. P or projection reconstruction An appendix lists VNMR commands macros and parameters used commonly for imaging and localized spectroscopy experiments VnmrIMAGE Interface Many new features and capabilities have been introduced with the VamrIMAGE interface The underlying philosophy of the software is to promote a friendly and convenient applications environment and improve the ease of use tools available within VNMR VnmrIMAGE highlights include e Automated setup and optimization of imaging gradients e RF calibration database for automatic selection of pulse power levels e Expanded pulse sequence library and pulse sequence programming capabilities including oblique angle imaging e Graphical planning of imaging and localized spectroscopy experiments 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 15 Introduction 16 Software Compatibility The new software described in this manual is designed to be compatible with already existing software Older style pulse sequences and macros both SISCO supplied and user written should continue to work as they always have We have consciously avoided names for pulse sequences and macros that have long standing definitions even though this sometimes meant creating new names that are perhaps slightly less descriptive The definitions of some parameters have changed but older parameter sets will continue to function properly with their corresponding pulse sequences Older sequences and
163. RERE 96 Figures 41 Fisto gram Window cic se sascscc cbs dss satsscesscaess cits E EREE EE E RE 97 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 7 List of Figures Figure 42 Figure 43 Figure 44 Figure 45 Figure 46 Figure 47 Figure 48 Figure 49 Figure 50 Figure 51 Figure 52 Figure 53 Figure 54 Figure 55 Figure 56 Figure 57 Figure 58 Figure 59 Figure 60 Figure 61 Figure 62 Figure 63 Figure 64 Figure 65 Figure 66 Figure 67 Figure 68 Figure 69 Figure 70 Figure 71 Figure 72 Figure 73 Figure 74 Figure 75 Figure 76 Figure 77 Figure 78 Figure 79 Figure 80 Figure 81 Figure 82 Figure 83 Figure 84 Figure 85 Figure 86 Figure 87 Figure 88 Figure 89 Cursor Data WIDNAOW asc sicciscisessdsvsnssantehik bss des du cesshet ARSE E REER NEE ASTE SEEE KESE 97 Line Data Window beissen oneee deen one sa aaae E E N aias 97 Macro Window ivissesses cease nan ne aE E E caetaeussblagcutese 98 File Browser for Loading Images eseseeseeseeeiesstseeesrserressrsrtrrerserestssesreretrreerersrsree 104 Slice Extraction Window w c cccscssesseecscessesesessuossseseccssessoosansevseroseceavecnesuesscesoesvoessees 105 Image Browser Math Panel 2 cc ccscsesesccissetessceasvecnsvceksdenseseadevecaveresveneonsessseasactavecsbies 111 Fragment of shamesfit c FIle x see scctcs tas opnceiss as sascss bay cetepecsunea R RE E arses 125 FUNCTION Specifications sssri iei ecaro soueen eas aE e
164. Selecting the Gamma button from the V Scale Properties menu allows corrections to be made according to the characteristics of a particular monitor Creating ROIs and Labels ROIs are created by selecting the ROI type to draw moving the cursor to the desired location pressing the left button and dragging out the desired ROI ROIs can also be read in from a file The Load button in the ROI Properties menu is selected with the right mouse button and dragged until a list of ROI files is displayed When the desired file has been chosen the ROIs stored in it are read in to all the selected Gframes The ROIs are all placed 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 75 Chapter 4 Image Browser in the same locations in data coordinates Their size and shape on the screen may differ depending on the aspect ratio of the data and the size of the Gframe This function is especially useful for calculating statistics on a number of files for the same region of interest When the size of an image is changed the label font size remains fixed in terms of screen pixels The left end of the text baseline is fixed on the data Storing ROIs and Labels ROIs and labels are stored into and retrieved from the directory BROWSERDIR roi or a subdirectory of roi similar to the way Gframes are saved in the gf rame directory see Storing and Retrieving Gframes page 72 All the selected ROIs and labels are stored in the chosen file Note that R
165. T RIGHT obtaining ECG signals Green The self adhesive electrodes supplied with the PGM 1000 kit require no electrode gel and can be directly applied to the bare skin Additional tape might be required to secure the electrodes to the limbs of larger animals Cardiac preamplifier The cardiac electrode leads can be clipped to the electrode Figure 106 Electrodes Connection tabs in order to connect the leads to the animal Avoid 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 215 Chapter 9 Physiological Gating Module clipping the electrode leads directly to the animal A diagram showing the connections to the animal and cardiac preamplifier is shown in Figure 106 The clips located at one end of the cardiac electrode leads are color coded to indicate the target limb for connection Clip Color Limb Electrode Black Left foreleg or left arm Green Right hind leg or left leg White Right foreleg or right arm Connect the plugs at the opposite end of the cardiac electrode leads to the cardiac preamplifier module These plugs are color coded to indicate both the corresponding limb electrode and socket on the preamp The connections are made as follows Plug Color Socket Socket Color Limb Electrode Black LA Black Left foreleg or right arm Green RL Green Right hind leg or right leg White RA White Right foreleg or right arm 9 3 Experimental Setup The is section describes the use of the physiological gating
166. VMR Command and Parameter Reference for information about the additional use of sw1 in nonimaging applications Related d2 Incremented delay in 1st indirectly detected dimension P imprep Set up rf pulses imaging and voxel selection gradients M nv Number of phase encode steps for 1st indirectly detected dim P sw Spectral width in directly detected dimension P sw2 Spectral width in 2nd indirectly detected dimension P sw3 Spectral width in 3rd indirectly detected dimension P tpe Duration of the phase encoding gradient pulse P sw2 Spectral width in 2nd indirectly detected dimension Description Spectral width for the second indirectly detected dimension of a multidimensional data set used in 3D volume imaging for the third spatial dimension or CSI for the second spatial dimension See sw1 for description except that number of phase encode steps is controlled by the parameter nv2 Refer to the manual VVMR Command and Parameter Reference for information about the additional use of sw2 in nonimaging applications Related imprep Set up rf pulses imaging and voxel selection gradients M nv2 Number of phase encode steps for 2nd indirectly detected dim P sw Spectral width in directly detected dimension P swl Spectral width in 1st indirectly detected dimension P sw3 Spectral width in 3rd indirectly detected dimension P tpe2 tpe3 Duration of 2nd and 3rd phase encoding gradient periods P 332 VNMR 6 1C User Guide Imaging 01
167. _contrast min_intensity max_intensity Sets display contrast to a linear ramp with minimum and maximum intensities specified Black is 0 and white is 1 display_contrast min_intensity max_intensity gamma Sets display contrast for gamma correction and linearity intensities steps with minimum and maximum intensities specified Black is 0 and white is 1 gamma is the exponent in the relation 7 k V display_contrast min_intensity max_intensity gamma contrast Same as previous command contrast is the ratio of maximum to minimum intensity displayable by a monitor display_saturation on off Turns on or off Show Saturation choice in Gamma Correction window Option Commands memory_warning_threshold level 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 101 Chapter 4 Image Browser 102 Sets a percentage threshold level for memory warnings If more than level percent of system memory is in use warnings might be generated when data is loaded The default is 80 Data File Commands data_header_set parname command Creates and sets new float type header variables in images already loaded into Image Browser These values are NOT put into the image files on disk UNLESS you save the modified images This command creates the header parameter parname if it does not exist in all selected images then sends the command line command to the UNIX shell The standard input of command is a list of name
168. a set from any arbitrarily ordered data that has been acquired under the control of an external AP table The data must have been acquired according to a table in the tablib directory The difference between t capply and tabc is that tcapply works on the first dimension transformed spectra residing in the VNMR data memory and t abc works on and changes the raw data in a FID file file is an optional argument specifying the AP table to be read the table must be in Svnmruser tablib lt file gt ftld 2 tcapply petable ft2d 2 tabc Convert data in table order to linear order C ftld Fourier transform along f dimension C ered Fourier transform 2D data C tcclose Close table conversion file C tcopen Open table convert file C Close table conversion file C tcclose Removes a table conversion file and frees the memory used to store the sorted table indices read in with the t copen command tcclose tcapply Apply table conversion reformatting to data C tcopen Open table convert file C Open table conversion file C tcopen lt x file gt Explicitly reads sorts and stores in memory a table conversion file in Svnmruser tablib lt file gt tcopen uses the file when tcapply is called file specifies the file to be read it must be in Svnmruser tablib lt file gt tcopen petable tcapply Apply table conversion reformatting to data C tcclose Close table convert file C Write a title to the plotter M
169. acro dslice displays up to 12 images at once from a multislice data set VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Chapter 2 Imaging Experiments Sections in this chapter e 2 1 Basic Imaging Principles this page e 2 2 Time Domain to Spatial Domain Conversion page 26 e 2 3 Slice Selection page 29 e 2 4 Frequency Encoding page 32 e 2 5 Phase Encoding page 34 e 2 6 Image Resolution page 35 e 2 7 Spatial Frame of Reference page 37 e 2 8 Image Reconstruction page 38 e 2 9 Important Imaging Parameters page 38 This chapter introduces the basic concepts necessary to understand MRI experiments You should be familiar with the terminology and principles in simple experiments in conventional NMR because this chapter focuses on MRI related topics NMR concepts can be easily understood when the process of a simple imaging experiment is analyzed The 2D spin warp imaging sequence that is commonly performed in MRI is used in this chapter as an example to illustrate principles and experimental aspects related to NMR The spin warp imaging sequence is based on the 2D Fourier transform principle for converting the time domain NMR signals into image data Most of the other imaging techniques are also based on the Fourier transform idea and can be regarded as variations of the spin warp method 2 1 Basic Imaging Principles This section contains a brief introduction to nuclear magnetic
170. ad file for all of your parameter setting operations Notice that when the decctool window is open the Load and Save buttons are disabled Load and Save perform their operations on your scratchpad file and also simultaneously overwrite the master file After you enter a file name the buttons become active but do not click on them now Read the following sections first and familiarize yourself with the interface Loading a File To load a file type a name in the ECC File field or click the pulldown menu arrow 4 to select a file then click on Load When you click the Load button the parameters in the parameter entry panels are simultaneously loaded from the file named in the ECC File field and also saved to the master file You can load a specific version of a file by including a version number extension in the file name e g test 7 If you do not specify a particular version the latest version is loaded Saving a File To save a file type a name in the ECC File field or click the pulldown menu arrow 4 to select a previously named file then click on Save When you click on the Save button the parameters in the parameter entry panels are simultaneously saved in the file named in the ECC File field and in the master file If you save over and over to a file of the same name previous copies are kept and named with an extension incremented by one from the previous version The number of the current version is listed below the
171. adout axis The readout position measured from the gradient coordinate origin pro is independent of imaging plane orientation and is the distance from the gradient origin to the center of the image along the readout direction pro is used by most imaging pulse sequences as an argument to the pof f set function which internally computes the spectrometer frequency required to center the readout axis at the value of pro The value of pro can be entered manually or graphically with movepro Number in cm Leo Field of view size for phase encode axis P movepro Move the imaging readout position C resto NMR resonance offset frequency P Euler angle for defining imaging plane orientation One of the three Euler angles used to define imaging plane orientation psi is the angle formed by the projection of a line normal to the imaging plane onto the magnet XY plane and the magnet Y axis psi is generally not set by the user directly but instead either by entering a string value into the orient parameter or through interactive graphical planning of a new imaging plane from an existing scout image 90 to 90 in degrees orient Slice plane orientation P phi Euler angle for defining imaging plane orientation P theta Euler angle for defining imaging plane orientation P Slice position Slice position measured from the gradient coordinate origin pss is independent of imaging plane orientation and is the distance from the gradient
172. aeeaee 169 Colormap Display Window 000 ee eeeeeeeseseecseesceceecneecnecssessecsseeseeesseceeseseseneesaseaes 170 Display Control Window ccsssissesscesieessescsdess vss enia eies eae Ea E EEEE E E ERE En 170 Sample Prior Knowledge PEAK File oo eee eeeeceeeeeeceeeeeeeeeeeeeecaeeeaesaeeaesseeaees 174 RF Shield Fitted on 183 mm HPAG Gradient Coil oe eee eeeeeeeceeeeeeeteeeeeeenes 177 Rear Housing of 183 mm HPAG Gradient Coil 0 ee eeeeseseeeececeeeeeaeeeeeeeeeeaees 177 HPAG Quick Disconnect BOX eeieeeceeseceseecssecesceceeeecseeeeeeeaecesaeceaeecsaeceaeeceeeeenaeeaees 179 System Gradient Coil Detail of Connection Points oo eee ee eseseecrecneecneeeeeeees 180 Front Panel of System Gradient Supply 0 ci cceeeseseesceecseeeeeeeceecaeeseesecaeeaeeecsaeeaeeees 182 Gradient Supply Internal Card Cage oo ceeeecsecsseceececeseceseeeeceeeeseseeeeeeseneeeesenes 182 Connections for System Gradient Coil in Standard Configuration eee 184 Connections for Auxiliary Configuration 0 eceeeeeseseceeceeeeessecaeeeeeseeaeeeseeeaeaeees 185 8 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 List of Figures Figure 90 Microimaging Cabinet with Gradient Control System oo eee eeeeeeceeeeeeeeeeees 190 Figure 91 Gradient Compensation Signal Flow ou eeeeeseesceseecseceseceeeaeeeeeeseeeeeeseeeeeeetees 192 Figure 92 Gradient System Cabling oo cee ceceseeeeceseceeseseeeeseseecaecnaecaecsaesaessaeeseseeeeseeeesens 193 Figure 93 ecc Tool Wind
173. aesesseceseeneeeseeeneesetens 253 iao E ee eee ee eee ree er 347 6 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 List of Figures Figure 1 Frequency Spectrum Produced by an NMR Signal oo ee eeeeeeeseesecseeesecneeeeeneensees 26 Figure 2 Effect of a Field Gradient Along Direction y o ieiececeseseesceecseeeesecsecateeeeaecaseeeeeesaeeees 27 Fig re 3 Frequency Ranges 2iici ic ceschcctesiscsszetasabscesscevcebvacstdastbelasaibensebsascessunsesnuendoasszacscaseabuacbaabe 28 Figure 4 2D Image Resulting from a Slice Selection oo eee eeeecceseeeeeceeeesecseaecnaeeseeneeeaees 29 Figure 3 Rectangular Profle speriene ean iiie rn oee EE EEE AER E ER O ER EE E EnS 29 Pir eG Slice Prole speresianenne ieies nean e rE eE oE aE EEEE EESE EO EERE 30 Figure 7 Sinc Function Truncated Sinc Pulse and Gaussian Shaped Slice Profiles 30 igure 8v Mu ltislice Excitation srsesecncicisreniin i no eE EEE E 31 Fig re 9 Signal Loss R stOrati n ssi cciessc ick dasicehveenscaess eni ee EEEE EEr E E E 32 Figure 10 Readout Gradient and Gradient Echo ssesseseseesesesererssrereresreereserrrseerrsererereseereneenresenens 33 Figure 11 Gradient Echo Imaging Sequence s sscseiioteusnicesrirerii ereeniisssrrikeirivekr siokiu 34 Figure 12 Image Resolution of Three Water Filled Spheres oo eee esses cseeesecsseeeeneeenees 36 Figure 13 Horizontal Magnet ccii ssicd cosieeies davacaedacaecisgscbdecisesenaqiessci skids EEE rE EE RE Si 37 Figure 14 Ver
174. aging 225 Chapter 10 2D and 3D Backprojection bp_3d Program that performs the 3D reconstruction Typical reconstruction time based on a SPARCstation 2 is 2 minutes for a 128 x 128 x 128 from 64 x 64 projections and 20 minutes for a 256 x 256 x 256 from 128 x 128 projections bp_mc Program that performs a magnitude calculation and is used prior to the program bp_2d or bp_3d bp_sort Program that shuffles the projections obtained using an arrayed parameter in the order required by the bp_3d program Be aware that 3D BP image data sets may require up to 70 Mbytes of hard disk space during acquisition and up to 100 Mbytes during the reconstruction 10 2 Backprojection Image Generation 226 Figure 109 depicts the basic approach for BP image generation Figure 109 Image Generation Using Backprojection Imagine a slice with a cylinder and a cube Applying a field gradient Gz x along the x axis case A results in a spatial one dimensional field dependence Bz By x Gz x along the probe Excitation of the probe with a short non selective rf pulse gives rise to a signal both from the cylinder and the cube The different resonance frequencies of the cylinder and the cube due to the applied gradient result after Fourier transform in a profile exhibiting the cube and the cylinder So far a mapping of the 2D object to a 1D profile has been achieved Note that the profile s intensities are determined by the line integrals
175. aging experiment steam Retrieves the standard parameters for the STEAM imaging experiment from vnmr parlib Create AP table for k space order M tabgen In imaging experiments creates an AP table for the k space phase encode order Conventional imaging experiments generally follow a monotonic phase encode order that begins at one extreme and progresses monotonically through zero to the opposite extreme For example the multipliers for the phase encode step might be 64 63 62 2 1 0 1 2 62 63 for an imaging experiment with 128 phase encode levels VNMR s pulse sequence capabilities allow the use of a k space order that is nonmonotonic through the use of external AP tables simple text files with a list of integer values tabgen can be used to create one of these tables for either a monotonic progression or a centrically ordered progression centric order starts at zero and progresses to the extremes in an alternating positive and negative fashion e g 0 1 1 2 2 3 3 tabgen prompts for the type of order the number of steps and a file name for the resulting table Imaging data acquired in nonmonotonic order must first be 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 2 1 Appendix A Commands Macros and Parameters Related tpwrcal Syntax Description Arguments Examples Related updtgcoil Applicability 272 Syntax Description processed with the tabc ro
176. ain processing functions The circles represent processing operations and the squares represent data Note that the data can be saved after each operation and retrieved for the next operation Also note that phase and baseline correction processing can be iterated Raw Metabolic Data Maps Curve Spatial Spectral Phase amp itt Correction Generation MVS MVS MVS Corrected Curvefit Figure 53 Processing Functions Data Flow The data is saved in global buffers after each processing step Data can always be redisplayed or reprocessed with an earlier step At any time during these operations a reference image can be processed and displayed with the current localized FID MVS or MVS curve fit data overlaid Other processes not shown in the diagram can be performed These processes include peak arithmetic pH maps and frequency difference maps Spatial Performs a Fast Fourier Transform FFT on the input raw data to Reconstruction obtain a set of localized FID voxels This set can be in one or two dimensions Weighting functions and zero filling can be applied to the data Voxel shifting can also be performed on the data Spectral Performs an FFT on the localized FIDs generated by spatial Reconstruction reconstruction to obtain the multivoxel spectra MVS data Weighting functions can be applied to the data zero filling can be applied before an
177. al and third spatial dimensions in higher dimensional imaging and CSI experiments As an example three dimensional volume imaging sequence have two independent phase encode axes controlled by tpe and tpe2 It is common to have a single phase encoding time block in which two independent phase encode gradients share the same time period In this case tpe and tpe2 would be equal nv2 Number of phase encode steps for 2nd indirectly detected dim P nv3 Number of phase encode steps for 3rd indirectly detected dim P sw2 Spectral width in 2nd indirectly detected dimension P tpe Duration of the phase encoding gradient pulse P Repetition time in imaging and localized spectroscopy experiments Repetition time of an experiment The definition of repetition time can vary somewhat from pulse sequence to pulse sequence In general for imaging experiments t r is the time required to complete one transient of one phase encode step including relaxation delay excitation data acquisition and any post acquire events such as rf spoiling phase encode rewinding and gradient turn off For multislice and or multiecho imaging sequences t r includes the complete multslice and multiecho train for standard arrayed slice acquisitions where the second character in seqcon is s the complete train is not included and t r is the repetition time for each slice position VNMR 6 1C User Guide Imaging 01 999163 00 A0800 A 5 Parameters Some 1D expe
178. al to become a local acquisition parameter Its value is the inner diameter of the active gradient coil in centimeters e Parameter BO has been moved from vnmrsys global and is now an acquisition parameter Its value is the strength of the static magnetic field in gauss e Parameter griserate has been created to accommodate the different rise time characteristics of the different gradient coils that can be used by a system griserate holds the value of the proportionality constant between the gradient strength expressed in DAC units and the ramp time from to the zero gradient expressed in seconds ramp time griserate X gradient strength The value of griserate is expressed in units of sec DAC unit The main function of griserate is to measure of the system slew rate Some pulse sequences use it for computing timing and gradient levels to refocus the NMR signal Running Experiments This section describes the changes in operation of the applications environment caused by installation of the HPAG accessory You must first be familiar with normal system operation in the standard gradient coil configuration in the absence of the HPAG accessory The HPAG accessory changes only minor details of system operation 1 The previously described software features allow parameters to be quickly reconfigured to accept the use of different gradient coils After changing gradient 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 187 Ch
179. allows slice select and volume imaging sequences in 2D and 3D The reconstruction of the acquired data covers the 2D and 3D case 10 1 Installation Note Before running the BP software make sure the imaging module is installed BP imaging software is included on the standard VNMR 5 3 installation CD ROM Loading BP software is accomplished the same as other VNMR software except the BP software requires a password Refer to the manual VNMR and Solaris Software Installation for detailed installation information The installation disk contains the following files bp3d c bp3d par bp3d bp2d c bp2d par bp2d bp_image c bp_image par bp_image bp_setup bp_reco bp_2d 01 999163 00 A0800 Pulse sequence parameter set and macro respectively written in obliquing style which support 2D and 3D BP image acquisition Pulse sequence parameter set and macro respectively which support obliquing 2D slice select spin echo BP image acquisition Pulse sequence parameter set and supporting macros respectively written in the original microimaging style which support 2D and 3D BP image acquisition along with the selected NMR weighting T saturation recovery and inversion recovery Tp and T3 Macro that executes the reconstruction of a 2D or 3D data set Program that performs the 2D reconstruction Typical reconstruction time based on a SPARCstation 2 is 2 seconds for a 256 x 256 from 128 projection VNMR 6 1C User Guide Im
180. allows the definition of scripts or macros that perform a sequence of Image Browser commands The MAGICAL language is described in detail in the manual VVMR User Programming this section covers only those aspects of macro programming that are unique to Image Browser The command syntax conditional statements and looping constructs which give the language its basic flavor are the same as in VNMR Note The macro capability included in VNMR version 5 3 is a partial implementation Many functions that should be callable from macros do not yet have macro commands and the user interface is a simple prototype version User Interface Click the Macro button to open the Macros window shown in Figure 44 Name The simplest way to use the Macro window is to type the name of the desired macro to Figure 44 Macro Window be run in the Name field then press Return The named macro which should be a built in command or in the directory SBROWSERDIR macro is run It is also possible to type any one line sequence of MAGICAL II commands or program constructs on Name and run it by pressing Return Although not a very convenient way to enter macros it can be very useful for quickly trying out a macro construction Used this way Name is essentially like the command line in VNMR Every time Return is pressed the macro is run it is not erased from the Name field Record Record On Off controls the automatic recording of macros Record On
181. alues in the first image are less than this threshold will not be fit and will be assigned values of zero in the synthesized resultant images expfit Make least squares fit to polynomial or exponential curve U makephf Transform arrayed imaging data and save as phasefiles M tlimage Compute a pixel by pixel 7 map M 296 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 lleft Syntax Description Related lright Syntax Description Related makephf Syntax Description Arguments Related markvs Syntax Description Related math Syntax 01 999163 00 A0800 Examples A 4 Commands and Macros for Processing and Display Set chart parameters to display 2D data in lower left corner M lleft Computes the chart position and size parameters sc sc2 wc and wc2 to place the 2D display area in the lower left quadrant of the VNMR graphics screen Iright Set chart parameters to display 2D data in lower right corner M uleft Set chart parameters to display 2D data in upper left corner M uright Set chart parameters to display 2D data in upper right corner M Set chart parameters to display 2D data in lower right corner M lright Computes the chart position and size parameters sc sc2 wc and wc2 to place the 2D display area in the lower right quadrant of the VNMR graphics screen lleft Set chart parameters to display 2D data in lower left corner M uleft Set chart parameters to
182. ame sign as gro for spin echo experiments e g SEMS In general the time integral for gror should be one half the time integral of gro in order to place the echo signal in the center of the AT window Because the refocusing gradient on time is internally computed in the pulse sequence independent of the acquisition time gror will not be exactly half of gro Sequence dependent specified in gauss cm up to tgmax gmax Maximum gradient strength P gro Read out fractional compensation P gssr Slice selection refocusing gradient P pilot Automatic sequence calculation P Readout dephasing gradient adjuster in EPI experiment P Systems with echo planar imaging EPI capabilities Correction gradient value added to the readout refocusing gradient G cm in EPI experiments to center the echo position in the acquisition window episet Set up parameters in EPI experiment M groa Readout gradient adjuster in EPI experiment P tep Post acquisition delay in EPI experiment P Slice selection gradient strength Controls the level of the slice select gradient if present imprep sets gss based on the slice thickness and rf pulse bandwidths or use set gss to update only gss Number less than tgmax in gauss cm gmax Maximum gradient strength P gssf Slice selection fractional gradient P gssr Slice selection refocusing gradient P imprep Set up rf pulses imaging and voxel selection gradients M setgss Select slice or voxel sel
183. ameter order and precedence P setarray Set up a parameter array M tpwr tpwrl tpwr5 Pulse power levels P Update gcoil and gradient calibration parameters Systems with three axis gradients updtgcoil Updates the gcoil parameter and gradient calibration parameters in imaging experiments updtgcoil is automatically called Gf gcoil exists in the new parameter set when a new parameter set is loaded or when an experiment is joined to update the experiment parameters B0 gcoil gmax and trise to match the calibration values specified by the configuration parameter sysgcoil updtgcoil first checks to see that gradients are present on the system then if sysgcoil is set to a value other than none assigns the value of sysgcoil to gcoil which forces the gradient calibration parameters to be updated with the values found in the corresponding gradtables entry If gcoil does not exist updtgcoil will create it VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Related A 3 Macros for Planning Experiments updtgcoil also computes the system field strength and assigns this to the parameter BO It is automatically called by the rt macro and by the jexp macro and is not normally directly executed by users BO Magnet main static field P gcoill Current gradient coil P gmax Maximum gradient strength P jexp Join existing experiment C re Retrieve FIDs M sysgcoil System gradient coil P trise Gradient rise time P A 3
184. ameter to n before running dmi imconi Display 2D data in interactive grayscale mode M imconn Display 2D data without erasing the screen M svib Generate and save images as Image Browser compatible FDF files M wysiwyg Set plot display or full display P Display current pss slice positions list M dpss Displays the current list of slice positions found in the parameter pss The list of slice positions in a multislice imaging experiment is stored in the arrayed parameter pss An acquisition parameter arrayed in this way normally results in an arrayed experiment in which each slice acquisition is treated as a separate array element pss is configured through its protection bits to prevent the execution of a conventional arrayed acquisition and instead to allow a compressed multislice acquisition that uses the arrayed pss values to specify the slice positions in a compressed multislice loop This unusual parameter protection also prevents da from displaying its values although a display of the array list can be forced by specifying the name of the parameter in an argument to da e g da pss dpss is exactly this macro and is provided to allow the list of pss values to be easily viewed da Display acquisition parameter arrays C pss Slice position P setprotect Set protection mode of a parameter C Display stacked spectra horizontally C dssh lt lt start finish lt step gt gt lt options gt gt Displays one
185. ample int get_image_height handle FDFptr handle Returns the number of pixels in the slow image dimension Example int get_image_depth handle FDFptr handle Returns the width of the region imaged in centimeters Example double get_object_width handle FDFptr handle VNMR 6 1C User Guide Imaging 119 Chapter 5 Image Browser Math Processing get_object_height Returns the height in cm of the region imaged Example double get_object_height handle FDFptr handle get_object_depth Returns the depth of the region imaged in centimeters Example double get_object_depth handle FDFptr handle get_dll_data Returns a pointer to the array of floats that represent the image Example float get_ddl_data handle FDFptr handle 5 4 The Fit Program The fit program is provided as a general purpose routine to fit a function to a series of images Output is one or more images that give the parameter value as a function of pixel location You can also add new functional forms to be fit as described in Adding New Functional Forms page 122 For example to run the fit program on t1 data type the following statement in the Image Browser Math window 11 17 fit 1 8 t1 ti 01 Look at the first two fields e 11 17 specifies the number of output images in this case seven These images contain respectively the three parameters of the fits the RMS residuals and the formal sigmas of the para
186. an be selected and the operation is executed according to the order given If one Gframe is selected that one is also the result image If two Gframes are selected the second Gframe gets the result Filtering Image Browser provides filtering Select a filtering operation by choosing Image Filtering from the Process menu When selected a Filter window as shown in Figure 39 opens Figure 39 Filter Window When Mean filtering is selected as in Figure 40 each data pixel in the image is replaced by the average of the surrounding 3 x 3 or 5 x 5 squares of pixels weighted according to the given filter mask The 3 x 3 filter is the default size when the window Figure 40 Filter Window with Data first opens The filter size is selectable using the right mouse button on the Mask field Filter files can be saved and retrieved in the same manner that ROI files are saved and retrieved The directory for Filter files is SBROWSERDIR filter Some example filters are provided but personal filters can be easily created When Median filtering is selected only the size of the mask is significant The weights are not used Each data pixel value is replaced by the median data value in the surrounding 3x3 or 5x 5 square A source Gframe with the image to filter must be selected before clicking on the Apply button to start the filter operation Optionally a second Gframe can be selected for the destination image If only one Gframe
187. an one data source To add two images select two sources graphic frames that contain images and a graphic frame destination Because no more than one destination can be selected the last selected graphic frame is always the destination To add a constant to an image select a source frame and a destination frame Be aware that the last selected frame is always the destination For example adding two images with one selected frame or more than three selected frames is not allowed However adding two images with two selected frames indicates that the image result destination should overwrite the second source image the second image selected When using Image Browser remember that statistics are performed on the actual image data pixels not on the displayed pixel values That is enhancing an image for viewing by using the Contrast tool or the Vertical Scaling Graphics tool does not change the statistical values However processing functions filtering histogram enhancement etc change the data values and hence the statistics from those images Statistics Statistics are always performed on ROIs not on images as a whole They can be performed on one ROI or a number of ROIs The ROIs can all be on one image or across a number of images If statistics are performed on one ROI a histogram is displayed along with the statistics If statistics are performed on a number of ROIs a graph is displayed with a selection of axes Statistics are
188. and can cause a significant larger central spike in the middle of the slice or volume which degrades the dynamic range of the whole slice or volume As a result you ll see a white dot or in case of a weighted FT a bright area in the center of the slice or volume Image Degradation from a Single Projection In BP imaging one faulty projection can spoil the reconstructed slice or volume There can be two reasons for a faulty projection e Saturation during the start of imaging sequence If the recovery time tr is too short and no dummy scans are used prior to acquisition a strong saturation takes place in the first projection This saturation results in high signal amplitude for the first projection compared to the following projections e Distortions for a projection caused by radiation from outside e g second spectrometer nearby or by arcing in the probe e g too much transmitter power Figure 127 shows the effect of saturation during the start of an imaging sequence on a 2D BP image The first projection dominates the complete image and its pattern is superimposed on it For comparison the correct image is shown on the right side To solve this problem use dummy scans to achieve steady state before acquisition and or to increase the time tr Circular Image Intensity Modulation BP imaging of semirigid or solid materials requires a short te thus moving the spin echo from the center of the signal to the left side and reduc
189. anges the system calibration and the value of the matching shim current because the gradient coils are often the linear shims If value of the matching shim current is changed the system gcal value may be in error and the linear shim will need to be re adjusted Setting gain to just over maximum common usage such as 10 over helps 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 191 Chapter 7 High Performance Auxiliary and Microimaging Gradients MOJ PUSTS uonesuoduop JUIIPePID 16 WINS Buz 0 Aus 10 au g au py g epua guoy en BU g au p L peog YOO au 15 auz g SuSE AVES OL pa BE AU ej h EE DUES G WSS JO SUOL O BUF L ea epua suo seu igaeag 104 WH OL aE F Jo auge q aU gz Ze Bep yuo e BWOOL O BUZE 10 LUGE O SUGE La Ge pu eeu Suu 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 192 7 4 Microimaging Hardware SUITGeD WAS S JUIIPVIN 7H IMSI ANELA YEB UAC Ly Jeo EPE 193 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Chapter 7 High Performance Auxiliary and Microimaging Gradients 194 improve gradient resolution and avoids compression of the preemphasis portion of gradient pulses Gain values of 50 are typical Duty cycle is a root mean square of the output voltage of the gradient compensation unit GCU over 100 ms If the duty cycle is above 80 the system is disabled a typical safe value is a 30 duty cycle The control is not linear in power but in the squa
190. animating 67 arithmetic 95 brightness and contrast adjusting 51 calctool 132 constructing an 103 degradation 245 displaying an 51 distortion 48 dividing an 67 77 95 enhancing 67 enhancing an 67 97 filtering 96 generation 226 getting image files 104 intensity modulation 246 math tool 75 reconstruction 38 132 reconstruction off resonance spin echoes 247 rescaling an 101 resolution 35 48 rotation 90 95 segmentation 92 storing an 106 Image Browser 65 109 file formats 107 math tool 111 Math problems with 127 opening Math 111 image files storing and getting 104 image planning interactive 253 Image Reconstruction window 165 image_file parameter keyword 251 352 VNMR 6 1C User Guide Imaging ImageMagick program 106 107 imageprint command 292 imaging application mode 342 basic concepts 25 coil 190 collecting data 44 concepts 25 experiments 25 macros and parameters 32 orientation Euler angles setting 268 parameters 38 plane orientation defining 63 pulse sequences 41 reference frequency parameter setting 42 setting up 62 slice plan 20 imark macro 292 imcalc macro 293 imcalci macro 294 imconi macro 295 imconn macro 295 imfit macro 295 imprep command 21 24 macro 42 50 62 64 231 258 in_memory_prof parameter keyword 251 increased temperature EPI 57 indicators PGM 223 info messages 108 Info Messages option 171 window 94 information display
191. annot be handled by the imfit macro it is possible to call the external imfit program directly as you would any other UNIX program The command line arguments must be constructed manually in this case The syntax required for a direct UNIX imfit call is imfit t1 t2 basename minthresh timel time2 timeN As an example with a set of phasefiles representing 7 data and named phantoml phantom2 use imfit tl phantom threshold To obtain a value for the noise threshold display an image place a cursor box over a region of noise and select the Mark button Divide the displayed value of height by vs and use the result as the threshold The macro makephf can be used to transform all of the images and save them as phasefiles t 1image automatically does this entire procedure prompting you for the required information Note that an error in imfit is that a T fitting type requires phase sensitive images progressing from negative to positive in the normal inversion recovery model t1 and t2 are keywords for the fitting type either t1 for inversion recovery or t2 for decaying exponential t2 can also be used for saturation recovery data basename is the name of a phasefile that represents the arrayed set of images The phasefile should reside in the planes directory and must end in consecutive integer extensions starting with 1 min_thresholdisa value for the lower limit for the fitting program Pixels whose v
192. antees that you will slice through the sample without having to hunt around e Set orient to trans sag or cor as appropriate Setting the pss Parameter Parameter pss determines the slice position relative to the gradient origin Setting pss automatically sets the related parameter ns the number of slices You cannot set ns directly but entering an array of slice positions into pss results in an update of ns to the proper value determined by the size of the pss array e Set pss as an array of slice positions in cm relative to the gradient origin you probably want to set pss 0 Checking the seqcon Parameter Some early SEMS parameter sets may have set the seqcon parameter to an incorrect although valid setting See Acquisition Loop Control on page 338 for more information on this parameter For proper multislice operation in SEMS e Check that seqcon ncsnn Update it to this value if necessary Selecting Values for the tr and te Parameters You may want to change the default values of t r and te Keep in mind that unlike d1 in the old IMAGE sequence t r is now the correct measure of the total repetition time for a multislice experiment i e the time between successive excitations of one slice e If desired set tr and te to new values in seconds Entering the imprep Command Everything necessary to set up an image is now done To proceed 1 Enter the command imprep This command takes the information ab
193. apter 7 High Performance Auxiliary and Microimaging Gradients 188 coil configuration reset the gcoil parameter to a value corresponding to the current configuration Table 11 lists gcoil values Table 11 Values of Parameter gcoil Main Coils Standard Design System std18 300 183 std31 85 310 100 310 std33 200 330 std40 200 400 Main Coils Actively Shielded Design shd18 300 183 shd31 85 310 100 310 shd33 200 330 shd40 200 400 HPAG Accessory Coils hpag18 85 310 100 310 200 330 200 400 2 Changing the value of gcoil resets the gradient coil dependent parameters in the current experiment Reset the following gradient levels to appropriate values for experimental conditions gpe gro gror gss gssr oF gx gy gz gxr gyr gzr In general the values of the gradient parameters need to be reduced when using the HPAG gradient coil because the coil intrinsically produces higher gradients for the same DAC setting than the main coil 3 Other parameters affected by the change of gradient coil hardware are the following frequency parameters resto tof slcto delto or tox to toz These parameters change either because of the different ZO sensitivities resto tof or because of different gradient strengths Determine the appropriate parameter values and reset them in the normal way The programs multislice setgpe setgro setgss setpoint etc remain fully functional in the 90 1 software release and can b
194. ard output Splitting FDF files The fdfsp1lit command takes an FDF file and splits the file into its data and header parts Use the syntax fdfsplit fdf_file data_fil header_file Note that the header can still have a checksum value in it If the header does have a checksum value remove it Prior Knowledge Peak Files Prior knowledge peak picking uses files in the csidir PEAK directory to define the expected peaks and their location Some files are already supplied for H1 and P31 Table 9 shows a list of menu selections followed by their corresponding file names Figure 81 shows a sample PEAK file for P31_standard 01 999163 00 A0800 Table 9 Prior Knowledge Menu Selections with Corresponding File Names Menu Selection File Name 1H in vivo standard 31P in vivo standard 13C in vivo standard 1H brain 31P brain 13C brain 1H muscle 31P muscle 13C muscle 1H liver 31P liver 13C liver 31P heart 1H kidney 1H phantom 31P phantom 13C phantom User defined 1 to 5 H1_ standard P31_ standard C13_standard H1_brain P31_brain C13_brain H1_muscle P31_muscle C13_muscle H1_liver P31_liver C13_liver P31_heart H1_kidney H1_phantom P31_phantom C13_phantom User to User5 VNMR 6 1C User Guide Imaging 173 Chapter 6 CSI Data Processing P31_standard Prior Knowledge of the peak information Nuclei 31P Tissue type standard in vivo Registe
195. are supported saturation recovery sr inversion recovery ir and aperiodic saturation recovery aps Reconstruction results in one or more image slices or a volume The acquisition and reconstruction of a series of slices or volume takes considerably longer than acquisition and reconstruction of a single slice Pulse Sequences The backprojection package has three pulse sequences e Sequence bp2d supports 2D slice select imaging and has an interface similar to the imaging module interface used to support oblique imaging 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 229 Chapter 10 2D and 3D Backprojection Sequence bp3d sequence supports 2D and 3D volume imaging and also has an interface similar to the imaging module interface used to support oblique imaging Sequence bp_image supports 2d slice select 2D volume and 3D volume imaging and has an interface similar to the microimaging module interface Table 21 provides data for each imaging method Table 21 Estimated Acquisition and Reconstruction Times Method np Acquisition Time Reconstruction Time Image Matrix 2D slice 128 32 x TE TR lt 1 second 64 x 64 2D slice 256 64 x TE TR 2 seconds 128 x 128 2D slice 512 128 x TE TR 5 seconds 256 x 256 2D vol 128 32 x TE TR lt 1 second 64 x 64 2D vol 256 64 x TE TR 2 seconds 128 x 128 2D vol 512 128 x TE TR 5 seconds 256 x 256 3D vol 128 1024 x TE TR 35 seconds 64 x 64 x 64 3D vol
196. at the dconi parameter is also available to control the dconi program display e dcon is a keyword to display a color intensity map this is the default mode but dcon is provided for compatibility with certain macros If dcon is the first argument it can be followed by any of the keywords linear phcolor avcolor gray and noaxis all of these keywords have the same meaning as when used with the dcon command e dpcon is a keyword to display a true contour plot If dpcon is the first argument it can be followed by any of the keywords pos neg and noaxis and then followed by values for levels and spacing All of these options have the same meaning as when used with the dpcon command e ds2d is a keyword to display a stacked plot in whitewash mode after the first spectra each spectra is blanked out in regions in which it is behind an earlier spectra If ds2d is the first argument it can be followed by any of the keywords nobase fill fillnb and noaxis All of these keywords have the same meaning as used with ds2d e again is a keyword to make dconi identify which display mode is currently being used and redraw the screen in that mode This option is useful when writing VNMR menus e restart is a keyword to activate dconi without redrawing the 2D data set This action causes dconi to make sure that 2D data is already displayed e toggle is a keyword to toggle between the cursor and box
197. ated pl Description Values Related patlist Description 340 Related nD Application dimension P ne Number of echoes to be acquired P ns Number of slices to be acquired P nv Number of phase encode steps for 1st indirectly detected dim P EE Total repetition time of an acquisition sequence P Pulse and Gradient List Parameters The list parameters provide information used in automated computation of rf power levels and slice or voxel selection gradient levels Each of these parameters can be arrayed to form a series of parameter names or values arraying these parameters does not cause arrayed data acquisition Every list has an entry corresponding to each rf pulse in the sequence providing sets of information about other parameters that are linked to each pulse event such as power level shaped pattern name etc All but the parameter fliplist are string parameters and the entries in these string lists are the names of the parameters that describe the corresponding attribute which can be inferred from the list parameter name itself Examples are given for the parameter set found in the SEMS imaging sequence Flip angle list Contains a list of the desired flip angles for each rf pulse Of the list parameters fliplist is the only numerical parameter the rest are string parameters Each entry in fliplist specifies the target flip angle that the corresponding pulse should achieve in the sequence The automated setup r
198. ates a new data trace that is concatenated with data from previous passes through that loop to form a single data block in acquisition memory Acquisition data memory must therefore be large enough to hold the total amount of data from any compressed acquisition loops before it is ultimately sent back to the host computer Compressed loops lie inside the signal averaging loop Pulse sequence loop execution can be easily toggled between compressed and standard modes by changing the appropriate character field in seqcon Changing the character field allows the same pulse sequence code to be used for different applications For example time course imaging studies are easily achieved by using a compressed phase encode mode which completes each image before the next begins Examples The following table lists some common seqcon settings e nD seqcon Application 1 nnnnn 1D spectroscopy 2 nesnn 2D imaging with compressed multislice standard phase encode 2 nscnn 2D imaging with compressed phase encode and arrayed slice position common in fast imaging sequences 2 cssnn 2D imaging with compressed multiecho and arrayed slice position 2 ccsnn 2D imaging with compressed multiecho and multislice 3 nncsn 3D imaging with compressed phase encode loop in 2D and standard phase encode loop in 3D 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 339 Appendix A Commands Macros and Parameters fliplist Description Rel
199. ation to be present in the pulsecal database The rfcoil parameter must be initialized to the entry in the pulsecal database Air or Water Cooling Turned On Air or water cooling systems must be enabled for gradient experiments Cooling is necessary to remove the heat buildup in the bore of the magnet caused by the gradient and shim coils Gradients systems are usually equipped with protection devices to detect and shut down the amplifier in the absence of either air or water flow 3 3 GEMS Multislice Imaging 44 This section describes the steps involved in setting up experiments and collecting imaging data using the gradient recalled echo sequence which is also known as FLASH or GRASS Because the setup procedure for most imaging experiments is similar to that of the GEMS sequence read this section before proceeding to other imaging sequences Requirements Your system must be configured for imaging and gradient calibration and eddy current compensation procedures must have been completed Gradient calibration and eddy current compensation are usually done during installation of the system so you do not need to repeat those procedures If those procedures have not been done contact your system administrator Description GEMS is essentially the same as the 2D spin warp sequence described in Basic Imaging Principles page 25 GEMS uses the Fourier transform principle to convert 2D time domain signals to a spatial frequency
200. ation used to display the data after the processing operation has completed Data interaction is different when processing individual spectra Individual spectra are usually selected and processed before performing a global operation in order to set up the processing attributes to use on the entire data set The currently selected frame should hold the desired spectrum to be processed Spectra can be inserted into this frame by using the Voxel Select tool described on page 154 or by selecting the voxel with the current processing window When processed the spectrum is stored back to the currently selected frame Select processing functions from the Process option in the CSI command panel with the right mouse button Click Process with the left mouse button to activate the current default process The current default process starts at Spatial Reconstruction and is incremented after each option until the Metabolic Map process Spatial Reconstruction The spatial reconstruction process performs a 1D or 2D transform along the spatial axes on the CSI Raw data set to form the localized FID data set The size of the spatial axes is the default Matrix size The Matrix field can then be expanded to provide for zero filling Figure 71 shows the window for the spatial reconstruction process Figure 71 Spatial Reconstruction Window The following list describes the functions of the spatial reconstruction processing attributes Dimension Defines the
201. aximum under these conditions Therefore any reset or power up of the acquisition system will leave the gradient compensation boards in a safe condition To return to the previously set conditions the eddysend macro will transmit the compensation values last used by the operator and clear any error lights on the gradient system The ranges for the time constants may be changed in eccsend by hand editing the maximum time of that time constant This mechanism is created to enable hardware changes of the time constants to be reflected into the software structure The gradient compensation boards each have five jumpers to change the range of the time constants A table of the jumpers and the matching time constant is furnished in the specific hardware documentation To match any changes to the hardware time constants eccTool produces a header section that tells eccsend the ranges for its calculations There are fifteen separate specifiers of the format tc_ x y z _ 1 2 3 4 5 where one of the items within each of the curly brackets is chosen The value is a floating point number in milliseconds An example entry is as follows max time constant for X channel 1 tG 250 0 Mixing software and hardware time constant definitions can cause confusion The windows time constants have default values If the time constants are changed in hardware the compensation file produced by eccTool must be changed manually to reflect these new values before calling e
202. ays image epiph Generates phasemap file epirs Reverses spectral data epirun Collects processes displays EPI data episet Collects EPI dataset episs Load default parameters episvib Saves images in Flexible Data Format for ImageBrowser go Acquires data pcmapapply Applies phase correction map to data used by epift pcmapclose Close phase correction map in EPI experiments pcmapgen Generates phase correction map used by epiph pcmapopen Open phase correction map in EPI experiments ssprep Calculates parameters gss tpwrl tpwr2 svf file Saves data Parameters eff_echo Sets effective echo position in phase dimension set to nv 2 gped Phase encode dephasing gradient increment groa Readout gradient adjuster in EPI experiment grora Readout refocusing gradient adjuster in EPI experiment image Phase encoding gradient flag O off 1 on tep Post acquisition delay in EPI experiment Unique to the episs c sequence Data Processing The echo signals correspond to the 2D k space data Note that every alternate echo is acquired with the readout gradient of opposite polarity Therefore each alternate echo must be time reversed before it is processed Time reversal is also equivalent to rotating the corresponding spatial frequency domain data about the center f2 0 After the odd echoes have been time reversed a dataset is similar to the time domain data collected in the spin warp imaging sequence After 2D Fourier trans
203. b ADC ADC M shames2 y BV SBV exp t alpha PS SBV BV PS 1 exp t alpha alpha 1 hct e tl and qt1 are alternative formulations for three parameter fits to T data e abst1 and absqt1 are alternative formulations for three parameter fits to absolute value T data e t2 is a standard two parameter fit to T data e adc is a two parameter fit to diffusion weighted images The fitted parameters are the Apparent Diffusion Coefficient and the reference level e shames2 is a two parameter fit for image enhancement by a contrast agent as a function of time The fitted parameters are for blood volume and permeability There are three fixed parameters that can be set from the command line alpha SBVO and hct The following command is an example 11 fit 1 8 shames2 x 0 01 0 136 0 13 0 37 In this command line the first constant 0 01 is interpreted as the threshold level any pixels with an absolute intensity less than this value are not fit but given zero values in the output images This first constant is read by the basic fitting routine any further constants can be read by the user function The next example sets the following parameter values alpha 0 136 SBV0 0 13 het 0 37 These parameters are also the default values 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 121 Chapter 5 Image Browser Math Processing You can also pass additional images on the command line The first extra ima
204. battery before beginning experiments e LOW BAT indicator on the PGM 1000 receiver unit lights during the course of an experiment it is assumed that the units are linked via the optical fiber and that the 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 211 Chapter 9 Physiological Gating Module cardiac preamplifier is located in the magnet Replace the battery The PGM system will continue to function during a low battery condition while the PGM 1000 receiver preamplifier ON LED remains lit e Ifthe preamplifier ON LED on the PGM 1000 receiver is not lit when the units are linked via the optical fiber the preamplifier unit might not be powered up the internal battery might be dead or the optical fiber system has developed a fault e If both the LED in the optical fiber output jack and the Low Bat indicator fail to light on power up the internal battery might be dead or the preamplifier optical fiber circuits might have failed Check the battery and if necessary replace it before experiments are started CAUTION When replacing the battery move the preamplifier away from the vicinity of the magnet bore Keep all tools outside the 5 gauss stray field To replace the battery turn off the power to the unit and perform the following steps which correspond with the numbered illustrations in Figure 103 Front Rear Front Bottom Rear 1 2 Of an Retaining Screws
205. bility This parameter is generally used to control a presaturation block that uses the parameters psat satfrq satpat and satpwr y means turn on execution n means turn it off psat Saturation pulse length P satira Presaturation frequency P satpat Presaturation pulse rf shape P satpwr Saturation presaturation pulse power level P RF spoiling on off Sets whether to turn on or off rf spoiling in sequences that include this capability This parameter is generally used to control an rf spoiling block in fast gradient echo sequences y means turn on rf spoiling n means turn it off rfphase Phase angle P Water suppression on off Sets whether to turn on or off water suppression in sequences that include this capability y means turn on water suppression n means turn off water suppression or to specify additional characters in some pulse sequences that provide more than one water suppression technique wsfrq Water suppression P Acquisition Loop Control Several special parameters common to all imaging experiments exist for providing information for automated setup or controlling pulse sequence execution These are seqcon and the list parameters fliplist patlist plist pwrlist and sslist The list parameters covered in the next section allow linking related parameters such as p1 tpwrl plpat together for use by automated setup macros VNMR 6 1C User Guide Imaging 01 999163 00 A0800 A 5 Para
206. bit frame buffer which can show only 256 colors or gray levels at a time on the screen The default structure is as follows grayscale 64 levels miscellaneous 12 levels CSI uses a colormap different from the standard colormap for overlaying metabolic maps over a reference image Its structure is as follows Display Control Use the Tools and the View command panel options to control the CSI display including images and spectra grayscale 64 levels bluescale 27 levels redscale 27 levels miscellaneous 12 levels greenscale 27 levels Various image display parameters can be manipulated with some of the graphics tools For example Vertical Scaling controls the intensity and contrast of the display and the Zooming tool allows magnification on individual spectra The View submenus in CSI provide viewing of localized FID MVS curve fit data sets and generated maps overlaid on reference images These viewing requests are useful because all the data is kept in global buffers but many times the display of the data has been overwritten These viewing requests allow the stored data to be reviewed Displaying and redisplaying overlaid images on CSI data sets is useful for drawing and getting ROI information by using the reference image The Colormap option in the View menu allows up to three different metabolic maps using red green blue intensity scales overlaid on a grayscale reference image to be displayed One of the options in the View m
207. both the main and auxiliary gradient coils if the eddy current compensation boards for the X Y and Z gradients are properly adjusted to suit the particular coil To avoid readjustment of the eddy current compensation each time the auxiliary gradient coil is used a second set of compensa tion 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 181 Chapter 7 High Performance Auxiliary and Microimaging Gradients boards is supplied as part of the HPAG accessory These boards are adjusted to compensate for the eddy currents generated in the magnet frame by the auxiliary coil Adjustment is made during the installation of the accessory To convert the power supply for use with a given gradient coil install only the appropriate set of eddy current compensation boards respectively labeled as X Y and Z Signal Con boards Exchanging eddy current compensation boards involves opening the control panel B of the gradient power supply and removing the existing set of boards from J N the internal card cage located behind the control panel To remove the set of boards from the internal card cage located behind the control panel take the following steps which correspond to the numbered callouts in Figure 86 1 Place the system gradient supply in Standby Figure 86 Front Panel of System 2 Turn off the Main Power Gradient Supply 3 Remove the pa
208. c motion of the object to be imaged Measurement of a physical property such as the electrocardiogram ECG is used to provide a physiological trigger to synchronize the imaging sequence to the motion Synchronization of NMR data collection with the motion period improves the image quality because data is always collected when the moving organ is in approximately the same position The organ appears to be static in terms of the NMR imaging process Different aspects of organ motion can be studied by introducing a fixed delay between the receipt of the physiological trigger and the NMR data collection Prospective gating is similar to the use of a stroboscopic light to view a rotating wheel If the pulse rate of the light matches the rotation period of the wheel then the wheel appears to be static Changing the point at which the light pulse is applied in the wheel s rotation cycle allows the wheel to be viewed in different positions The Physiological Gating Module 1000 PGM 1000 detects the ECG of the experimental subject analyzes the incoming signal and provides a trigger pulse to the spectrometer for prospective gating experiments 9 1 Cardiac Anatomy and Electrocardiography This section contains descriptions of cardiac anatomy and electrocardiography The following information might be helpful when planning and executing experiments Cardiac Anatomy In mammals the heart see Figure 99 is a four chambered organ located in the c
209. c just prior to the P wave of the next cardiac cycle The association between the electrical and mechanical events is known as electromechanical coupling Electromechanical coupling allows prediction of the heart motion state based on knowledge of the electrocardiogram Such a prediction is extremely helpful in setting up delay parameters so that images can be acquired at desired points in the cardiac motion cycle The phenomenon of electromechanical coupling leads to a link between the duration of the QT interval ventricular systole and the R to R interval or heart period The QT interval is commonly found to be between 33 and 50 of the R to R interval in normal hearts The PGM 1000 can be adjusted to detect the QRS complex and provide a trigger pulse from the electrocardiogram A sequence delay parameter called hold in the standard imaging pulse sequences can be used to delay execution of the pulse sequence after the reception of a specified number of external trigger pulses 9 2 Hardware Description This section describes the hardware components of the PGM 1000 including the function of all controls jacks and ports and PGM preamplifier battery replacement Parts List Table 17 lists the parts shipped with the PGM 1000 module 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 209 Chapter 9 Physiological Gating Module 210 Table 17 PGM 1000 Parts List Part Number Quantity Description 74 122907 00 01 000009 00 Prea
210. cbbaotsasabessas ssasdcgacsabeasedsosauavsonetoVy cus stevodadeaasdevobuversscuesabesosasts 133 TOONS isch e E E I E 147 OA Processing Functions 22 36 scisieessbstssiecsoessssbsceecd sscaactdgecuacseuevsclacasdecsies dti eos Eoi as ieia 156 6 5 Files and Other Items ee ee eesceeecesecenceceeeecsaceeeceseeeececescecsaeceaeeceeeeesaeeeeeesseeeeasens 167 Chapter 7 High Performance Auxiliary and Microimaging Gradients 175 hell HPAG 183 Hard ware sccissscsscicigcesaecssvceasdseiedecsiiesecasekcsdaanssedsaescsehseeceseasasededees aeeneeeon 175 Moe Expermental SOUP croeer deve cpecsacees equvod vane egatiesiasavnenseucngateusetussetecteosigeveanceacesys 183 7 3 Performance Specifications 2 0 0 eesceeeeessccesceceseecsseesececeeceeseceeneesseeesaeceeeecsseeeneesnees 189 TA Microimaging HardWare icicscsccssscicasvessscats stcsscnstesuccsonsebeacesseevodh sonvaseveantdevagnsseuvevnsests 190 Chapter 8 Digital Eddy Current Compensation c cccsssseeeeeseeeereeenees 199 8 1 The DECC Module 0 c ccssccsssessssssssesssseesecsssecsnsessecsssesssesensesusesesessaecesssesaecenseses 199 82 Theory Of Preemnp Wass svcd cscsrcs cecsscesve dyes sacenousheguecnspsus sebbacetvoasscuvtepscnbcateaGiascrevsress 199 8 3 Using the decctool Interface oo eeccececseceeeeeeecenseceececeeeecsaeceaeeceeeeneeeeneeneeeeaeens 202 8 4 Exercising decctool Using an Oscilloscope eeeceesecesceceeeeenseceececneeeeeeeeeeenteeeeneens 206 Chapter 9 Ph
211. ccsend Old values may be present to other compensation sets and the files should be named in a manner that distinguishes them from defaults and other probes The macro eccsend takes a text file in the subdirectory imaging eddy1lib of the VNMR system directory and produces an output binary file The output of eccTool is a text file that can be used as an input file foreccsend Arguments for eccsend enable several options The first argument is the input file name either full or relative If no second file name is given eccsend makes a file eddy out in the subdirectory acqqueue of the VNMR system directory otherwise it places that output in the named second file The contents of this file may be incomplete values not set will be left alone Lines beginning with the delimiters or are treated as comments Blank lines and lines that do not contain data are ignored Each channel s data starts with a letter followed by a colon e g X or Y or Z 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 197 Chapter 7 High Performance Auxiliary and Microimaging Gradients 198 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Chapter 8 Digital Eddy Current Compensation Sections in this chapter e 8 1 The DECC Module this page e 8 2 Theory of Preemphasis this page e 8 3 Using the decctool Interface page 202 e 8 4 Exercising decctool Using an Oscilloscope page 206 This chapter describes the digital eddy cur
212. ch as statistics The window automatically opens when statistics or other information is output to it The desired information can be then be selected and output to a file and the messages can be deleted The window can be closed or moved to a different location Reading VNMR Image Files The VNMR data that can be read are not files but directories which must contain a phasefile anda procpar file Currently the directories are either the current experiment directory or the directories saved with the command svdat To reada VNMR image use File Browser to select the directory that contains the phasefile file and the parameter file then select the Load button in File Browser To read experiment images the expl exp2 or exp9 directory must be selected Working with FDF Files The Flexible Data Format FDF file consists of a header and data e The header is an ASCII header and its fields are defined by a DDL Data Definition Language Having a ASCII header makes it easy to decipher the image content and add new fields Also the format of the header is the same as the ASCII format of the procpar file e The data portion is binary data described by the header fields It is separated from the header by a null character 108 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 4 6 Files and Other Items For a definition of all the fields see the section FDF File Specification in the manual VNMR User Programming Creating FDF files
213. cifications of the last displayed metabolic map View Menu The following subsections describe the CSI Image Image MV MVSI Image and Colormap options listed in the View menu on the CSI main command panel shown in Figure 54 on page 135 CSI Option The CSI option displays one of the following global CSI buffers in the currently selected graphics frame e MVS data e Localized FID data e Raw data e MVS curve fit data Image Option The Image option displays a global image buffer in the currently selected graphics frame e Reference image data e Metabolic map image data Image MVS Option The Image MVS option displays the global reference image buffer overlaid on one of the following global CSI buffers in the currently selected graphics frame e MVS data e MVS curve fit data e Localized FID data 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 169 Chapter 6 CSI Data Processing Image MVS can be used for obtaining ROI Spectrum information by using the reference image MVS Image Option The MVSI Image option displays one of the following global CSI buffers overlaid on a global reference image buffer in the currently selected graphics frame e MVS data e MVS curve fit data e Localized FID data Colormap Option The Colormap option opens the Colormap Figure 79 Colormap Display Window Display window shown in Figure 79 to create color metabolic maps and overlays Up to three different peaks can be displa
214. ckets and slide the auxiliary gradient coil out of the magnet through the rear entrance The auxiliary coil is heavy and requires the help of an additional person to lift and manipulate it Set aside the locking screws for future use Restore the water supply to the gradient coil at the main water shut off valve Check the HPAG quick disconnect box for potential leaks Exchange the eddy current boards in the system gradient power supply for the set calibrated for the main gradient coil Verify that the system connections are in the standard configuration shown in Figure 7 before powering on the system shim and gradient power supplies The ZO shim manual operation only can be reset to a value that places the transmitter offset for proton operation close to zero frequency Otherwise remember to compensate for the frequency shift that will be observed when using the main gradient coil Replace the system rf shield doors on the front and rear of the main gradient coil after loading the bore equipment in to the magnet VNMR 6 1C User Guide Imaging 01 999163 00 A0800 7 2 Experimental Setup HPAG Software Support This section outlines the software support for the HPAG accessory provided by the Spectroscopy Imaging Systems 90 1 release of system software This software release marks a major change in the handling of gradient calibration parameters so that a variety of new gradient coil types can be supported Features relevant to the contro
215. com for precompiled binaries 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 107 Chapter 4 Image Browser Flexible Image Transport System The Flexible Image Transport System FITS file format specification is available by anonymous FTP from fits cv nrao edu in the directory fits documents standards FITS was selected as the standard format because it is a true data format rather than just an image format It supports integer and floating point data and has header entries to specify the original image scale and aspect ratio More information is available at www gsfc nasa gov astro fits fits_home html Redisplaying Graphics Frames The Refresh option on the control panel refreshes and redisplays all graphics frames Displaying Error and Info Messages The Messages pulldown menu on the control panel contains the options Error Messages and Info Messages Error Messages The Error Messages option opens an Error Messages text window This window is scrollable so that all previous error messages can be viewed If there is an error the Error Message window automatically opens on the screen The window can stay on the screen or be closed Error messages can be saved into a file or all messages can be deleted Info Messages The Info Messages option opens an Info Messages text window This window is scrollable so that all previous info messages can be viewed The Info Messages window is for output of information from a particular task su
216. control point is on the y 0 5 line When the control point is in region 3 or 4 the curves for regions 2 or 1 respectively are reflected through the x y 1 line Linear Mode The linear mode allows the user to specify a piecewise linear function that passes through all of the control points Any additional number of control points can be added by clicking the left mouse button anywhere on the canvas away from an existing control point Control points can be deleted by clicking on them with the middle mouse button It is a good idea to avoid large discontinuities in the slope of this function at the control points Due to the characteristics of human vision these discontinuities can make a surface that increases smoothly in intensity across a picture appear to be non monotonic in intensity For this reason the third mode might be more useful VNMR 6 1C User Guide Imaging 01 999163 00 A0800 6 3 Tools Spline Mode The spline mode is like linear mode except that a spline curve is drawn through the control points instead of straight lines The spline mode is also coupled to the linear mode in that the two modes share the same control points changing the control points in one mode also changes them in the other The spline function used here interpolates between control points with cubic polynomials arranging that the slopes match at the control points The final curve is continuous up to the second derivative At the endpoints second
217. correctly sets the threshold voltage Observe the filtered electrocardiogram on channel and the signal from the PGM 1000 receiver output jack marked THRESHOLD OUT The threshold voltage signal should coincide with the baseline of the ECG signal Increase the ECG threshold voltage until the trace observed on channel 2 lies midway between the top of the baseline features and the maximum of the QRS complex as observed in the ECG Disconnect the threshold voltage output from channel 2 of the oscilloscope and begin to observe the inhibit output signal This signal should respond in a periodic fashion as each QRS complex is detected The response pattern should be the same as that described above for proper cardiac triggering Once proper cardiac triggering has been obtained by one of the methods described above proceed to adjust the inhibit delay Adjusting the Inhibit Delay If proper cardiac triggering has been obtained the inhibit delay can be adjusted by observing the electrocardiogram and inhibit output signals on channels and 2 of the oscilloscope as illustrated in Figure 108 With the inhibit delay set to its minimum value the inhibit output should decrease from 5 V to 0 V for a period of 50 ms every time a QRS complex is detected In this state shown in Figure 108 the PGM 1000 receiver supplies the spectrometer with a trigger pulse for every QRS complex that appears in the ECG If the pulse is not desirable increase the inhibit
218. cription Related sslist Description Related A 5 Parameters pat list isa list of the shape file names not the shape file names themselves e g pat List would not be set to the explicit names sinc gauss fliplist Flip angle list P imprep Set up rf pulses imaging and voxel selection gradients M plist Pulse length parameter list P pwrlist Pulse power level parameter list P sslist Gradient parameter names list P Pulse length parameter list Contains a list of the rf pulse length parameter names used by the sequence For example the SEMS sequence has a 90 pulse p1 and a 180 refocusing pulse p2 with plist p1 p2 fliplist Flip angle list P imprep Set up rf pulses imaging and voxel selection gradients M patlist Pulse shape parameter list P pwrlist Pulse power level parameter list P sslist Conjugate gradient list P Pulse power level parameter list Contains a list of the rf power parameter names used for each pulse in the sequence The SEMS sequence uses the parameters tpwr1 and tpwr2 to specify the power for the two corresponding pulses p1 and p2 for example pwrlist tpwrl tpwr2 fliplist Standard flip angle list P imprep Set up rf pulses imaging and voxel selection gradients M patlist Pulse shape parameter list P plist Pulse length parameter list P ssilist Gradient parameter names list P Gradient parameter names list Contains a list of the gradient param
219. cro 41 43 62 264 s2puls macro 42 safety interlock board 194 safety precautions 11 13 sagittal image orientation 20 63 sample probe preparation 248 temperature 316 sat parameter 238 242 244 saturation function 86 saturation recovery 229 241 Save Check window 146 saving data 102 301 ECC files 203 EPI data 61 FIDs in current experiment 301 files 105 graphic frames 81 101 105 image files 104 images 105 parameters from current experiment 302 ROIs 69 88 105 VNMR images 73 scout image 17 screen graphics region 66 SDAC board 204 sediff macro 264 SELECT button 69 134 selectable large signal mode preamplifier 344 selecting graphic frames 71 81 101 SEMS PAR parameter set 19 macro 264 pulse sequence 17 seqcon parameter 21 336 339 sequentially display images 67 setarray macro 42 51 62 265 setflip macro 265 setgcal macro 265 setgcoil macro 266 setgn macro 42 50 63 300 setloop macro 267 setof macro 42 49 62 63 setorient macro 268 setpgrad macro 268 setrgrad macro 269 setsgrad macro 270 setting compensation 205 duty cycle 62 204 eddy current 62 gain on gradients 205 imaging orientation Euler angles 268 limits for gradient pulses 204 reference frequency parameter 42 rise time 204 shims 205 slew rate 62 setting up array of pulse width values 42 experiments 44 01 999163 00 A0800 imaging experiments 41 imaging gradients 62 rf pulses 62 vox
220. ct the QRS complex in the electrocardiogram The signal is a constant voltage that ranges from 0 V to 12 V e GATE OUT carries the signal used to gate the spectrometer For normal operation connect it to the port labeled Biological Gate J8120 on the spectrometers patch panel The gate pulse signal is held at 5 volts This voltage is reduced to 0 V ground for a period of 1 ms in order to generate a trigger pulse for the spectrometer e CARDIAC OUT FILTERED carries the filtered ECG signal e CARDIAC OUT UNFILTERED carries the ECG signal in the unfiltered state 115VAC 50 60Hz is the power cord for a 115 Vac 50 60 Hz power input Suitable power output sockets are located on the rear panels of the spectrometer Use these sockets for voltage compatibility and correct electrical grounding of the PGM 1000 units e 250 A FUSE holds a 0 25 A 1 25 in fuse Check the fuse if the PGM 1000 receiver fails to power up Cardiac Electrode Leads Electrode Connections The set of cardiac electrode leads provided with the PGM 1000 are designed to be connected to the subject to form a standard limb lead configuration Connect electrodes to a region of exposed skin on the right Animal in supine position foreleg hind leg and the left Uppermost foreleg of the subject Suitable Right Left signals can often be obtained White foreleg foreleg Black from the pads on the surface es of the subject s feet Shaved regions are suitable for LEF
221. cted voxel spectrum Anything done locally does not affect the data in the MVS data until you select the Store button Select the desired Phase Order and Auto Go to perform automatic phase correction on a spectrum in a selected Gframe Select the Spectrum tool to perform manual phasing After the tool is selected click on the voxel to phase For more information see Spectrum Tool page 154 and Adjusting the Phase with the Spectrum Tool page 142 If the phasing results are satisfactory select the OK option to save the phase values to be used with the Write all global phase mode The following list describes the functions of the Local Phase Correction processing attributes shown in Figure 59 Phase Order Selects the type of Phase Correction Constant Linear or Both Auto Go Selects Automatic phasing Set rp Sets the rp field to 180 or clears the field Set Ip Sets the 1p field to Marker Marker np echo or clear Marker searches for a line marker in a currently selected gframe and sets the 1p value to 360 n where n is the nth complex data point specified by the Line Marker location This option is useful for phasing an echo To use Marker do the following steps 1 Voxel select a localized fid corresponding to spectra for phasing 2 Put a Line Marker in the middle of the echo and press Marker 3 Select gframe that the desired spectrum is in and apply 1p phase Marker is same as Marker except it sets a negative
222. ction to proceed In the 2 D case the window does not appear 3 The following messages appear allowing you to monitor the reconstruction process Magni Profi 2D 3D 2D 3D tude calculation is running le generation finished BP is running BP is finished See BP Macros and Programs Details page 249 for a detailed description of the individual settings passed between the program constituting the reconstruction Sometimes errors might appear in the magnitude calculation section for example bp_mc can t read bhead This error generally results when the initial Fourier transform has been performed on only one projection or a subset of the total projections To fix the problem enter ft or wft again and rerun bp_reco Displaying the Dataset At the end of the reconstruction process the data is written out for display e Fora2D dataset the first slice or only slice is copied into the data and phasefile files in expn datdir so that the slice can be viewed by VNMR Also the single or multislice data is reconstructed into FDF files for viewing by ImageBrowser These files are also located in expn datdir with the names lt seqfile gt 000 fdf lt seqfil l gt 001 fdf lt seqfile gt nnn fdf e Fora 3D dataset the data is written out to a FDF file in expn datdir named lt seqfil can imme Le gt fdf The display program disp3dis also started with the data so you diately view the 3D dataset This
223. current compensation uses exponential preemphasis 5 50 signal conditioning The compensation boards have the 10 10 capacity to set five time constant and amplitude values for the preemphasis These are calibrated for the system lifetime upon installation 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 189 Chapter 7 High Performance Auxiliary and Microimaging Gradients Shim Coils The shim set for the auxiliary gradient coil has windings for Z0 Z1 Z2 Z3 Z4 X ZX Z2X Y ZY Z2Y XY X2 Y2 ZXY and Z X2 Y2 shims Imaging Coil The imaging coil has a nominal diameter of 8 cm with a 90 flip time of less than 100 us for a square pulse The coil is tuned at the following system proton frequencies e 200 057 MHz for 200 330 and 200 400 systems e 85 500 MHz for 85 310 systems 7 4 Microimaging Hardware The principal unit of the microimaging module is the cabinet containing the gradient control system shown in Figure 90 which contains the gradient control circuits and power amplifiers The power amplifiers supply the high current pulses to the gradient coils in the magnet bore The microimaging module installation manual describes microimaging hardware in detail oT Status panel o SERVICE Qa o o T UUTETIIVETTINTITIITIM X gradient DUOUUTDOOOIUTOO INEDI amplifier a TECHRON 7700 SERIES 9 atea a TTA Y gradient AOIOCOTOOOIIOOOTIIOOIIIOTIIONII
224. curve fit on the selected peak or on the total spectrum depending on which item was selected in the Interactive Fitting Tool window Curve Check uses the displayed parameters to draw the curve Auto Curve Fit performs a curve fit on the selected spectrum Click Peak Reg to register all the peaks if the peak values are satisfactory Use Mmap No Set to register the peaks desired for metabolic maps Peaks are selected by Figure 73 Interactive Fitting Tool Window assigning a number in the Metabolic Map No area The value 0 deselects that peak Fitting OK registers the fitting parameters for the defined peaks These options only need to be selected when the local curve fit is satisfactory The following list describes the functions of the processing attributes that appear in the Interactive Fitting Tool window The attributes Peak No Edit from Marker Gaussian Factor Assign No Name and Metabolic Map No are peak specific Peak No Assigns a number to the current peak being fitted Fitted curve is automatically displayed over spectrum Frequency Intensity and Width are fields associated with this peak Edit from Marker Updates and displays Peak No and associated fields with peak and information from selected cross hair markers Gaussian Factor Assigns curve fitting factor 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 163 Chapter 6 CSI Data Processing 164 Assign No Name Metabolic Map No Max BO Shift Max
225. d x and y for the data and for the grey level values d and g These variables are defined as E d d nin Eq 21 d max d nin and 8 Emin Eq 22 Emax Emin Therefore both x and y vary from 0 to 1 Note that with the appropriate gamma correction discussed in the next section the actual screen intensity will vary exponentially with y For any type of mapping function the Negative button can be selected to invert the intensity scale that is the minimum grey value will be white and the maximum black 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 83 Chapter 4 Image Browser 84 Curve Mode The type of mapping function is selected by the buttons at the upper left of the Vertical Scaling window The default is curve which provides a flexible functional form that includes power functions and a close approximation to exponential functions The two parameter family of curves are controlled by moving the curve s control point around with the left mouse button The left and right ends of the line can also be moved up and down The form of the function depends on which regions of the graph the control point is in If the control point is in region 1 as shown in the Figure 32 the following equation shows the defining function for these curves b Eq 23 ax z where a and b are the two adjustable parameters The ranges of a and b are a gt 0 1 lt b lt 10 Eq 24 N 4 ty 3 va rN Za X4 4
226. d Z and the other sample II centered in X and Y but offset from the Z center For this simple case assume that the samples are point like and have very narrow linewidths Also assume that the NMR frequency for each sample can be measured at any time and independently of each other A simple pulse acquire is applied to either sample at a time T following a BO field gradient pulse as shown in Figure 96 If the rf pulse acquire sequence is short compared to the gradient and eddy current times then by varying the time T between the gradient and the rf pulse a series of spectra result where the spectral lines are offset from the zero gradient spectrum and converge to the zero gradient frequency for long time T e t Gradient O a RF Pulse D Acquire Figure 96 RF Pulse Acquire Sequence Experience has shown that frequency of the line as a function of time follows Eq 33 N T T f T f i A k 1 where A and T are characteristic of conducting structures in the magnet within which the eddy currents reside According to Lenz s law eddy currents act to oppose the field that caused them for shielded gradients A can be negative In general there are several conducting structures in the magnet and each gives rise to a term in the summation in Equation 33 Eddy current fields contain for all practical purposes two components a BO component and a gradient component first order or linear term Each co
227. d after the data Phase and Baseline Perform phase and baseline correction on the spectra Correction Correction can be done manually or automatically on a spectrum by spectrum basis or automatically on all the spectra in the MVS data 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 131 Chapter 6 CSI Data Processing 132 Metabolic Map Generates a metabolic map from the MVS data The data must be curve fitted before metabolic maps can be generated curve fitting can be done on a local or global basis Image Allows reference images to be reconstructed from raw data Reconstruction Image Calctool Does calculations using spectral peaks for generating metabolic maps by using combinations of peaks and scalar values pH Map Calculates pH maps and frequency difference maps between selected peaks in the spectra ROI Spectrum Extracts a series of spectra along a defined line or extracts an averaged spectrum from inside a rectangular ROI Graphics Functions Tools are provided to allow the creation and modification of various types of objects in the graphics region CSI uses the same tools as ImageBrowser Frame Zooming Vertical Scaling and Contrast ROI and Text Annotation However CSI has some differences from ImageBrowser CSI only implements box and line ROIs and has added graphics functions to perform voxel selection of spectra peak picking curve fitting and interactive filtering The ImageBrowser standard colormap uses an 8
228. d images Adjust the zoom lines to all selected images The zoom lines are the lines that control the portion of images to be zoomed Controls the real time tracking of the zoom line positions in other selected Gframes when zoom binding is enabled You can set the maximum number of tracking frames If you set the number to 0 only the zoom lines in the Gframe in which the mouse is dragged will change in real time When you release the mouse button the zoom lines in all selected frames will snap to the new position If you set the number of frames to a number n that is less than the number of selected Gframes only the first n selected Gframes will track in real time Allows you to set the number that controls the zooming magnification factor See the Using Keyboard Accelerators page 79 for more information Controls the sensitivity of the cursor for the zoom lines This specifies how close the mouse cursor must be to a zoom line to select it When Pixel Interpolation is displayed in the menu it means that pixel replication is being used to expand the size of the images to display on the screen not just when zooming but at any time an image is redisplayed If Pixel Replication is displayed it means that pixel interpolation is currently selected and cubic spline interpolation is used to display the images Note that the pixel interpolation takes much longer than pixel replication Some Zoom functions are available by
229. d in compressed mode with nf M ftnt Fourier transforms data acquired in compressed mode with parameter nf ft nf is for one dimensional data ft2d nf is for two dimensional data flashe Convert compressed 2D data to standard 2D format M ft Fourier transform 1D data C CE2D Fourier transform 2D data C Submit experiment to acquisition and FT the result M ga lt lt nocheck gt lt next gt lt wait gt gt Performs experiment described by the current acquisition parameters checking parameters loc spin gain wshim load and method to determine the necessity to perform various actions in addition to simple data acquisition This may involve a single FID or multiple FIDs as in the case of arrays or 2D experiments ga causes the data to be automatically weighted and Fourier transformed wft at the end of each FID data acquisition Before starting the experiment ga executes two user created macros if they exist The first is usergo a macro that allows the user to set up general conditions for the experiment The second is a macro whose name is formed by go_ followed by the name of the pulse sequence from seqfil to be used e g go_S2pul go_dept The second macro allows a user to set up experiment conditions suited to a particular sequence nocheck is a keyword to override checking if there is insufficient free disk space for the complete 1D or 2D FID data set to be acquired next is a keyword to put
230. d move the cursor down the list of commands 2 When the desired command is highlighted release the button Figure 27 Frame Properties Menu 3 Pin the menu by selecting the pushpin icon EA in the top left hand corner of the menu Creating Gframes To create new graphics frames 1 Position the mouse pointer in the graphics window outside of any existing Gframe 2 Hold the eft mouse button down and drag the pointer across the screen This action draws a box 3 When the left button is released the box is completed and selected Notice that a frame must not overlap any part of another frame Another way to create a Gframe is to load an image when no frames exist A Gframe the size of the whole graphics region is created and an image is loaded into it An array of Gframes can be created from an empty graphics region with the Gframe splitting routine described in Splitting Gframes page 72 If no Gframes exist the entire graphics region is split up into the requested matrix of frames Selecting Gframes To select a graphics frame e Position the pointer within the frame and click the left button The frame s corners become highlighted to show that it is selected and any other selected frames are deselected To select a number of frames e Press the middle mouse button to select a frame if it is not selected or deselect it if it is already selected To select a number of Gframes and append each fram
231. d the acquisition time In this type of acquisition only hard pulses are used for excitation thus taking the signal of the whole probe in each projection step Depending on the available measurement time signal to noise considerations and the properties of the probe a 2D method bp2d or 3D method bp3d image can be acquired In case of a 2D image acquisition the reconstructed intensity in each pixel refers to the summed up intensities along a line perpendicular to the chosen image plane This non slice selective approach results in a short measurement time for a 3D object and is useful in cases of poor signal to noise or it can serve as a scout view In case of a 3D image acquisition each voxel in the reconstructed volume series of slices refers to the signal obtained from the particular pixel position x y Z Both the 2D and 3D type of acquisition use the same pulse sequence T Weighted 2D and 3D BP Pulse Sequence The T weighted pulse sequence is shown in Figure 118 The preparation phase A contains only the recovery time t r After phase A the gradients are switched on and allowed to settle as set by trise T gt weighting is achieved during acquisition phase B by setting the spin echo time te If te is smaller than the sum of dy and half of the acquisition time the echo occurs left shifted T Weighting Using Inversion Recovery or Saturation Recovery T weighting in the preparation phase A is achieved by a 90 pul
232. d to by handle The value of the variable is put into the integer pointed to by pvalue Returns a logically true nonzero value on success and a logically false zero value on failure Example int get_header_int handle name pvalue FDFptr handle char name int pvalue Gets the value of an double type header variable The variable name is read from the image referred to by handle The value of the variable is put into the location pointed to by pvalue Returns a logically true nonzero value on success and a logically false zero value on failure Example int get_header_double handle name pvalue FDFptr handle char name double pvalue Gets the value of an character array type header variable The variable name is read from the image referred to by handle A pointer to the character string is put into the location pointed to by pst ring Returns a logically true nonzero value on success and a logically false zero value on failure Example int get_header_string handle name pstring FDFptr handle char name char pstring 01 999163 00 A0800 get_header_array_int get_header_array_double get_header_array_string get_image_width get_image_height get_image_depth get_object_width 01 999163 00 A0800 5 3 Image Browser Math Functions Gets the value of one element of an integer array type header variable The index member of the variable name is read from the image referred
233. dacsesscehdacavedscessesabscveasdspabsasveceaapedacsysanseaicnss 146 Graphics Tools Window c cc ccescsscscasesesssscasestescossscsazseveasosbuscevasecsseaatesusestasssedbesbns cess 147 Vertical Scale Properties Window ooo eee ceeeseceeceseceeeeseeeeeeeeeeeeeseeeseeseecaecaecaeesaeeaees 148 Vertical Scaling Window ctacescesccseccodetevagecss ascideccevecuateiceduesseesdercsgevigcesctassus casgecreessees 149 Curve Control PONE sesscesecasecdecestoseesvesseteecsdescasescerscerssanseusagastuseciecaseeseesseesorestsapecsessees 150 Gamma Correction Window oo eececeseeseessessecssessecaeceaeceecseeseceseeeeceeeseeseaeseaeeaaeeaseaee 151 Spatial Reconstruction Window ou ce esceceseceeceseeeeeeseeeeceseeeeeeaeeeeecaeecaesaeeaesseesaees 157 Spectral Reconstruction Window ou eee ceceseceeceseeeeeeseeeeceeeeeeeeaeeeeecaeecaecaeesaesneesaees 158 Interactive Fitting Tool Window ou eee cseeese teense ceeceseeseceaeeeeeeeeeseceeeeseseeeeeesenes 163 Metabolic Map Display Window ooo eee eeeeeceeeeeeeeseeeeecaeecaecsaeeaecsacaeceeteeeeeees 164 Image Reconstruction Window ou eeecesessecssessececeseceeeseeeeeseeeeceeeseeeeseseaeeaaeeaeeaee 165 PH Map Control Window ou cece eceeceseeeeceseeeeeeseeeaecaeecaecaaesaeceaeaeseeeseeeeeeeeseeeees 166 FileBrowser Window i sec cccsscescocssecdessectsostensesbnescenesevoeetuosecborenesscosdaseedenessaseneosessbes 168 FileBrowser Save Tool Window ou eee ceceesecsesseceecesececeseeeceseeeeceeeseeseaeseaseaaee
234. data to a compressed format can be highly beneficial Compressed to Standard Format flashc can convert a compressed compressed multislice multiecho or multi image sequence It can also convert a rare type sequence with a compressed phase encode echo train Processing and Displaying Reformatted Data After the data has been reformatted use the ft 2d command to process and display the 2D image Instead of using flashc and the ft 2d the command use ft nf to double Fourier transform the 2D data set When ft nf is used the data is not reformatted Use the dconi command to redisplay the image for further analysis Converting Table Ordered Data It is possible to acquire data from imaging and 2D experiments in nonmonotonic order either by explicitly coding the desired progression into a pulse sequence or by using an external AP table to control the order In either case VNMR is not able to properly process the resulting data In such cases the t abc macro is useful tabc converts data obtained in table order to linear monotonic order so that the data is suitable for processing in VNMR The data must have been acquired according to a table in the tablib directory tabc reads the file fid in the acqfil subdirectory of the current experiment Before data is reordered this file is written to another file named fid origin the same acqfil directory Therefore if for any reason t abc fails or results in an unpredictable or unde
235. dataset must contain the reference scan This scan must be acquired with the phase encode gradient turned off browser Start Image Browser application U Display list of current experiments in VNMR text window M explib2 Displays a summary list of the available experiments similar to exp1ib in the text window For each experiment the experiment number name of the pulse sequence and the first part of the text file are displayed There are three main differences between the macros explib2 and exp1lib e explib2 isa macro which can be modified by users while explibisa VNMR command e explib2 is somewhat faster than exp1ib primarily because it does not obtain and display the size of each experiment in kilobytes e explib2 does not display any acquisition status information such as queued experiments as does explib explib Display experiment library M 01 999163 00 A0800 filter Syntax Description Arguments Examples Related findpw Syntax Description Arguments Examples Related flashc Syntax Description A 4 Commands and Macros for Processing and Display Set apodization parameters to give Gaussian LP filter for wft2d M filter weighting_value Computes the Gaussian weighting parameters gf gfs gf1 and gfs1 to give a Gaussian low pass smoothing filter for the w t 2d command weighting_value specifies the degree of weighting and results in a reduction at the edge o
236. delay to reduce the triggering frequency Slowly adjust the inhibit delay control to increase the inhibit delay time while observing the oscilloscope traces Allow a few heart beats to pass between each adjustment Carefully note the response of the inhibit output trace At first increasing the inhibit control simply lengthens the period of time the inhibit delay spends at 0 V after R wave detection As soon as the length of the inhibit delay period approaches the value of the heart period the inhibit output signal appears to respond erratically The erratic response is caused by natural variations in the heart rate A further increase of the inhibit delay causes the erratic pattern to disappear and a new periodic response shown in Figure 108 to appear The new response of the inhibit output signal appears as a level change from 5 V to 0 V as a QRS complex is detected in the ECG This change is followed by a delay greater than VNMR 6 1C User Guide Imaging 01 999163 00 A0800 9 3 Experimental Setup A Inhibit Out Signal Inhibit DelayTime Figure 108 ECG and Inhibit Out Trigger on A Each Heart Beat B Every Other Beat one heart period in which the inhibit output signal is held at 0 V During this interval a second QRS complex appears in the ECG The inhibit output then returns to the 5 V level in the second heart period In this state the PGM receiver outputs a trigger pulse for every second QRS complex detected in th
237. dient pulses Timing parameter to control the separation of a pair of diffusion sensitizing gradient pulses Most diffusion weighted imaging sequences use a pair of gradient pulses to achieve contrast based on diffusion each of length tdelta The separation in time between these gradient pulses is normally defined as 316 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Related tdiff te Description Related Description Related tep Applicability Description Values Related tflow Description Related Description A 5 Parameters tDELTA in an attempt to correspond to the original definitions of Stejkal and Tanner 6 and A gdiff Diffusion gradient level P tdelta Control diffusion sensitizing gradient pulse length P tdi fe Diffusion sensitizing gradient pulse length control P Diffusion sensitizing gradient pulse length control Timing parameter available to control the length of a diffusion sensitizing gradient pulse Standard Varian pulse sequences more commonly use the parameter t delta for this purpose gaiftt Diffusion gradient level P tdelta Control diffusion sensitizing gradient pulse length P tDELTA Control separation of two diffusion sensitizing gradient pulses P Echo time Echo time for imaging and some localized spectroscopy experiments For gradient and spin echo imaging sequences te is usually defined as the time measured from the middle of the initial
238. ding Save All command ms140 fdf The File Browser window displays the currently selected file on the top line Below that file is the current directory 5 The number of files in the directory is 9 files listed at the bottom There is a scrolling window that contains the names of all the files in the directory Subdirectories Figure 45 File Browser for Loading Images are indicated with a at the end of their name To select a name in the scrolling list position the cursor over the desired name and click the eft mouse button Changing Directories To change directories use the left mouse button to double click on the directory name Select the name so it appears in the top line then press the Return key Changing directories can also be accomplished by entering the name directly in the top line and pressing Return The UNIX prefix works in File Browser The entry moves you to the parent directory Loading Files Select the Load pulldown menu item from the File command panel item to open a File Browser window for loading files To load a file into Image Browser select the desired file and click on the Load button Files are loaded into the next available graphics frame To select a particular frame to load an image into that frame should be selected immediately VNMR 6 1C User Guide Imaging 01 999163 00 A0800 4 6 Files and Other Items before clicking the Load button If there are no Gframes a si
239. directions in the horizontal magnets and refer to the left right and top bottom orientations respectively as shown in Figure 13 Top Supine pS y Back Front A Right i Left Vale v Bottom Prone Figure 13 Horizontal Magnet However the x and y directions in vertical bore magnets are less obvious because of the cylindrical symmetry of those magnets shown in Figure 14 During installation the gradient coils and shim coils are aligned and fixed so that they are symmetrical with respect to the center of the magnet For imaging you must place the rf coil in the magnet center and position the sample within the rf coil 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 37 Chapter 2 Imaging Experiments The image planes are referenced with respect to the gradient frame of reference Top we The three commonly referenced planes are sagittal coronal and transverse and they respectively refer to the planes that are perpendicular to the x y and z axes as shown in Figure 14 Images can also be X obtained from arbitrary or oblique planes The plan macro in VNMR y allows you to define oblique planes by Z using a graphical tool and a reference u image For some applications you might aa want to collect a3D volume image instead Bottom of a 2D slice image For a 3D volume image it is possible to analyze or view the data by using 3D image analysis routines Figure 14 Vertical Magnet
240. dy arrayed array is updated If more advanced array capabilities such a simultaneous arrays have been specified through array its value might need to be corrected after use of setarray To repeat an experiment several times using the same parameter values e g to perform a stability test use set array to array any parameter with an increment of 0 If no arguments are entered the macro prompts for argument values parameter is the name of parameter to be arrayed start is the value of the first array element increment is the increment between successive arrayed elements number is the total number of array values setarray setarray pw 10 10 4 sets pw 10 20 30 40 setarray tof 1000 500 4 sets tof 1000 500 0 500 setarray nt 1 0 10 setsnt 1 1 1 1 1 1 1 1 1 1 array Parameter order and precedence P exparray Array a numeric parameter M Set rf power levels to desired flip angle setflip lt parameter pattern power flip_angle gt Computes the power level required to achieve a specified flip angle for any rf pulse A valid entry in the pulsecal calibration file specified through rfcoil is also required set flip uses the pulse calibration together with the integral of the pulse shape found in the header of the shape file to compute the power level necessary to obtain the required flip angle If no arguments are entered the macro prompts for argument values parameter is the pulse length parameter pattern
241. e along the readout direction in the magnet It can also be used for pulse calibration and for setting the receiver gain t tr p te p rf gss gro ge A ADC Figure 17 Gradient Echo Imaging Sequence Data Collection Set nv the number 64 or 128 of phase encode steps before entering go to acquire the image For efficiency the GEMS sequence collects the data in a compressed format seqcon nscnn If the data is collected in the standard noncompressed format seqcon nssnn the overhead in the end of scan operation can influence the true recycle time in the pulse sequence This situation is particularly true for experiments such as GEMS which is often run with very short t r values for recycle time about 5 msec to 20 msec In a case when data is collected in the standard format errors can be significant Reformat Process and Display After data collection use the lashc command to convert 2D FID data files from compressed formats seqcon nncsn seqcon ncecnn seqcon nnccn to the standard format seqcon ncsnn or from the standard format to compressed formats flashc reads the file fidin the acqfil subdirectory of the current experiment Because data is reordered and the original fid file is overwritten and therefore Jost flashc is written so that in the event of an error during processing the original f id file is preserved Also before flashc runs the command does a s
242. e data 1pe2 is used for the fast x direction when processing CSI data In this discussion the fast medium and slow directions are considered to be the order that the fast Fourier transforms are performed and are analogous to the x y and z directions Default value is 8 thk Although thk is not in the old standard parameter sets and is an oblique imaging parameter it is currently the only method to define slice thickness Default value is 1 Spatial Parameters for Non Oblique Sequences The location for these data sets is currently always assumed to be at 0 0 0 coordinates orient String parameter used with gro gpe gpe2 to determine orientation Default value is xyz gss gpe gpe2 The signs of the gradient values along with the orient parameter are used to determine the orientation of the data set These are used for CSI data sets Default value is 1 gss gpe gro Gradient parameters used to determine the orientation for reference images Default value is 1 Spatial Parameters for Oblique Sequences psi phi theta Euler angles to determine data set orientation Default value is 0 PSS ppe2 ppe Position parameters for CSI data sets Default value is 0 PSS pro ppe Position parameters for reference image data sets Default value is 0 FDF Files The CSI tool saves data as FDF Flexible Data Format files The FDF file consists of a header and data e The header is an ASCII header and its fields are defined by a Da
243. e if required An example is the parameter group p1 topwr1 and plpat These are in fact three independent parameters and there is no hard rule that requires them to be associated It is convenient to write a pulse sequence so that for example the power level for pulse p1 is tpwr1 and the parameter specifying the shape of p1 is named plpat Standard Varian imaging sequences are written in an attempt to have pulse names follow the obvious progression of the sequence and where possible to use names that are descriptive of their function For example an inversion recovery spin echo sequence would start with an inversion pulse of length pi with a power level specified by tpwri and pattern specified by pipat followed by the 90 slice selective excitation pulse p1 tpwrl plpat and ending with the 180 refocusing pulse p2 tpwr2 p2pat All pulse length parameters are defined in VNMR as type pulse meaning that pulse durations are entered in us The standard limit on maximum pulse length is 8190 us Use the set 1imit command to increase the upper limit on length Remember that pulse durations are internally converted to seconds for purposes of pulse sequence calculations refer to the manuals VNMR Command and Parameter Reference and VNMR User Programming for more detailed information The predefined pulse power parameters have maximum and minimum values derived from the global configuration parameters parmax and parmin These li
244. e parameters lro lpe and 1pe2 respectively After loading the data a 3D volume appears in the display panel fdf_file is the name of a file containing FDF data appmode Application mode P fn Fourier number in directly detected dimension P Eni Fourier number in 1st indirectly detected dimension P fn2 Fourier number in 2nd indirectly detected dimension P ft3d Perform a 3D Fourier transform on a 3D FID data set M U lpe Field of view size for phase encode axis P 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 279 Appendix A Commands Macros and Parameters dmi Syntax Description Related dpss Syntax Description Related dssh Syntax Description 280 lpe2 Field of view size for 2nd phase encode axis P lro Field of view size for readout axis P Transform and display multiple images in VNMR graphics window M dmi Transforms and displays a series of multiple images from an arrayed multislice or multiecho imaging experiment in the VNMR graphics window Because the resulting image display is noninteractive changes in expansion vertical scale window and level must be made on a single interactive display before executing dmi The layout and size of the images are optimized to maximize the image display on the usable graphics region Images can be displayed in either the trace f1 orthetrace f2 mode in either full or zoomed modes To force VNMR to use the entire graphics window set the wysiwyg par
245. e 18 Gradient Echo Version of EPI Pulse Sequence k space along the phase encode direction is determined by gped the phase encode dephasing gradient parameter gped is usually set so that the effective echo ef _echo appears at the center of the phase encode dimension t1 Artifacts Unless special data processing is used images are usually affected by severe artifacts Because the EPI is prone to artifacts the technique is seldom used for routine work It is useful to know the nature and source of these artifacts in order to understand the steps that are necessary to minimize the artifacts when running EPI experiments Half FOV Ghosts In an ideal case all echoes appear at the middle t2 0 of the acquisition window However because of the nonideal behavior of gradients and spurious gradient fields the echo positions of the odd and even echoes might appear shifted from the 12 0 position which contributes to the phase shifts between the odd and even echo signals Half field of view FOV ghosts are one of the more common and notorious artifacts in EPI images These ghosts are caused by incorrect matching of odd and even echoes As discussed in Data Processing page 52 the evolution of odd and even echoes are time reversed with respect to each other because they are acquired with gradients of opposite polarity Therefore external effects such as inhomogeneity and eddy currents etc influence the amplitude and phase of odd and
246. e 68 for details about Image Browser initialization Before adjusting the gamma correction adjust the monitor Some monitors have no easily accessible brightness control therefore monitor adjustment should be performed by a service person The most common problem with monitor adjustment is that the black level is set too dark making everything near the bottom end of the intensity scale appear black Set the brightness control labeled X on some monitors just low enough so that the blackest level at the left of the grayscale ramps pixel value 0 is indistinguishable from the unscanned black background at the edge of the monitor screen To accomplish this adjustment it might be convenient to move the Gamma Correction window slightly off the bottom of the screen so that the bottom row of steps directly merges with the unscanned margin Once monitor brightness has been adjusted correctly the perceived prominence of the intensity steps in the Gamma Correction window should be roughly equal with no gamma correction The gamma correction described in the following paragraph is still effective on a poorly adjusted monitor although if the brightness is set too high there is no way that the lowest gray level can be made entirely black Two forms of gamma correction are available When the Gamma and Log switches are both set to ON Image Browser attempts to make each step in the colormap index an equal step in the log of the screen inte
247. e C by setting the spin echo time te The spin echo might appear left shifted because of a time constraint imposed by setting te too small VNMR 6 1C User Guide Imaging 01 999163 00 A0800 10 4 Routine Usage ms _ 2 0 3 7 2 0 wif ii j us j 1 I ia 20 o ON BOL Oi O 20 tr trise hrm90 pi tpe p1 dx trise hrm90 trise dy trise 1 5 2 0__ j 2 0 1 0 EAL 2 0 2 0 3 7 2 0 ni tr trise hrm90 pi tpe pi dx trise hrm90 trise dy trise BACKPROJECTION SPECIAL ptype slice 50000 gain ACQUISITION 02000 temp 402 175 90000 i 00300 il trise 00200 in GRADIENTS PROCESSIN cp orient xyz sb 0 002 SAMPLE hrm90 gcal 0 002000 sbs 0 000 date Mar 30 94 2000 0 lro 0 80 phfid 0 1 file home1fpe 47 gro 4000 fn not used ter BP AR_2 Schlau hrm90 grof 1 450 proc Ft chi 2000 0 gss 5000 math f solvent none gssf 0 500 CONTRAST DERIVED prep n sw 50000 0 Figure 123 T Weighted 2D Slice Selective Pulse Sequence T1 Weighting Using Inversion Recovery or Saturation Recovery T weighting in the preparation phase A is achieved by a 90 pulse saturation recovery sr or by a 180 pulse inversion recovery ir The pulse is controlled by pi and tpwri In acquisition phases B and C set te to a small value to reduce the T weighting influence Figure 124 shows an example of T1 weighting using ir or sr 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 241 Chapter 10 2D and 3D Backprojection A B BACKPROJECTION TRANSIENTS TIM
248. e ECG Increasing the value of the inhibit delay progressively reduces the triggering frequency Each time the inhibit delay approaches an integer number of heart periods the inhibit output makes a transition to erratic behavior because of normal variations in the heart rate To prevent erratic triggering increase or decrease the inhibit delay Obtaining Images Cardiac gated images can be obtained with most of the standard imaging pulse sequences The operation of each sequence and its compatibility with gating operation is described in the manual VNMR User Programming The slice profile projection modes of all sequences operate exclusively in the nongated mode Gating is usually activated through the parameter t icks The value of ticks is the number of trigger pulses the system detects before proceeding to carry out the current scan 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 221 Chapter 9 Physiological Gating Module 222 Using a value of ticks greater than 0 provides a gated image A value of ticks greater than 1 reduces the effective triggering frequency by a factor of 1 ticks Generally it is better to use the inhibit delay feature of the PGM 1000 because this feature provides protection against false triggering and leads to a more stable triggering frequency The pulse sequence statement used to control gating xgate is inserted into sequence codes just prior to the active portion of the sequence usually after the
249. e Execute button is equivalent to pressing Return on the Name line Note that the contents of the Name line not the contents of the scrolling window are executed Macro Capabilities Parameters operators and reserved words and VNMR and Image Browser commands can be run as macros Parameters Parameters are supported the same as in VNMR as are multiple parameter trees and parameter groups However Image Browser makes no distinction between different trees and groups Operators and Reserved Words Image Browser MAGICAL II has the same reserved words and operators as VNMR MAGICAL II as listed in the manual VNMR User Programming except that the two special operators typeof and size are not operational Built in Commands Most VNMR commands are inappropriate for Image Browser and are unavailable many of these commands acquire and analyze NMR data A small number of VNMR commands are of a more general nature The following VNMR commands are also available in Image Browser Each command is used exactly the same as in VNMR see the format listing regarding an extension Command Action create Create new parameter in a parameter tree destroy Destroy a parameter destroygroup Destroy parameters of a group in a tree echo Output from echo appears in Info Messages window and is searched for relative to BROWSERDIR roi directory 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 99 Chapter 4 Image Browser 100 Command
250. e Network Graphics PS Adobe PostScript file PS2 Adobe Level 2 PostScript file SGI Irix RGB image file SUN Sun Rasterfile TGA Truevision Targa image file TIFF Tagged Image File Format VIFF Khoros Visualization image file XBM X11 bitmap file XPM X11 pixmap file XWD X Window System window dump image file label Conversion scripts are currently limited to one line of at most 1000 characters Before the script is run the symbol 1 is expanded into the name of a FITS format input file containing the data The output file name is represented by 2 In this case the script includes a quality flag that controls the amount of data compression to be done The data line specifies the type and size of data that JPEG supports but it is currently ignored One limitation of dumping files in a non FDF format is that the aspect ratio of the image is not preserved Image Browser dumps out the actual data rather than an image of it Most image formats assume that the individual pixels are square and do not have x and y scaling information in their headers The FITS format does have such information in its header and it is filled in appropriately by Image Browser but convert ignores it and most viewers ignore it when they display the FITS file ImageMagick Package The ImageMagick package is free by anonymous FTP from various Internet sites such as ftp x org in the directory contrib applications ImageMagick Also see www wizards dupont
251. e an image by entering the command svib image 4T Loading Images Images are easily loaded in Image Browser Select the File button which opens a File Browser Data window You can now browse directories and data files and can load images When you load an image the vertical scaling for the display is automatically set so that the range of data values in the image spans the full range of grayscale values Image Browser accepts images in the Flexible Data Format FDF which is the type of data file created by the macros svib or svsis described in the previous section Saving Images from VNMR for Image Browser Image Browser also accepts some types of images in the VNMR Phasefile format 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 73 Chapter 4 Image Browser FDF Files The FDF file is the file format of choice because all the information to describe the image is in the file and there is no directory structure necessary An FDF file can be loaded by double clicking by selecting the file and pressing the Return key or by selecting the file and clicking on the Load button VNMR Phasefiles To retrieve images stored as VNMR phasefiles select the directory that stores datdir phasefile and curpar and then select Load For example to analyze an image in VNMR in exp3 start Image Browser select exp3 and load the image Note that double clicking on the directory or pressing Return after its name opens that directory but doe
252. e because echo time depends on the acquisition time and the rf and gradient pulse delays in the sequence The shortest achievable echo time depends mainly on maximum gradient performances such as maximum gradient strengths rise times and residual eddy currents However te delay can also be used to enhance the T or T gt contrast in images For example in functional MRI brain activity causes localized susceptibility in the brain which is enhanced by using the 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 39 Chapter 2 Imaging Experiments 40 gradient echo imaging techniques The T gt effects of solid materials are very short lt 100 us so special experimental techniques need to be used to obtain images from such samples ti Inversion Time ti is an important contrast parameter in imaging The inversion time contrast between different components in the sample can be enhanced by performing a t i inversion recovery sequence ti ir The ti ir imaging sequence involves applying a 180 inversion pulse and a delay t i at the beginning of a conventional imaging sequence The inversion pulse flips the magnetization to the z direction The spins return to equilibrium exponentially with a time constant inversion time as illustrated in Figure 16 180 Exponential recovery of the longitudinal magnetization gt t 0 tnull 0 69T Figure 16 Equilibrium Magnetization Sampling the magnetization after the
253. e data set There are three methods for baseline correction e Spline e Polynomial e SINC For faster performance in baseline correction select Write all mode in the Global Baseline Correction field The Automatic mode can take tens of minutes To register the correction values for the Write all mode select Correction OK after the sampled points and the correction method are satisfactory then select Apply To All Figure 60 Baseline Correction Window Baseline Sampling With Baseline sampling as a default select the Sampling Go option A baseline sampling on the spectrum in the selected Gframe is performed and a number of sampling points are displayed If these sampled points are satisfactory choose either the Spline or Polynomial correction method then select Correction Go The corrected spectrum is displayed in the current Gframe with the baseline curve used for correction overlaid on it VNMR 6 1C User Guide Imaging 01 999163 00 A0800 6 2 Getting Started If the sampled points are not satisfactory points can be added by performing the following procedure Add Points 1 Select the Picking tool E described on page 155 and insert a point at the desired location on the spectrum by clicking the left mouse button on the mouse 2 After you add a point the G Tools window defaults to the ROI Select tool El described on page 153 To add more points select the Picking tool again Move Points To move points do the
254. e gradient levels M tpe2 tpe3 Duration of the 2nd and 3rd phase encoding gradient periods P gpe3 3rd phase encode gradient increment Description Phase encode gradient increment for 3D or 4D phase encoded applications gpe3 should be used when a third phase encode gradient is required It is available for use in a 4D CSI experiment three spatial dimensions one chemical shift Related imprep Set up rf pulses imaging and voxel selection gradients M gpe Phase encoding gradient increment P gpe2 2nd phase encoding gradient increment P lpe3 Field of view size for 3rd phase encode axis P setgpe Set phase encode gradient levels M tpe2 tpe3 Duration of the 2nd and 3rd phase encoding gradient periods P gped Phase encode dephasing gradient in the EPI sequence P Applicability Systems with imaging capabilities Description Determines echo position in the phase encode direction A blipped gradient phase encodes the signal with respect to the phase encode direction gped determines the center of the k space along the phase encode direction gped is usually set so that ef f_echo appears at the center of the phase encode dimension t1 Related eff_echo Effective echo position in EPI experiments P gro Readout gradient strength Description Controls the level of the readout gradient if present imprep sets gro based on its internal algorithm or use the macro set gro value which sets gro to a specific value and updates at and sw gro
255. e microimaging cabinet e Arching in the probe during the acquisition VNMR 6 1C User Guide Imaging 01 999163 00 A0800 10 5 Artifacts in BP Imaging Figure 129 Image Intensity Modulation e Incomplete coverage of the angle for phi or theta set by the user To solve this problem redo the acquisition and remedy the reason for the faulty or missing projections Image Reconstruction Using Off resonance Spin Echoes BP imaging requires an on resonance condition to align all profiles in one central point If profiles are acquired in off resonance condition the information in the profiles is shifted on the profiles axis according to the gradient This misalignment results after reconstruction in an image like the one shown in Figure 130 It is obvious that the contributions of each profile to a particular pixel position were smeared on a half circle The only solution for this problem is to redo the scan and adjust a proper on resonance condition Figure 130 Misaligned Profiles Profile Degradation Induced by Gradient Switching Theoretically the two projections from 0 and from 180 of the same object should be the same except that one is the mirror image of the other Figure 131 shows a projection from 0 on the left side and a projection of 180 on the right side Mirroring the projection of the right side and superimposing them results in Figure 131 Notice that both projections originate from the sa
256. e phasemap is used to correct phase errors in EPI data phasemap must be present in the current experiment directory Use dconi to view the data index is the array number of the image dconi Interactive 2D data display C epiph Generate phase correction map in EPI experiments M pcmapapply Apply phase correction map to data in EPI experiments C Generate phasemap file in EPI experiments M Systems with echo planar imaging EPI capabilities epiph Generates the phasemap file from the EPI reference scan The file is generated in the current experiment directory for EPI processing The first data array must correspond to the reference scan which is collected with the phase encode gradient turned off image 0 episet Set up parameters for EPI experiments M image Control phase encoding gradient in EPI experiments P pcmapgen Generate phase correction map in EPI experiments M Reverse spectral data in EPI experiments C Systems with echo planar imaging EPI capabilities epirs Reverses spectral data It is used by epift epift Process and display images in EPI experiments M Collect process and display EPI data M Systems with echo planar imaging EPI capabilities epirun 283 VNMR 6 1C User Guide Imaging Appendix A Commands Macros and Parameters Description Related episet Applicability Syntax Description Related episs Applicability Syntax Description episvib Applicabi
257. e pulse labels in ascending numerical order to correspond with rf pulses as they occur in the timeline of sequence events Number in us pwpat plpat p5pat Pulse shape P tpwr tpwr5 Pulse power levels P Inversion pulse length Pulse length for an inversion pulse often used as an optional first pulse preceding the main sequence to provide contrast based on T relaxation A pi pulse is often programmed so that it can be toggled on or off by the user with the inversion recovery flag ir irf Inversion recovery mode P pipat Inversion pulse shape P ti Inversion recovery time P tpwri Inversion pulse power P Magnetization pulse length Pulse length for a magnetization transfer pulse often used as an optional first pulse preceding the main sequence to provide magnetization transfer contrast A pmt pulse is often programmed so that it can be toggled on or off by the user with the flag mt mt Magnetization transfer on off P mtpat Magnetization transfer pulse rf shape P mtpwr Magnetization transfer pulse power level P Saturation pulse length Pulse length for a saturation pulse often used as an optional first pulse preceding the main sequence to provide water fat or solvent suppression A psat pulse is often programmed so that it can be toggled on or off by the user with the flags ws or presat presat Presaturation pulse execution on off P satira Presaturation frequency P satpat Presaturation pulse rf shape P
258. e to a selection list e Enable the Frame tool and select each frame with the middle mouse button There is also a selection in the Frame Properties menu that selects all Gframes Gframes can also be selected when the ROI Tools button designated by an arrow is enabled in the Tools popup window Moving Gframes To move a Gframe 1 Select the frame 2 Position the cursor within the selected Gframe and hold down the left mouse button 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 71 Chapter 4 Image Browser 72 3 Drag the frame to a new location Gframes can be dragged across other Gframes but must not be dropped where they would overlap with another Gframe Resizing Gframes To resize a Gframe 1 Select the frame 2 Position the cursor on the desired highlighted corner and hold down the left mouse button 3 Drag the corner to the desired position Splitting Gframes Splitting Gframes into a number of smaller frames allows viewing formats to be quickly and easily set up To split a Gframe 1 Enable the Frame tool 2 Select the Gframe or frames to be split 3 Choose the desired split from the Split Selected Frames menu in Frame Properties Saving Currently Displayed Gframes To save all currently displayed Gframes e Select the Save Frame Layout option It switches the File Browser to Graphics Frame Save mode Use the File Browser to go to the desired directory and save the frames Storing and Retr
259. e used the same way as they are used in previous software releases To help speed up the gradient coil changeover process e Reset the ZO shim to place the resonance offset for protons water to a standard value which is the same for both gradient coil configurations Resetting the shim reduces the time needed to recalibrate the resonance frequency and helps reduce confusion over frequency offsets when using the different configurations for multinuclear experiments Keep a record of the ZO shim values Place a copy of this record on or at the shim supply e Prepare custom parameter sets for commonly used experiments for both standard and auxiliary gradient coil configurations Custom sets reduce the time needed to reset the parameters and decrease the probability of set up mistakes e Save a basic set of shim values for some standard object such as a large uniform phantom for each gradient coil configuration Load the set before reshimming after the VNMR 6 1C User Guide Imaging 01 999163 00 A0800 7 3 Performance Specifications hardware change over A saved set of shim values reduces the need to shim from scratch each time the gradient coil configuration is changed e Post a copy of the procedure for exchanging gradient coils so that it is always available to users 7 3 Performance Specifications The purpose of the HPAG accessory is to provide an auxiliary gradient coil that can be easily connected to and disconnected from ima
260. each rf pulse Together with the bandwidth for each pulse found in the header of each shape file imprep computes the slice or voxel selection gradient to achieve the appropriate slice thickness or voxel dimension imprep assumes that the slice thickness for imaging experiments is specified by the parameter t hk and that voxel dimensions for voxel experiments are specified by the three parameters vox1 vox2 and vox3 Gradient levels are then calculated from the relationship gs s BW y thk for slice selection or gvox1 BW y vox1 for voxel selection Where there are two or more pulses used with the same slice select gradient gs s is determined by the rf pulse with the narrowest excitation bandwidth fliplist Flip angle list P gro Readout gradient strength P gvoxl gvox2 gvox3 Gradient strength for voxel selection P plist Pulse length parameter list P patlist Pulse shape parameter list P pwrlist Pulse power level parameter list P pulsecal Create modify delete entry in pulsecal rf calib file M tfegil RF pulse calibration identity P setgpe Set phase encode gradient levels M setgro Set readout gradient strength and spectral width M setgss Select slice or voxel selection gradient levels M setvgrad Set voxel selection gradient strengths M sslist Gradient parameter names list P sw Spectral width in directly directed dimension P swl Spectral width in first indirectly detected dimension P sw2 Spectral width in
261. eal Imaginary or Both Correction Method Selects spline polynomial or SINC Spline and Polynomial are used after baseline sampling has been done SINC is used when peak sampling has been done Polynomial Order Sets the order for polynomial correction Correction Go Performs the selected correction on the data Correction OK Saves correction values for use with global Write all correction 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 161 Chapter 6 CSI Data Processing 162 Global Baseline Correction is done by ensuring that Item and Mode are correct and clicking the Apply option Use the Box ROI tool to select a subset of the total number of voxels Mode Set to Write all or Automatic Write all uses the last set of local phase or baseline corrections and applies it to all the spectra Automatic does everything automatically Metabolic Map Calculation Metabolic Map Mmap Calculation performs the curve fitting and peak picking necessary to create a metabolic map After peaks have been selected and fitted metabolic maps of selected peaks can be made See Figure 61 for the Mmap Calculation window which contains curve fitting Mmap calculation and curve fitting works the same way phase and baseline correction works It is best to select a spectrum perform local peak picking and curve fitting on the local spectrum and then perform global curve fitting The following sections describe the functions of Mmap calculation process
262. eated and resized in the graphic region with the mouse The Frame tool properties menu consists of the following options Split Selected Frames Splits each selected graphics frame into an array of smaller frames If there are no Gframes in the graphics region the entire region is split into the selected matrix of frames Select the desired nxm entry from the submenu to make an array of n rows by m columns Or select Other to split frames into an arbitrary number of rows and columns VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Delete Clear Select All Frames Load Frame Layout Save Frame Layout Zooming Tool 4 3 Graphics Tools Deletes all graphics frames all selected graphics frames or all unselected graphics frames Clears all graphics frames all selected graphics frames or all unselected graphics frames Selects all graphics frames Loads graphics frames from a file in the directory SBROWSERDIR gframe or a subdirectory Saves graphics frames into a file in the directory SBROWSERDIR gframe or a subdirectory The Zooming tool is used to select a portion of an image to be expanded Box cursors are displayed on all the currently selected Gframes The cursors are XORed to the image The zooming tool menu consists of the following zoom properties Zoom Unzoom Bind Unbind Zoom Tracking Zoom Factor Cursor Tolerance Pixel Interpolation Pixel Replication Zooms selected images Unzooms selecte
263. ecification is required to start with the manual mode to register the peaks and metabolic map information Click on Specify CurveFit and Mmap to open the Interactive Fitting Tool window shown in Figure 73 you must have MVS data to open this window VNMR 6 1C User Guide Imaging 01 999163 00 A0800 6 4 Processing Functions The following list describes the functions of the attributes that appear in the Local Specification portion of the Mmap calculation window e Item Specific Total Spectrum fits either one line at a time or the entire spectrum e Curve Type Gauss Lornz SINC Lrnz Const S L selects the type of line shape to fit Interactive Fitting Tool The Interactive Fitting Tool allows peaks and curve fits to be checked curve fits to be adjusted and peaks and curve fits to be registered A frame with a voxel spectrum must be selected before this tool can be activated To register the peaks and metabolic maps this tool must be activated when initially processing data After this information is registered it can be used to process other data sets The tool need not be activated again until curve fitting or map information is to be changed Select Fitting Go in the Manual mode to activate this tool The Interactive Fitting Tool window shown in Figure 73 allows curves for each peak to be viewed curve parameters to be changed metabolite names to be assigned and numbers to be mapped Fitting Tool Curve Check displays a
264. ection gradient levels M thk 2D imaging plane slice thickness P Slice selection fractional refocusing Fractional multiplier used as a fine tuning adjustment for the gssr slice refocusing gradient level 312 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Values Related gssr Description Values Related gss2 gss3 Description Related image Applicability Description Values Examples A 5 Parameters 1 0 when the theoretical gradient calculations are correct gss Slice selection gradient strength P gssr Slice selection refocusing gradient P Slice selection refocusing gradient Controls the level of the slice select refocusing gradient when pilot n When pilot y gssr is ignored by the pulse sequence and internally computed The internal value is printed in the window used to start VNMR gssr is normally opposite in sign to gss In general the time integral for gssr should be very close to one half the time integral of gss to properly refocus spins that have dephased during the rf slice selection pulse Because the refocusing gradient on time is internally computed in the pulse sequence independent of the rf pulse length gssr will not be exactly half of gss Number in gauss cm up to gmax Nominal value is gssr 0 5 gss gmax Maximum gradient strength P gss Slice selection gradient strength P gssf Slice selection fractional gradient P gror Read out dephasing
265. ections obtained for one image To set on resonance perform the following steps 1 Enter gro 0 to disable gradients 2 Enter go to acquire one scan You should see a signal If no signal is seen check te echo time and gain receiver gain To increase the signal decrease te or gain The echo may not be centered in the time domain 3 Enter t to Fourier transform the data and then move the cursor on the line in the spectrum and enter movet of to set the spectrometer frequency to the cursor value Your display should be similar to the display in Figure 115 Setting BP Image Acquisition The next step is to run the bp_setup macro You should now set up the BP imaging sequence according to your needs as follows 1 Enter bp_setup to run the macro The following questions are asked 234 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 10 4 Routine Usage a cr vs delta 371 80 136 4 Figure 115 On Resonance Condition a BP type bp3d bp2d bp2ds According to Table 20 you may select volume excitation schemes bp3d or bp2d or the slice selective excitations scheme bp2ds b Preparation none sr ir aps tir Table 20 summarizes the selections available in the preparation phase The selection none disables any excitation in the preparation phase thereby allowing only T weighting sr ir or aps result in T weighting using saturation recovery inversion recovery or aperiodic saturation respectively
266. ectors are described in the following subsections RF Shield Filter Box Shim Connector Water Hoses and Connectors Gradient Power Cable Figure 85 System Gradient Coil Detail of Connection Points Gradient Power Cable When connected to the gradient connector port J59X1 of the HPAG quick disconnect box the gradient power cable P5901 supplies power from the system gradient power supply to the X Y and Z gradient coils and shims 180 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 7 1 HPAG 183 Hardware WARNING Do not connect or disconnect the gradient power cable to or from the HPAG quick disconnect box unless both the system gradient and shim supply have been switched off Gradient connector port J59X1 of the HPAG quick disconnect box presents a risk of electrocution if the gradient power cable is disconnected while the system gradient supply is switched on CAUTION Do not connect or disconnect this cable to or from the HPAG quick disconnect box unless both the system gradient and system shim supply have been switched off Severe damage can occur to both gradient and shim supply if the supplies are powered up as connections are being modified Shim Connector Port The shim connector port J5902 receives power from the system shim power supply via the shim power cable P59X2 Power is supplied to all shims except to X Y and Z which obtain power through the gradient connector cable CAUTION Never discon
267. ed and optionally a destination Gframe can be selected The first Gframe selected is the operand the second frame added is the operator and the third is the destination frame To select frames do the following procedure 1 Select a source Gframe by moving the cursor into the desired Gframe and pressing the eft mouse button the Frame tool does not need to be active 2 Obtain a destination Gframe by pressing the middle button when the cursor is positioned in the desired frame In the case of the Arithmetic function when two images are source frames a third frame can be selected using the middle button as the destination frame 3 After the frames have been selected the Rotation function can be activated Rotation Reflect images and rotate in 90 increments This function operates on the images in the selected Gframes Using the Movie Mode A number of images can be chained together and sequentially displayed to produce an animated image by using the Movie mode The movie mode is started by selecting the Movie button in the control panel This opens a Movie Control panel Before the movie can be run the desired image frames for the movie must be selected These frames are designated by means of a playlist A playlist is a list of the image files that make up a movie It can be saved and retrieved so the movie need not be specified every time 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 77 Chapter 4 Image Browser 78
268. ed by the multislice ms or multi image mi value e arraydimis set to the product of its original value and the original value of nf e arrayelemts is set to 1 if no parameters were arrayed during data acquisition or to 2 if any parameter was arrayed during data acquisition Arguments nf is the number of FIDs in the second dimension of a 2D experiment When converting data in the standard format to a compressed format nf must always be the first argument When converting compressed compressed or rare type sequences the first argument must be a string defining the type of compression e mi is a keyword for the multi image type of compression e ms is a keyword for the multislice type of compression e rare isakeyword for the rare multiecho rare type fast imaging data sets Standard to compressed ns is the number of images slices or array elements to be retained Compressed compressed or rare to standard t races is the number of compressed traces to retain for each ni The parameter nf is set to this number after lashc has run Compressed compressed or rare to standard echoes is the number of compressed echoes used with rare type formatting Examples Compressed compressed or Standard Format to Compressed Format flashc nf standard to compressed flashc nf ms ns compressed phase encode and multi slice flashce nf mi ns compressed multi image and phase encode Compressed
269. ed pulse with its amplitude modulated in the form of a sinc function as shown in Equation 5 sin 0 0 Eq 5 The phase 9 is given in Equation 6 0 27vt Eq 6 In Equation 6 v is the modulation frequency of the sinc function and is the time axis Theoretically the resulting excitation profile can be predicted by taking the Fourier transform of the sinc function which in Equation 5 is rectangular in the frequency domain as shown in Figure 7 FT Sinc 5 function t f Truncated gt ie sinc f Gaussian J gt J t f Figure 7 Sinc Function Truncated Sinc Pulse and Gaussian Shaped Slice Profiles However in practice because of experimental limitations such as T gt the pulses are limited to about 4 ms or less The resulting truncated sinc function has an excitation profile as shown in Figure 7 Gaussian shaped pulses are also used for slice selection purposes The Gaussian pulse produces a profile that is also a Gaussian as shown in Figure 7 In general this simplified approach is only true for short about 30 or less flip angles At larger flip angles pulses VNMR 6 1C User Guide Imaging 01 999163 00 A0800 2 3 Slice Selection show large behavior that is not ideal because of the nonlinear response of the NMR spins The pulse shapes can be optimized to produce more ideal pulse characteristic for specific applications For example the rf pulses can be optimized
270. eeeeeeeseneeeeeseeneeeeeesneeesensenenenensneeees 65 Al OVERVICW sic 25 sosscs2s vies eorr ea ra PE EEE n IEE EEE E Er EE EERE AEE PAES EEA EEEE E EERE EENE ERE ERT RS 65 42 Getinge Started ocseesuriecireen in as vers beh sented E eE EE REEERE E EES EE ES 68 4 3 Graphics LOOMS vssisesseessetsavacscesevonsceevecisebavesscaanseiscedsassavsesaseseduscsvastsaanysavedapusbiaes EOS aiasbes 80 FA Data Processing sssini e e EEEE EEE SS 90 AES Macros coarae a E E E T EE RE E R 98 4 6 Files and Other Items sirsiran iaaea E oE EES tiia 104 Chapter 5 Image Browser Math Processing cccsseecsssseeeeesseeeeeeesees 111 5 1 Opening Image Browser Math ssseseseeseseseesesesrrrrsrrressesresreseseeeerteserrestereeseeerseeeesee 111 5 2 Image Browser Math Expressions sesessesesessesrsersrssrssrsresresesreerreserrrsreresreresreeesre 112 5 3 Image Browser Math Functions sssssssesosicssesristeressrresviriescivisereiisrno dee tisis rasio siere risrs 113 DA The Fit Program i cacseiecssvdcaseescaasccbeszssasscscecancssuncetaacsasdesshucepibesnavie base astesieasbesasbandibsadst 120 5 5 Problems with Image Browser Math eee ese ceecseceseeseceaeeeceeceseceeeeseseeeesetees 127 Chapter 6 CSI Data Processing ccssesecesssseeeeessseeeeeenseneeeeensneeeeenene 129 Ol Overview of CSI Moeroa assesi eaeoe nerea eoa dee aes cet en otra gaan 129 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 5 Table of Contents 62 GEIS Started sacs shivcieses sh
271. efined a plane that is oblique If you want to make sure your two points lie along one of the major axes here s a hint Move the cursors to the first point you want to mark keep the mouse inside the image boundaries but place the mouse arrow outside the blue image box to define the second point This method causes only one cursor to move and ensures that the two points properly lie along one of the major orthogonal planes If you want to define a multislice experiment you can use the ns and Gap buttons to specify the number of slices and the gap between slices respectively When you compute the target slice the correct slice positions are entered into pss automatically These slice positions are defined in monotonic order not in interleaved order But unlike the older imaging sequences the slice order is not computed inside the sequence but defined by the array order of pss You can enter the values of pss in any order that you like or use the macro sliceorder to record slices automatically Computing and Displaying the New Target Parameters At this point you have specified the target imaging plane or planes on the scout image You now need to compute the new orientation and slice position for these planes e Select the Compute Target button 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 23 Chapter 1 First Steps Making an Image 24 This button places the results in a set of target parameters that will be transferred in
272. el selection gradients 62 Setup button 195 sfrq parameter 234 SGI file format 107 shell command 100 shim coils 190 shims controlling gain of 205 showing 2D data interactively 278 3D FDF file 279 datasets 232 EPI data 284 GEMS images 51 Image Browser menus 70 si_low_pass filter 251 signal detection PGM 223 intensity 39 loss 39 48 56 PGM modulation 223 PGM transfer 223 restoring lost 32 separating 35 simulated data generating 137 single pulse sequence parameters load 62 63 SISCO 93 1 software 22 slew rate 194 197 204 slew rate setting 62 slice acquiring and reconstructing 229 and voxel selection 275 based BP acquisition 240 distances 97 extracting one 345 offset 44 parameters define 62 plane 23 plane orientation 324 positions 21 24 63 326 selective excitations scheme 235 thickness 44 48 63 327 to be acquired 334 Slice Extraction window 105 slice gradient and slice selection calculation 300 slice selection 29 fractional refocusing 312 gradient level 313 gradient strength 312 refocusing gradient 313 slicemark macro 275 sliceorder macro 23 275 sliceplan macro 276 Smart DAC SDAC board 199 Snapshot program 94 solids high power amplifiers caution 14 solvent parameter 22 spatial frame of reference 37 spatial information obtaining 26 spatial reconstruction 131 157 spatial reference position defining 42 01 999163 00 A0800 Index setting 6
273. elective pulse Related offset Calculate and display absolute frequency offset at cursor M resto NMR resonance offset frequency P NMR resonance offset frequency Description Frequency offset used as a chemical shift reference by most imaging and 330 localized spectroscopy sequences typically set to the offset of the water resonance in biological samples Selection of the desired slice or voxel position is accomplished internally by the poffset and poffset_list pulse sequence elements by computing the frequency offset required to excite at a position in space that is the product of the position and the gradient strength used A chemical shift reference offset resto must be added to this offset for example offset restoty pss gss As an example suppose the chemical shift offset for water is 4000 Hz and the desired slice position is 3 cm from center with a 2 G cm gradient The offset required to position the slice 3 cm from the gradient origin is 25 548 Hz y pss gss 4258 3 2 The 4 kHz water resonance offset must be added to this value to avoid an error of 4 7 mm in the slice position Thus resto must be added to the gradient produced offset to give the proper frequency offset 29 548 Hz The of f set macro may be used to determine the value of resto from a one dimensional spectrum In samples where more than one chemical shift species exists such as water and fat in biological samples there is always some error in spatial p
274. ent If only one numerical argument follows the t ype argument the current experiment is the scout experiment and the numerical argument is the experiment number of the target experiment transfer s 6 transfer v 2 7 Target Parameters page 341 mp Move parameters between experiments C mvfov Move the field of view from one experiment to another M plan Interactive slice and voxel selection M phi Euler angle for defining imaging plane orientation P psi Euler angle for defining imaging plane orientation P resto NMR resonance offset frequency P ee COr 1 RF pulse calibration identity P theta Euler angle for defining imaging plane orientation P thk 2D imaging plane slice thickness P Store marked positions for planning target voxels voxmark lt reset gt Stores the locations of points selected during the planning of new voxel positions and dimensions in the parameter t_mark voxmark is called by the Mark button in the Voxel planning menu and is not normally executed from the command line reset is a keyword to clear any previously marked positions by zeroing t_mark Target Parameters page 341 plan Interactive slice and voxel selection M Compute position and orientation for new target voxel voxplan Computes the position dimensions and orientation for a new target voxel from a set of marked positions found in the t_mark parameter Multiple voxels previously selected with the voxe
275. ent only the signals from a predetermined slice are pulsed so that only those excited spins contribute to the resulting image Slice selection involves using a selective rf pulse in combination with a slice selection gradient zZ Z N tea y Slice selection 2D Image Figure 4 2D Image Resulting from a Slice Selection The section Time Domain to Spatial Domain Conversion page 26 described how the presence of a field gradient causes a spatial frequency spread profile along the gradient direction shown in Figure 3 In the example shown in Figure 5 the profile along the z direction is rectangular because the signal intensities from the sample at various points along z are equal rf Figure 5 Rectangular Profile The use of the hard pulse excites all of the spins in the sample because the excitation bandwidth is wider than the frequency spread of the profile However if a soft selective pulse is used a narrow bandwidth of the profile at the carrier frequency is excited In other words spins corresponding to a narrow Slice at z 0 are selectively excited The resulting profile referred to as the slice profile is shown in Figure 6 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 29 Chapter 2 Imaging Experiments 30 Figure 6 Slice Profile Ideally a rectangular slice profile is preferred A rectangular profile can be achieved by using a shap
276. ent Procedure o oo eee ceeceseeeeceseeeeceeeeeeeeeeeeeesaeeeaesaeesaecseeeaees 212 Front Panel of PGM 1000 Receiver eceeeeseescsecseeseesecseceeeseeaecaeeeesaeeaeeesseeeaeneees 213 Back Panel of PGM 1000 Receiver oo ceeeceseseeseeecseeeeeeesecseeeceaesaeseeeecsacsaseeseeenee 214 Electrodes Comnecton ciisicsseviastan tien save EER E AE EEEE EE 215 Unit Interconnection Diagram oe cece ceeceseeeeceseeeeceseeeeeeseeeaecaeecaecssesaeenaeeaees 217 ECG and Inhibit Out Trigger on A Each Heart Beat B Every Other Beat 221 Image Generation Using Backprojection o ic eee eeeeeeceseeeeceeeeeecaeecaecsseeaeenseeaees 226 Parameter Set for Dp2d 0 0 0 cscsssscsssesssessesscessessesesnensssecsssseneconessessonsovessessoesnsessess 227 Profile of Fourier Transform of One Projection ceeeeeesecseeeesecseeeeeeenseeeseeeeeenee 228 Setting the Weighting civsccccevsescssvecssesssanscdsssdsnchossengnacsorsssbnsonsuncagnh csvecsbostaassedaesseienys 231 Unweighted and Weighted Fourier Transform o eeecesssesecseeeceseceeeeeeeesaeeeeeeeeeenee 232 Parameters for Sequence dp_image oo eeeceseseeesseecseeseeseeseceeeeceseaeeeeeecaceaeeeeeeenes 234 On Resonance Condition cessisccsscceccscesseesssesesvs couse aE nET EERE EEEE EEE REEE iiS 235 Macro bp_setup Values Display sesssessesesseseeesssresesreersrreserreerresresesreersreererreresrssee 236 Phases A Preparation and B Acquisition sesseeeeeseeeseseesresrsesesersesreesresseses
277. ents and damage to the system carefully follow the steps in order The initial configuration of the hardware should be the same configuration shown in Figure 88 with the main gradient coil as the active coil This is the standard configuration Verify that the system is functional in the standard configuration before proceeding to install the HPAG auxiliary gradient coil If the connections are not made as shown in Figure 88 the system is in an incorrect configuration and might be damaged In this situation perform the following three SAFETY steps and then correct the cabling error so that the connections match those shown in Figure 88 The system can then be powered up 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 183 Chapter 7 High Performance Auxiliary and Microimaging Gradients Gradient P Shim Current Thermocouple Gradient Current Magnet Water Hoses from Main Supply OD Figure 88 Connections for System Gradient Coil in Standard Configuration 2 SAFETY Use the power on off button located on the front panel of the system shim power supply to turn it off 3 SAFETY Use the STOP button and the main power switch to turn off the system gradient supply 4 SAFETY Turn off the water flow to the gradient coil at the main water shut off valves WARNING Do not proceed with the following steps until the three previous steps marked SAFETY have been performed 5 Remove the rf shield do
278. ents can be entered on the command line e The string quick can be used to force nonlinear fits to bypass the iterative fitting procedure and use the initial guess for the parameter values as the final result Depending on the accuracy of the initial guess function this result might be useless or 120 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 5 4 The Fit Program nearly as good as the results of the nonlinear fitting procedure quick is also useful for checking the accuracy of a guessing function e The string noderiv directs the nonlinear fitting routine not to use derivatives of the fitting function with respect to the parameters that might be provided In this case the fitting routines will estimate derivatives numerically from finite differences This option is mainly useful for testing The strings prev or noprev are used to force the USE_PREVIOUS_PARAMETERS flag on or off Be aware that prev breaks the abst 1 and absqt1 routines because their guess routines modify the data prev Types of Fits As shown in the Table 8 the types of fits available are t1 qt 1 abst 1 absqt1 t2 adc and shames2 Table 8 Fit Types Fit Parameters Name Functional Form PO Pl P2 t1 y M 0 M exp t T1 M T1 M 0 M qt1 y A 1 2 Q exp t T1 T1 A Q abst1 y M 0 M exp t T1 Mg T1 M 0 Mo absqt1 y A 1 2 Q exp t T1 Tl A Q t2 y M 0 exp t T2 T2 M 0 adc y M exp
279. enu is Properties which allows some of the display functions including fixed or automatic scaling of spectra to be customized VNMR 6 1C User Guide Imaging 01 999163 00 A0800 6 2 Getting Started Data Formats CSI supports two data formats e VNMR raw data FID Format that enables reading raw CSI data for processing or raw image data for image reconstruction e Flexible Data Format FDF Format that CSI uses to output all data CSI adds fields to the original FDF specification Localized FID MVS reference images and metabolic map data can also be read in this format The CSI product has utilities that allow FDF files to be created from other data files 6 2 Getting Started This section describes the process of verifying the correct user environment starting CSI and performing some of the basic functions Setting the User Environment CSI has been designed to run in an X Window System environment This means that any X terminal can be used as the user interface as long as it supports the 8 bit graphics The host system that actually runs CSI must be a Sun workstation with Solaris 2 3 or higher Host systems should have as much memory and swap space as possible CSI data sets tend to be very large and after each processing step the data set is saved in memory Environment Variable The CSIDIR variable contains the directory path to the user s initialization directory The following command should be in your Lo
280. er common way to improve the image appearance is to interpolate the image during the display process Interpolation is also equivalent to zero filling the data in the time domain 2 9 Important Imaging Parameters 38 This section describes three important timing parameters t r te and t i that are used during the performance of imaging experiments tr Recycle Time The tr parameter defines the time between the beginning of one scan and the next VNMR 6 1C User Guide Imaging 01 999163 00 A0800 2 9 Important Imaging Parameters It is important to allow sufficient recycling time so that the excited spins have sufficient time to return to equilibrium In the case of a 90 excitation pulse a recycle time of gt 4 T must be allowed If the recycle time is too short the signal gets saturated which results in a gradual loss of signal intensity eventually reaching an equilibrium or steady state condition However this 7 dependent signal variation can be exploited to enhance T contrast in the images In experiments involving quantitative work such as relaxation studies and pulse power Table 2 Relaxation Times and receiver gain calibration t r must be set to greater than 4 7 to avoid erroneous Liquid Time results In experiments such as FLASH the Doped water 1 g CuS04 lit 0 6 flip angle is set to approximately oped water Lg Cu iter 5 cocoto 30 and tr is set to small values Vegetable oil Oas abou
281. er is first started the macro st art up is executed This macro allows customizing some aspects of Image Browser s operation 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 103 Chapter 4 Image Browser 4 6 Files and Other Items 104 This section describes file input and output and the error and information displays File Browser The File Browser is a standard interface used for storing and retrieving files Itis used when saving files and when retrieving image files The Gframe ROI and Filter interfaces use the File Browser for saving files but they do not use it for retrieving files because the Load interfaces are built for quick access and always assume a specified directory For more information about the particular directory for these interfaces see Getting Started page 68 Figure 45 is an example of a File _ Browser window for loading images Ne File Browser Data The basic File Browser window is the Load File From Load same for most operations Load All ms060 fdf The title of the window in this case chris p sw ib DATADIRS HEARTDATA File Browser Data describes the use of the current File Browser window In f J di A e x ms000 the case of loading movie images the EAN E title is Movie Frame Loader for ROIs ms040 fdf it is File Browser ROI When files are ms060 fdf saved Load is replaced by Save Load ms080 fdf All does not change because there is no ae eae correspon
282. er to shut off the main water supply when making the water connections Shutting off the main water supply provides protection against valve failure in the fittings located in the HPAG quick disconnect box which would lead to a leak at full system water pressure 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 179 Chapter 7 High Performance Auxiliary and Microimaging Gradients Gradient Power Line Conduit Power lines from the system gradient supply enter the HPAG quick disconnect box through a conduit located on the inside of the box These power lines are not part of the quick disconnect system regard the lines as permanent connections HPAG Probe and Sample Handling Equipment The HPAG accessory includes additional probe and sample handling equipment to facilitate experiments using the auxiliary gradient coil This equipment is designed to integrate with the main system probe and sampling handling equipment to avoid unnecessary duplication of parts The sample handling equipment is similar to that provided for standard imaging systems equipped with 183 mm gradient coils System Gradient Coil The standard system gradient coil is modified upon installation of the HPAG accessory to allow quick and simple disconnection from the system gradient and shim supplies The water connections and hoses to the main gradient coil are also modified for quick disconnection Figure 85 is a diagram of the modified arrangement The functions of these conn
283. eretserressesreretsreererersreererse 253 999163 00 A0800 VNMR 6 1C User Guide Imaging 9 List of Tables Table 1 Experimental Macros and Parameters o eececceeeescesseeeceeeeeeceseeeeecaeecaecaeesaecsaeeaeeeenaees 32 Table 2 Relaxation TIMES iii i cesessatesce hae Ee a shee Shes stews EEE EREE E E ebuede 39 Table 3 EPI Related Commands and Parameters ssesseeseseseeeseeeeseeresrsreserresteersreereresesrssenrsseeees 52 Table 4 Imaging Parameters sensorn oiii ieste aE e a E EE S E E aE Eio iasi 59 Table 5 Imaging Pulse Sequence Commands Macros and Parameters s sseeseeesseeeeesreereeeeeeee 62 Table 0 ROL Select r Tool Properties sssscsssnsvesssetsceesassetscsoesesaises sobiveienasesssnacevseecesiseaecesanouans 88 Table 7 Formats Available in Image Browser e eseseesesesersrseresrrrereresserresenresenrererererreresrnrenresene 107 Tbk By Fit VY Pes iscessssscesceasceshessinesealeelgsasensocevecsaasadeescasceeancscaatveddes EEEE EEEE E EE a RE ie E EEEREN E t 121 Table 9 Prior Knowledge Menu Selections with Corresponding File Names eee 173 Table 10 HPAG 183 Accessory Parts List 00 ee ceceeeesseseseeseseeeeceseecaecnaecaecnaeaessaeeseseeeeseeeetees 176 Table 11 Values of Parameter G GOT A vicsscsctetssaccssectickscstcetaccduthas ae nai iaie a eiai 188 Table 12 Gradient Coil Length and Weight 2 0 0 eee eeeeseeeeeeceseeeeeceeecaecneesaessaesaesseeeseeseeeas 189 Table 13 Gradient Channels D
284. ering the line e Because pressing the Return key is required at the end of almost every command or line of text you type on the keyboard use of the Return key will be mentioned only in cases where it is not used This convention avoids repeating the instruction press the Return key throughout most of this manual e Text with a change bar like this paragraph identifies material new to VNMR that was not in the previous version of VNMR Refer to the VNMR Release Notes for a description of new features to the software Purpose of This Manual This manual should instruct both new and experienced SISCO users If you are a new user this should be your reference for imaging and localized spectroscopy applications Because we want to spare new users the duplication of effort required to learn both old and new we have explicitly left out references to the older methods in most of this manual Other VNMR manuals you will find useful include e VNMR Command and Parameter Reference e VNMR User Programming e VNMR and Solaris Software Installation VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Chapter 1 First Steps Making an Image Sections in this chapter e 1 1 Making an Initial Scout Image this page e 1 2 Using the Scout Image to Plan a New Target Image page 22 This chapter describes the typical steps in setting up and running a VnmrIMAGE pulse sequence The SEMS Spin Echo Multislice pulse sequence is used as an examp
285. es 1 2 and 3 and puts the result in Gframe number 4 4 1 2 3 3 After typing the expression you must click on the Execute button to carry out the operation The expression is evaluated for each data pixel to calculate the output image The first time an expression is entered and executed it is edited and inserted into a C program which is then compiled and stored in the directory SBROWSERDIR math expressions bin as a dynamically loadable library This library is then linked to the running Image Browser program and the input images are passed to the routine containing the user s new expression This routine calculates the output image and then returns to the main Image Browser which loads it into the appropriate Gframe Finally the library is unloaded If the same expression is used a second time possibly with different image numbers the compilation step is skipped in the above sequence because the precompiled program can be used Precompiled expressions are stored in BROWSERDIR math expressions bin A list of these programs is available in the Expression menu Each choice is the right side of a precompiled equation with the Gframe numbers but not the s and any spaces removed When an expression is selected it replaces whatever is in the window prefaced with and the cursor is placed after the first The Tools panel is also put into Math mode To use a precompiled expression do the following steps 1 Selec
286. es to the data e Line ROI drawing e Point ROI drawing e Box ROI drawing e Polygon or freehand ROI drawing e Annotation 74 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 4 2 Getting Started e Image math To activate a tool point to its button with the cursor and click the left mouse button Once a graphics tool is activated the corresponding function can be initiated in the graphics region with the eft mouse button Commands can be performed by opening the Properties menus with the right mouse button Typical commands are load save or delete in the case of Gframes or ROIs The commands zoom or unzoom are typical in the case of zooming Zooming When Zooming is selected in the Tools window a box cursor appears on all the selected Gframes This function allows one image or a number of images to be magnified zoomed when zoom is selected from the Zoom Properties menu The zoom function can also be bound together across all selected Gframes so that when the cursor on one frame is manipulated the cursors on all the selected frames change Binding is enabled or disabled by selecting Bind from the Zoom Properties menu Image display can be performed either by Pixel Replication or by Pixel Interpolation Once again this is a property that can be selected from the Zoom Properties menu If Pixel Interpolation is selected a cubic spline interpolation is performed Be careful when selecting Pixel Interpolation because interpolation
287. es warning 13 removable quench tubes warning 13 removing graphic frames 72 81 100 VNMR 6 1C User Guide Imaging 355 Index repetition time experiments 318 requirements for using GEMS 44 rescal macro 263 rescaling an image 51 resizing graphic frames 72 resolution EPI 57 phase encode dimension 36 readout dimension 36 resonance frequency definition 27 offset frequency 330 offset frequency loading 268 resto parameter 20 22 24 32 42 49 62 63 retrieving FIDs 264 parameters 264 Return key 16 rf power for desired flip angle 265 rf pulses calibration identity 345 loading power calibration parameters 62 setting up 62 rfcoil parameter 19 24 44 49 63 rise time setting on SDAC board 204 rm command 100 ROI tools ROI 87 selector 153 roi_ commands 100 ROIs 66 69 75 153 annotation tool 90 area 91 binding turning on off 100 button 76 directories 68 directory 69 file 134 getting statistics from 77 intensities histogram limits spanning 91 manipulation tool 74 math tool 87 roi_ commands 100 save 105 saving 100 select and adjust 87 selector tool 87 set font size 88 spectrum 132 statistics 90 storing 76 tools 130 updating statistics 91 rotate command 103 rotating images 67 77 95 103 rotation function 77 panel 95 rt macro 62 264 rtp command 47 macro 62 264 rtphf command 299 356 VNMR 6 1C User Guide Imaging S S2PUL button 264 s2pul ma
288. escteiscsicovsosscbscssbaessessesonsectersessdesdecbscscbeieeuseos 71 Figure 28 Zoom Magnification Factor Window ou eeeeeseesceceesceeeeeeeeaeeeeecaeesaecaaesaecnsseaeeneensees 79 Figure 29 Tools Window ssenseiisccniiie snie ee tsaer EEEE EE E RE E EUERE EE iN 80 Figure 30 Vertical Scale Properties Window oo cece cece eescesseeeceseeeeeeseeeeecaeecaecaaesaecsaeeaeeneeenees 82 Figure 31 Vertical Scaling Window oo eeeeeecseceseeseceseeseceeeeeceeeeseecseeaecoeesaecaaesaesnessaeeeegees 83 Figure 32 Curve Control Pot sissssesccssscssischousescnsebiescascssiaenasnes caicssvesnenseddecabvsebousenaessdacsedbes ESEE 84 Figure 33 Gamma Correction Window o0 ccceeesceceseessceseeeeceeeeeeceeeeeeeeaeeeeecaeesaecaaesaecneesaeeeeaees 85 Figure 34 Statistics Window with One ROI 000 eee eeeeeeeeeceeceeeceeeeeeecaeeseecaeesaecaeesaecnesnaeeeeeaees 91 Figure 35 Statistics Window with Multiple ROIs oo eee eeeeceeeceseeeeecaeeceeceesaecsaeeaeeneeeaees 93 Figure 36 3D Volume Calculations scciscusissssccvcassssecscssssecssesaivescsoceesecducsstssnesszssessucessesssassarsseriesniees 93 Figure 37 Statistics Output Generated by Print Stats Button oo cee cecseeeeecnseeeeneeesees 94 Piste 28 Rotation Panel seseina ede cecestessais o EE AE EEEE E NOE EEE 95 Figuro 39 Filter Window ccs ccietin ieiencisseicbide satesban er i E ERARE E REE OE E E 96 Pioure 40 Filter Window With Data cccsciscsessicteceepscnesstvcgs ited aebahces caleesasvat sabedd ea EE a
289. ese connectors are described in the following subsections VNMR 6 1C User Guide Imaging 01 999163 00 A0800 7 1 HPAG 183 Hardware Rear Housin i i g Spacing Rings RF Shield Door Thermocouple Connector Water Hoses and ee Connectors Gradient Power Cable Figure 82 RF Shield Fitted on 183 mm HPAG Gradient Coil Rear RF Shield Door Locking Mechanism Shim Connector ee Water Hose Gradient Power Cable Figure 83 Rear Housing of 183 mm HPAG Gradient Coil Gradient Power Cable The gradient power cable P5911 supplies power from the system gradient supply to the X Y and Z gradient coils and shims when the cable is connected to the gradient connector port J59X1 of the HPAG quick disconnect box WARNING Do not connect or disconnect the gradient power cable to or from the HPAG quick disconnect box unless both the system gradient and shim supply have been switched off The gradient port connector of the HPAG quick disconnect box presents a risk of electrocution if the gradient power cable is disconnected while the system gradient supply is switched on 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 177 Chapter 7 High Performance Auxiliary and Microimaging Gradients 178 CAUTION Do not connect or disconnect the gradient power cable to or from the HPAG quick disconnect box unless both the system gradient and shim supply have been switched off Severe damage ca
290. essees 237 T2 Weighted 2D and 3D Pulse Sequence oo eee eee eeeseeeseeseecneceecaecnseeseenseeaees 238 TI Weighting Preparation Phase ooo cee eeeseeeecseecsececeesecseesecneceseceeeeseseneeeeseaes 239 TI Weighting aps Sequence sic isesiesssscases antes cashestcvesiacbescugstevoabsossacaviessatencavtdabevneneets 239 Elo Weis iting cis sasekeksteesshi ieee eect ceeds ees EEOAE REE 240 Slice based BP ACQUISITION lt s ssivcciisciescduiks heeiekiedhecinsci sasudatdaseasoevtsavonzanesseusonanneys 241 T2 Weighted 2D Slice Selective Pulse Sequence oo eee ee eeeeeeseseecnecesetneeeeeeees 241 T1 Weighting Inversion or Saturation Recovery oe eee ee eeeseeeneeeeeceeeseeeeeaeenees 242 T1 Weighting Inversion or Saturation Recovery oe eee ee eseseeereeseecseenseeneenaeenees 243 Distorted Images crnce nna e E REE E E 245 Saturation in First Projection eee ceeeeceeeeeeceseeeeeeseeceecaeecaecseeaecsaesaesneeeeeeeeeees 246 Circular or Spherical Modulation oo ee ceeceseeeeceseeesceeeeeeeeeeeeeeeaeeeeecaeesaeceeeaees 246 Image Intensity Modulation ooo eee cee eeseceeceseeeeeeseeeeceeeeeeeeeeeeeeeaeeeeecaeesaesaeeeaees 247 Misalion d Profiles cc c si0 sisessececsianticrre nas sa ctepivima never ens eto ecn eastern tani 247 By Field Sieci EE A OAA E EEA 248 Phantom Setup for BP Imaging eesseesseseseesesrssrsreesreersrreserresesreserresrerrsreereresserrssee 248 Interactive Image Planning Interface eseeseeecseeseseeeereseisre
291. essing 146 Both menu panels are straightforward Select a frame a peak and the display option The images can be interpolated to provide a smoother image The Display Mmap Info option shows a list of the register maps in the Info Messages window The Colormap Display window allows up to three metabolic map images using RGB colors to be simultaneously displayed and overlaid on a reference image if desired See Image Reconstruction page 165 for instructions on creating a reference image For this simulated data however a reference image was created along with the CSI data and can be displayed along with the Mmaps by using the Colormap Display window Image Peak Arithmetic Peaks can be operated on to form new peaks which can be saved and displayed as new maps Perform the following steps to run the Image Arithmetic process 1 Use the right mouse button to select Process from the command panel then select Image Calctool 2 Select a Gframe 3 Use the cursor and the left mouse button to enter an arithmetic expression such as 1 2 8 This expression subtracts peak two from peak one and creates a new peak 8 Select the Return option al to run the calculation When al is selected a new map is formed and displayed in the selected frame by using the arithmetic expression But the map is not registered or saved as a metabolic map display peak until Save is selected Figure 64 shows the Image Figure 64 Image Calctool Wi
292. et frequency in Hz It must be set so that the transmitter is on the resonance frequency of the imaging component usually water ldof can be used to set this value from the global value in Hloffset rfcoil Contains rf pulse calibration entry in pulsecal database tcapply Apply table conversion reformatting to data tcclose Close table conversion file tcopen Open table conversion file te Specifies echo time in sec For GEMS it is usually set to less than 0 01 sec to minimize T effects thk Specifies slice thickness in mm tpwr Specifies pulse power output in dB units 63 dB is the maximum value 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 63 Chapter 3 Imaging Pulse Sequences Table 5 Imaging Pulse Sequence Commands Macros and Parameters continued tpwrl Specifies pulse power for the excitation pulse The imprep macro sets the pulse power to the value specified by fliplist For GEMS set tpwr1 to correspond to a 10 to 20 flip If the tpwr1 value is reduced by 6 dB the flip angle is reduced by 50 For example reduction in the power by 12 dB corresponds to a flip angle of 22 5 90 4 liplist provides a easy way to change the flip angle tr Specifies recycle time in sec It must be set to allow for spins to return to their equilibrium state For GEMS it can be reduced to about 0 025 sec to 0 1 sec because of the low flip angle 5 to 30 used for excitation 64 VNMR 6 1C User Guide Imaging 01
293. et image In this case enter mp 6 Starting the Planning Session To start planning 1 Enter the command plan 2 Click on the Slice menu button 3 Inthe new row of menu buttons click on Clear to remove any previous planning information The third button is now Mark 1 Marking the Target Slice Plane To define a slice plane 1 Move the cursors to the first point you want to lie in the target image slice plane 2 Select the Mark 1 button 3 Move the cursors to the second point on the line that will define the slice plane 4 Select Mark 2 You have just selected two points that describe a line through the current scout image The target image will be perpendicular to the scout slice plane on the line you have defined Selecting Compute Target shows this If you decide you want to change one or both of the marked points select Clear again and follow the above procedure once more to define your new slice plane If you are working on a system that has gradient waveshaping capabilities your slice plane may lie at any angle Slice planes that do not lie along one of the three major axes are said to be oblique If your system does not have gradient waveshaping the gradient DAC resolution is limited to 12 bits which is in general not adequate to define arbitrary slice planes with sufficient resolution in readout phase encode and slice select directions and so the software will at this point prevent you from continuing if you have d
294. eter names used for slice or voxel selection with each rf pulse in the sequence The SEMS sequence uses the parameter gss to define the slice select gradient level for both rf pulses giving sslist gss gss Some rf pulses in a sequence may not be slice or voxel selective such as a presaturation or inversion pulses The corresponding entry in sslist for these pulses should be n Another example is the ISIS sequence which has a total of four pulses The first three are voxel selective with levels specified by the parameters gvox1 gvox2 and gvox3 asin sslist gvoxl gvox2 gvox3 n fliplist Standard flip angle list P gss Slice selection gradient strength P imprep Set up rf pulses imaging and voxel selection gradients M patlist Pulse shape parameter list P plist Pulse length parameter list P pwrlist Pulse power level parameter list P Target Parameters 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 341 Appendix A Commands Macros and Parameters Each imaging and localized spectroscopy experiment contains a group of parameters that are used to hold information on a temporary basis during the planning of new imaging slices or spectroscopy voxels These are called target parameters because they are used to transfer positional and orientational values planned from an existing scout image to a new target experiment Each of the normal parameters that describe positions dimensions and orientations has a correspo
295. eter tn and the value of tof Thus if a point at the center of the spectrum is used of fset returns a value equal to tof and not zero CAUTION Because most imaging spectrometers either do not have lock Arguments Examples Related pulsecal Syntax Description hardware or run imaging in unlocked mode the solvent parameter should be set to none in both the imaging experiment and any 1D spectral experiment used to determine frequency offsets Having solvent CDCI3 for example results in improper frequency assignments in any imaging experiment with solvent none This can result in errors in slice and readout position or failure of frequency dependent functions such as water suppression silent isa keyword to not display the frequency offset value The default is to display the value parameter is a variable such as the parameter t of in the example below that if present is loaded with the calculated offset frequency value offset offset satfrg cr Cursor position in directly detected dimension P resto NMR resonance offset frequency P sfrq Transmitter frequency of observe nucleus P solvent Lock solvent P tof Frequency offset for observe transmitter P Create modify or delete entry in pulsecal rf calibration file 1 pulsecal lt name pattern length flip power gt 2 pulsecal name remove Adds new entries into an rf pulse calibration database file Th
296. etting Started Related at Acquisition time P axis Axis label for displays and plots P imprep Set up rf pulses imaging and voxel selection gradients M Ira Field of view size for readout axis np Number of data points P setgrad Set readout gradient M swl Spectral width in 1st indirectly detected dimension P swl Spectral width in 1st indirectly detected dimension Description Spectral width for the first indirectly detected dimension of a multidimensional image data set as in conventional analytical spectroscopy In imaging sw1 is generally a phase encoding dimension created by stepping through a range of phase encode gradient levels with a constant time gradient pulse number of steps set by the parameter nv instead of incrementing a delay as in analytical 2D spectroscopy Because phase encoding is a function of both time and gradient sw1 has no real significance as it generally does in 2D spectroscopy where sw1 1 d2 other than to act as an artificial value for use by image display and processing routines The choice of value for sw1 is therefore somewhat arbitrary and is generally set to 1 tpe by imprep Even though d2 is not used as an incremental delay in imaging sequences its value may in fact be automatically incremental in noncompressed sequences For this reason imaging pulse sequences should never use d2 unless an incremental delay dependent on the value of sw1 is specifically required Refer to the manual V
297. etup The values are finally programmed into the gradient compensation units This button is active only when eccTool is started from VNMR save Writes out and updates values in the file field file When a file is written preceding values in the file not the window are lost To prevent accidental overwriting lock a file with the files button read Allows the user to read an existing file Enter the file name or use the eccTool Files window defaults Sets all values to defaults that are an uncompensated starting point quit Quit the eccTool program Channels The eccTool window shows the settings of one channel at a time To display each channel in turn click the cycle button next to the Gradient field 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 195 Chapter 7 High Performance Auxiliary and Microimaging Gradients 196 Values To change a value in the window do the following steps 1 Move the mouse to the relevant field 2 Delete the existing field 3 Type in the new value The file name also can be manually entered If the value is within the correct range itis accepted If not an error message appears at the bottom of the window with the valid range and the erroneous value The value should be corrected Accelerators Within each field certain keys function as accelerators e Typing a produces a message about the valid range of the field Additionally typing a d or D sets the field to its default val
298. even signals in different ways 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 53 Chapter 3 Imaging Pulse Sequences 90 _ tpwrt 180 22 tpwr2 RF rae RF lt lt a p tspoil q lt spoi slice gss me ap A gssr phase tped gt li ke A A eee gpeb gt tblip trod gt gror gror amp grora at gt roa amp gro read NX man vate ie signal i pom npn eee ADC 0 0 Figure 19 Spin Echo Variant of the EPI Pulse Sequence The amplitude and phase variations between odd and even echoes cause a ghost artifact to appear along the phase encode dimension as shown in Figure 21 The ghost image appears shifted from the primary image by lpe 2 hence the image is referred to as a half FOV ghost Most half FOV ghosting can be reduced by the EPI phase correction routines discussed in Phase Correction page 57 Figure 21 Ghost Artifact 54 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 3 5 Echo Planar Imaging and Phase Correction Map Files t t pcmapgen FT t2 p _ generate phase map t2 F2 phase map Reference Scan p p ui i z FT t2 pemapapply e e phase correct F2 F2 EPI data p p q p p p q p F1 t1 z os FT t1 e epirs bd lt lt e F2 F2 ze EPI image Figure 20 Time Domain Data Processing Steps Chemical Shift Ef
299. f data in the spatial dimension can only be looked at However a filtering function can be looked at and constructed To use the tool select an empty Gframe Select Tools Graphics and then the Filtering tool The selected Gframe splits into three Localized FID sections as shown in Figure 58 P Filtering or To manipulate the filtering function Wee O Weighting middle window press the left and Function middle mouse buttons All parameter changes appear in the Spatial Reconstruction window Resulting Parameters can also be changed in Spectrum the window changes appear in the filter Gframe Figure 58 Filtering Display Spectral Reconstruction After spatial reconstruction has been completed select the Process option in the command panel to open the Spectral Reconstruction window The window can also always be opened from the submenus with the right mouse button The window appears with default values specified in all the fields Select the Apply To All option to process the localized FID data and display the MVS data in the currently selected Gframe Processing parameters associated with spectral reconstruction are zero filling filtering and left or right shifting of the FID To reprocess the data set and redisplay the MVS data in the currently selected frame change the desired field or fields and select the Apply To All option Filtering or Weighting The Filtering or Weighting tool is fully a
300. f macro can be used to set the transmitter frequency t of to the cursor position 6 Calibrate the pulse power Measure the 90 or 180 pulse and enter it into the pulsecal database The setarray macro can be used to set up an array of pulse width values for the calibration experiment The macro ga collects and displays the Fourier transformed data The command dssh allows you to display the arrayed spectra The indpw macro lets you more conveniently calibrate the pulse powers f indpw automatically determines the maximum and minimum signal from a set of ten predefined pulse lengths and enters the calibration values into the pulsecal database Once the pulse power is calibrated pulse parameters such as pulse width pw and shape e g pwpat in imaging pulse sequences can be easily changed Pulse powers are automatically computed by the imprep routine Different imaging samples can affect the tuning Q of the imaging coil Therefore it is necessary to calibrate the pulse with each sample so that the proper pulse powers are calculated for the imaging sequences 3 2 Conditions for Use 42 This section lists the conditions that are necessary to use imaging pulse sequences and information on the Lock and spin parameters and the spuls and s2puls macros Receiver Gain Adjusted Imaging samples generally produce excessive NMR signals that often saturate the receiver If the ADC overload error message is displayed you must set the gain
301. f phase encode steps for 3rd indirectly detected dim P seqcon Acquisition loop control P setloop Set values for ni and nf to control arrayed and real time looping M Number of phase encode steps for 3rd indirectly detected dimension The number of phase encode steps for the third indirectly detected dimension in a multidimensional experiment In a 3D CSI experiment three spatial dimensions one chemical shift dimension nv3 controls the third spatial dimension 1pe3 The lower level parameters ni and nf are set automatically each time a value of nv3 is entered through the macro set loop which uses the seqcon parameter to determine if the acquisition is standard or compressed in the dimension controlled by nv3 and appropriately sets either ni or nf Because nv3 is explicitly used in most imaging pulse sequences to specify the number of phase encode steps the user should never directly set ni or nf but instead set nv3 and let the software automatically assign ni and nf flashe Convert compressed 2D data to standard 2D format C imprep Set up rf pulses imaging and voxel selection gradients M VNMR 6 1C User Guide Imaging 01 999163 00 A0800 A 5 Parameters lpe3 Field of view size for 3rd phase encode axis P nf Number of FIDs P ni Number of increments in 1st indirectly detected dim P nv Number of phase encode steps for 1st indirectly detected dim P nv2 Number of phase encode steps for 2nd indirectly detected dim
302. f the data approximately equal to the argument value in dB The higher the value the more the weighting and apparent smoothing smaller values give less apodization and apparent smoothing A weighting value of zero turns off the Gaussian weighting parameters filter 10 gf Gaussian function in directly detected dimension P gfl Gaussian function in 1st indirectly detected dimension P gfs Gaussian function in directly detected dimension P gfsl Gaussian shift const in Ist indirectly detected dimension P wft2d Weight and Fourier transform 2D data C Measure 180 pulse update pulsecal database M findpw Measures a 180 pulse and updates the pulsecal database findpw automatically determines the maximum and minimum signal from a set of ten predefined pulse lengths and enters the calibration values into the pulsecal database The s2pu1 sequence should already be loaded and running Before the new pulse parameters are entered into the pul secal database the results are displayed on the screen and you are prompted for a response When you type y you are asked for a file name then the pulsecal database is updated start_pw_value specifies the starting pw value end_pw_value specifies the ending pw value findpw findpw start_pw_value end_pw_value pulsecal Create modify or delete entry in pulsecal rf calibration file P pw Pulse width P s2pul Set up parameters for standard two pulse sequence Convert compressed
303. f the magnet The strong magnetic field surrounding a superconducting magnet can erase magnetic media such as floppy disks and tapes The field can also damage the strip of magnetic media found on credit cards automatic teller machine ATM cards and similar plastic cards Many wrist and pocket watches are also susceptible to damage from intense magnetism Refer to the manuals supplied with the magnet for the size of a typical 5 gauss stray field This gauss level should be checked after the magnet is installed 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 13 SAFETY PRECAUTIONS Caution Notices continued CAUTION CAUTION CAUTION CAUTION Keep the PCs including the LC STAR workstation beyond the 5 gauss perimeter of the magnet Avoid equipment damage or data loss by keeping PCs including the LC workstation PC well away from the magnet Generally keep the PC beyond the 5 gauss perimeter of the magnet Refer to the Installation Planning Guide for magnet field plots Check helium and nitrogen gas flowmeters daily Record the readings to establish the operating level The readings will vary somewhat because of changes in barometric pressure from weather fronts If the readings for either gas should change abruptly contact qualified maintenance personnel Failure to correct the cause of abnormal readings could result in extensive equipment damage Never operate solids high power amplifiers with liquids probes
304. f the magnet and gradients e Set resto to the value you found in Determining the Reference Offset Frequency page 18 Setting the Field of View Parameters Choose values for the image field of view FOV and enter them as follows 1 Set lro to the readout length in cm 2 Set lpe to the phase encode length in cm Do not use the old macros set gro and setgpe Setting the Slice Thickness The parameter thk sets the slice thickness for an image e Set thk to the slice thickness in mm A value of 2 or 3 is a good place to start Selecting the Image Orientation The parameter orient defines the imaging slice plane and indirectly controls a set of three Euler angle parameters that the pulse sequence uses internally to achieve the desired orientation orient has allowed values of trans sag and cor short for transverse Z slice gradient sagittal X slice gradient and coronal Y slice gradient respectively A fourth entry of oblique is also possible but cannot be entered directly The entry for orient in the appendix see page 324 describes oblique slice selection Because it is common for the sample to be fairly well centered on the X axis even if it is off center in Y and Z you might start by entering orient sag For a vertical bore VNMR 6 1C User Guide Imaging 01 999163 00 A0800 1 1 Making an Initial Scout Image magnet Z is more likely to be the on center axis so enter orient trans This nearly guar
305. fects Unlike the conventional spin warp sequence EPI echoes evolve as a function of time This evolution means that if different chemical components e g oil and water are present in the sample each of the echoes in the echo train is also chemical shift encoded Therefore the phase encode dimension represents both chemical shift and spatial dimensions which result in multiple images corresponding to the different chemical shift components in the sample The readout dimension also shows chemical shift artifacts similar to those seen in conventional spin warp images but the effects are much less severe when compared to those seen in the phase encode dimension Special pulse techniques are necessary to selectively suppress unwanted resonances Alternatively the desired components to be imaged can be selectively excited which avoids any interference chemical shift artifacts from the unwanted resonances Phase modulation of the echo signals caused by samples with multiple resonances has another undesirable side effect Phase modulation caused by the chemical shift effect interferes with the phase correction routines used to correct for the echo shifts along the t2 direction The pcmapgen routine that is used to calculate the phase maps is unable to distinguish the difference between phase shift caused by incorrect alignment of echoes and phase shift caused by chemical shift 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 55 Chapter
306. files M Save FIDs in current experiment M svfi lt file lt nolog gt lt arch gt gt Saves parameters text and FID data in the current experiment to a file No data is removed from the current experiment sv f merely saves a copy of the data in a different file You can enter rt to retrieve the complete data set or enter rtp to retrieve parameters only file is the name of the file with the suffix fid added to be created to save the data The default is the system prompts for a file name You are warned if you attempt to overwrite a file that already exists In fact if data has been acquired with the file parameter set the data does not need to be saved It is already stored in a named file nolog is a keyword to not save the log file with the data The default is to save the log file 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 301 Appendix A Commands Macros and Parameters Examples Related svib Svp 302 Syntax Description Arguments Examples Related Syntax Description Arguments Examples Related arch is a keyword to assume that the data goes to a database and appends to the or creates a doneQ file with information that can be used by the command status SvE svf home vnmr1 mydatafile file File name P PE Retrieve FID M rtp Retrieve parameters M status Display status of all experiments C Generate and save images as Image Browser c
307. filter Filters 2 3 and 4 are used to suppress high spatial frequencies Specifies the bandwidth of the filter function i1lter_bw is valid for 1 0 or less For a value of 1 0 no additional spatial frequency cutoff is performed with regard to the filter function used Smaller values lead to a cutoff and a smoothed image For a Hamming filter filter_bw 0 54 is recommended Name of the intermediate file between the first and second cascade of the 3D BP If met a_image is not specified it is automatically set up Intermediate files within the first and second cascade respectively Name mask for the resulting slices of the 3D volume Each slice is indicated by an extension to image_file with i1ii 000 001 002 i_size 2 i_size 1 If image_file is not set the default mask is prof_file Any subsequent reconstruction overwrites the already reconstructed slices Provides partial reconstruction facilities to assist in off resonance conditions r_size must be greater than or equal to 0 and must be less than m_size to achieve full support on the unit ball given by m_size Measurement center definitions that allow compensation for different definitions used for the position of frequency 0 in the profile the center value Typically they are set tom_size 2 0 Reconstruction center definitions used to compensate an offset in an off resonance condition In the case of no off resonance condition they are set tom_size 2 0 VNMR 6 1C U
308. for installation on site by an Varian Field Service representative Part Functions During installation the gradient coil spacing rings and rf shield doors are adjusted and assembled to form a single unit collectively known as the auxiliary gradient coil This unit 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 175 Chapter 7 High Performance Auxiliary and Microimaging Gradients 176 Table 10 HPAG 183 Accessory Parts List Part Number Part Count Description x 1 183 mm auxiliary coil x 2 Spacing rings 00 967610 00 2 RF shield doors 00 967702 01 1 Gradient power cable aux coil 00 967702 02 1 Gradient power cable main coil 00 967636 00 1 Quick disconnect box 00 967219 91 3 Eddy current compensation boards 1 Probe and bore equipment kit Part number is different for each system and is available upon request is loaded into the system magnet during use and held in place on the rear flange of the system rf shield by the locking screws The coil is connected to the gradient supply via a gradient power cable 00 967702 01 which is cabled to the HPAG quick disconnect box The shim power water and thermocouple sensor lines are also connected to the auxiliary coil during use The eddy current compensation boards are calibrated during installation to provide eddy current control for the HPAG gradient coil These boards are installed into the system gradient supply by the user when the HPAG gradient coil is in use
309. formation the time domain data yields an EPI image Figure 20 summarizes the basic data processing steps EPI Limitations Even though EPI is potentially a powerful technique its has not been widely used because of limitations that include the stringent demands of EPI on gradient hardware and the large gradient fields needed with negligible eddy current effects Another major limitation is that EPI is prone to artifacts caused by inhomogeneity and the less than ideal nature of field gradients In practice the NMR signal rapidly loses phase coherence because of field inhomogeneity effects and spin spin relaxation Therefore the echo train must be collected in a very short period of time before the signals of interest are lost dephased Lost signals can be minimized by shortening the acquisition time However if the acquisition time is reduced the strength of the readout gradient must also be increased by about the same factor Consequently EPI experiments often run into the gradient strength limits Each blipped gradient phase encodes each echo according to the phase encode direction The center of VNMR 6 1C User Guide Imaging 01 999163 00 A0800 3 5 Echo Planar Imaging and Phase Correction Map Files 90 tpwrt RF p1 p1 gss slice gssr lt tped gt phase A A A AN eee lt gt gpeb tblip lt at gt gro amp groa trod gt aa eee read VS NS gror amp grora gro signal 0 0 ADC eee Figur
310. functions that do not have any of the previous forms The most desirable functions might be in this category Set to the name of the subroutine that calculates the function values The specifications for this function are on page 124 Always optional and is useful only for NONLINEAR functions It is set to the name of the subroutine supplied by you that calculates derivatives of the function with respect to each parameter If a you do not provide a routine derivatives are estimated by the nonlinear fit routines Providing derivatives normally only slightly speeds up fit routines VNMR 6 1C User Guide Imaging 123 Chapter 5 Image Browser Math Processing 124 GUESS Used only for NONLINEAR functions It is set to the name of a routine supplied by you that calculates an initial guess for the parameter values Sometimes fixed initial guesses might work for all sets of data In such cases you can omit setting GUESS and instead specify default values with the following command set_default_parameters 3 0 0 1 0 0 0 where the first argument 3 is the number of following arguments the remaining arguments are the default values You must provide at least as many values as there are parameters in the fit If completely fixed guesses do not work but the same guess can be used for every pixel in the image you can specify the command GUESS fixed_guess which allows the initial guesses to be passed on the command line These guesses wo
311. g dgm allows menu selection of the various dg screens in any experiment by searching for all parameter names that begin with the two letters dg and presenting a menu of all such names To display any of these parameter groups select the button with the desired name or description The Print button in the dgm menu prints the currently displayed parameter group dg Display group of acquisition processing parameters C Display 3D data U From UNIX disp3d lt fdf_file gt Displays a 3D FDF Flexible Data Format file or a raw 8 bit 3D data file with no header Compatible FDF files are produced by ft 3d withthe fdf option or by default if appmode imaging FDF data can also be loaded either by entering the file name as an argument to disp3d or by typing the file name into the File field in the disp3d control panel and clicking the Load button If the FDF data word size is larger than 8 bits the data are scaled and truncated to 8 bits for display Raw data files can only be loaded from the control panel Besides the file name the user must enter the size of the data matrix in the fast medium and slow dimensions in the Data size field Typically these would be the values fn 2 fn1 2 and fn2 2 respectively Furthermore the desired size of the image in screen pixels also in the fast medium and slow dimensions must be entered in the Display size fields Typically these values would be near 100 and the relative ratio of th
312. g f1iplist is a more convenient way of setting the pulse flip angle Check the NMR signal At this stage all parameters should have been set and should be ready for imaging Before proceeding any further check the NMR signal gradient echo by typing the command go The df command displays the FID echo on the screen The command ft displays the Fourier transformed signal in the absolute value mode which is the profile along the readout dimension If necessary the sample can be positioned by observing the profile The gradient echo profile can often appear distorted because of inhomogeneity effects Optimize the receiver gain To optimize the receiver gain set gain n and then execute go After autogain has been adjusted reset the gain parameter gain y To automatically determine receiver gain use the set gn macro The image profile can be used to optimize the receiver gain Set the number of phase encoding steps e g nv 128 Acquire the image by entering go Process the compressed GEMS data by entering the command ft nf or the macro ftnf If necessary use the lashc command to convert the compressed data to the standard array format 50 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 3 5 Echo Planar Imaging and Phase Correction Map Files The t 2d command double Fourier transforms the standard arrayed 2D data sets The w t2d command applies apodization functions along the readout and phase encode dimen
313. g function to the same position ouse buttons Left weighting Center vf vs i vf vs 2 1b 3 sb 4 sbs o gf 8458 469 1 1e 05 MUET 6 7e 04 Bees er unused unused 0 0e 00 Figure 112 Setting the Weighting Use the following guidelines to adjust the weighting 1 Choose the width of the weighting function to be at least 5 to 10 times broader than the width of the echo signal and 2 Make sure the weighting function has decreased to nearly zero at the left and right side of the scan If it is truncated with a large nonzero value artifacts in the reconstruction will appear An example of the effect of the weighting appears in Figure 113 which shows a comparison of an unweighted and a weighted FT It is obvious that the course of the profile is smoother after the weighted transform 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 231 Chapter 10 2D and 3D Backprojection 232 Figure 113 Unweighted and Weighted Fourier Transform Performing Reconstruction The macro bp reconstruction 1 Enter b _reco takes care of the reconstruction process For the duration of the refer to Table 21 p_ reco to start the reconstruction process 2 When running a 3D reconstruction a text file appears with settings that will be used for the reconstruction You can modify the text file at this time if you want to change any of the default settings In any case you must quit or exit the editing window in order for the reconstru
314. gative phase encode gradients are applied during the phase encode time tpe For example if nv 4 the gradient amplitudes are stepped in half integral units of 1 5 0 5 0 5 41 5 The phase modulated nature of the imaging experiment would normally produce unwanted dispersion components in the final image This problem is avoided by phase encoding with both positive and negative values of the gradient to create a pseudo echo signal along the phase encode dimension that is transformed with pure absorption components Therefore as in the case of the gradient echo signal an absolute value calculation yields an image without the need for any phase correction The field of view along the phase dimension is related to the step size of the phase encode gradient and is defined by the following equation Ipe 1 Y pestep Eq 18 In Equation 18 1pe is the field of view along the phase encode dimension in cm It is important to choose the parameters so that the field of view lpe is greater than the spatial frequency spread along the phase encode dimension or else the spatial components that lie outside the field of view will cause fold over artifacts 2 6 Image Resolution Image resolution defines the ability to separate the signal arising from adjacent regions in the object being imaged Decreasing the resolution improves the appearance of the actual shapes of the separate parts of an object An image is displayed as a 2D digitized pic
315. ge page 107 to do the conversion convert always produces an 8 bit precision maximum output file even if the format supports more bits and they are present in the input To add new formats obtain a program that converts from the FITS format or any supported format to the desired format see the section Flexible Image Transport System Then add lines to the SBROWERDIR fileformats init file and specify the new name and the conversion script The following example entry produces JPEG files format JPEG compressed format script convert quality 85 fits 1 jpeg 2 data integer 8 The label JPEG appears in the popup menu of format types the comment on the remainder of the format line is ignored The conversion script is everything on the line after the script VNMR 6 1C User Guide Imaging 01 999163 00 A0800 4 6 Files and Other Items Table 7 Formats Available in Image Browser Format Description AVS AVS X image file BMP Microsoft Windows bitmap image file EPS Adobe Encapsulated PostScript file FAX Group 3 FAX FITS Flexible Image Transport System GIF Compuserve Graphics Interchange Format version 89a GIF87 Compuserve Graphics Interchange Format version 87a JPEG Compressed format from Joint Photographic Experts Group MIFF Magick image file format PCD Photo CD PCX ZSoft IBM PC Paintbrush file PDF Portable Document Format PICT Apple Macintosh QuickDraw PICT file PGM Portable gray map PNG Portabl
316. ge is used as a baseline reference its pixel value is subtracted from all the normal input images The following command is an example 11 fit 1 8 9 Shames2 x Here the fit routine uses 9 as the reference image Up to three more additional images can be specified to set pixel dependent values of alpha SBVO and hct these values override any constant values specified on the command line such as 11 fit 1 8 9 10 Shames2 x Now the fit routine sets alpha differently for each pixel according to the value in image 10 The fit routine also uses 9 for a baseline User variables are defined in the second section of a fitting file as static local to the current file However on compilation all your xfit c files are combined with fit c into one file so names should be unique among all fitting functions Adding New Functional Forms Additional functional forms can be handled by supplying a C language file that defines the function and how to fit it Take the following steps to add new fitting functions 1 Create a file of C source code containing your fitting function The format of this file is described in detail in Function Definition Files page 122 2 Edit the file userfit c to include your new file 3 Entermake depend to update makefile to recognize your new file The command make depend changes the makemathfunc file a warning fit c includes userfit c more than once appears wh
317. gh pass frequency is increased The best initial setting of the high pass frequency is 0 5 Hz When the recommended initial frequencies for the bandpass filter controls have been set the electrocardiogram is close to the unfiltered state Increase the high pass frequency until any baseline undulations are removed Typical low frequency baseline undulations have a period greater than one heart period Baseline undulations often arise from the motion of the animals limbs due to respiration and can be minimized by securing the limbs and electrode clips to the side of the animal bed with tape The polarity of the QRS complex might invert for higher settings of the high pass frequency Correct any inversion with the polarity switch When the high pass filter has been adjusted decrease the low pass filter only if the ECG is noisy Setting the ECG Detection Voltage Threshold There are three ways to adjust the ECG detection voltage threshold The simplest way is to take advantage of the automatic threshold feature e Automatic Threshold To set up the automatic threshold first reduce the inhibit delay time control of the PGM 1000 receiver to the minimum value Reducing inhibit delay time causes it to trigger on every event that exceeds the value of the ECG detection threshold Switch the ECG detection threshold to automatic mode while observing the inhibit output signal on channel 2 of the oscilloscope After a few heart beats the automatic th
318. gin file setenv CSIDIR SHOME csi_initdir If a new user is created with the makeuser script this variable is automatically set CSIDIR points at a user initialization directory Initialization Directory The initialization directory in vnmr user_templates contains files bitmaps frame directory ROI directory and PEAK directory used for starting up tuning and running CSI This directory is copied into the user s home directory when makeuser is run It can be copied into any location within the user s area as long as the environment variable CSIDIR is set to point to the new location Within the initialization directory all files ending with the suffix m are bitmap files and must not be changed The initialization directory contains the following relevant files and directories colormap init Contains the colormap definition Colors for graphics frames Gframes can be defined as can ROIs and text annotation fonts window init Contains the default positions for the main CSI window and various subwindows csiparam init Contains processing factors and parameters for tuning certain CSI processing functions 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 133 Chapter 6 CSI Data Processing 134 gframe Directory containing graphics frames layouts The file with the name default is the set of Gframes that are loaded at bootup This is the directory where sets of Gframes can be saved A personal default set of Gframes can be
319. ging and voxel selection gradients M setgss Select slice or voxel selection gradient levels M Voxel Dimension Position and Orientation Parameters posl pos3 Description Position of voxel center Voxel position measured from the gradient coordinate origin pos1 pos2 and pos3 are independent of voxel orientation and are the distances from the gradient origin to the center of the desired voxel along the three axes of the rotated coordinate frame specified by the voxel orientation Voxel positions are most often be determined through the interactive voxel planning procedure from a scout image but can be entered manually through the command line The voxel position ultimately used during pulse sequence execution to compute the spectrometer offset frequency required to place the center of the voxel at the correct spatial position in the presence of a voxel selection gradient is described by the equation offset restoty posl gvoxl 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 327 Appendix A Commands Macros and Parameters Values Related vox1 vox3 Description Values Related vorient Description Values Related This simple calculation is the basis for the pulse sequence statement poffset Because the frequency offset is determined internally by the pulse sequence at run time it is not necessary to run the imprep macro after changing pos1 Number in cm gvoxl gvox3 Gradient strength fo
320. ging 01 999163 00 A0800 Examples Related setvgrad Syntax Description Related steam Syntax Description tabgen Syntax Description A 2 Macros for Setting Up Experiments setgss setgss gss thk setgss gvoxl voxl1 fliplist Flip angle list P patlist Pulse shape parameter list P sslist Gradient parameter names list P gmax Maximum gradient strength P gss Slice selection gradient strength P imprep Set up rf pulses imaging and pulse power levels M plist Pulse length parameter list P setgpe Set phase encode gradient levels and timing M setgro Set readout gradient strength and spectral width M Set voxel selection gradient strengths setvgrad In localized spectroscopy experiments automatically computes and sets the voxel selection gradients in G cm to achieve the required voxel dimensions setvgrad calls the macro set gss for each of the three voxel axes using the parameters gvox1 gvox2 and gvox3 for the gradient strength parameters and vox1 vox2 and vox3 for the voxel dimension parameters If any of the voxel dimensions are arrayed set vgrad configures the array parameter to give the proper diagonally arrayed experiment gvoxl gvox2 gvox3 Gradient strength for voxel selection P imprep Set up rf pulses imaging and pulse power levels M setgss Set slice selection gradient strength M voxl vox2 vox3 Voxel dimensions P Retrieve parameters for STEAM im
321. ging Gradients Sections in this chapter e 7 1 HPAG 183 Hardware this page e 7 2 Experimental Setup page 183 e 7 3 Performance Specifications page 189 e 7 4 Microimaging Hardware page 190 This chapter describes high performance auxiliary and microimaging gradients The concept behind the high performance auxiliary gradient HPAG accessory is to provide dedicated gradient coils to increase system performance The accessory provides performance improvements for e Maximum gradient strength e Gradient rise and fall times e Duty cycle e Eddy current compensation These attributes provide access to higher image resolution shorter echo times thinner slices faster sequences and better localized spectroscopy lineshape in smaller voxels HPAG hardware is designed to provide easy and simple changeover between the system s main gradient coil and the auxiliary gradient coil Changeover time is typically less than 20 minutes The VNMR system software provides full support so that simple configurational changes allow the HPAG to function with all standard sequences Pulse sequences provided by the user are easily modified for use with the HPAG gradients 7 1 HPAG 183 Hardware This section describes the hardware components of the HPAG 183 accessory Parts List Table 10 is a list of parts that make up the HPAG 183 accessory These parts should be received preinstalled with a new imaging system or as a retrofit kit
322. ging system The auxiliary gradient coil provides access to higher gradient strengths and faster slew rates The smaller diameter of the HPAG auxiliary coil leads to a reduction in the level of eddy currents induced in surrounding metal parts in particular the magnet cryostat The effects of eddy currents are compensated by three additional compensation boards calibrated for the auxiliary gradient coil and by physical adjustment of the coil position within the magnet Cabling to both the standard and auxiliary gradient coils is routed through the HPAG quick disconnect box allowing connections to be easily made to either coil Gradient Coil Physical Dimensions On all systems the inner diameter is 123 mm and the outer diameter is 183 mm Table 12 gives the length and weight for standard systems Table 12 Gradient Coil Length and Weight Gradient Strength System Length Weight f mm kg The gradient strength is 10 G cm 100 mT m on the X Y and Z axes 200 400 Mk HI 2005 47 200 330 Mk II 1888 44 200 330 Mk II 1680 38 Gradient Rise Time ae ine 33 Gradient rise times of 500 us to 10 G cm on X Y and Z axes This time is equivalent to a gradient slew rate of 200 T m Duty Cycle and Heat Dissipation Table 13 Gradient Table 13 summarizes the duty cycle specification for Channels Duty Cycles simultaneous use of all three gradient channels Gradient Duty Cycle G cm Eddy Current Compensation 3 100 Eddy
323. gion that does not give an NMR signal The lack of NMR signal causes the edges of the object to be poorly defined and can cause overlap between adjacent structures so that the separate objects cannot be distinguished from one another As the number of data points and or gradient frequency spread is increased the signal from any given point is better able to be confined to a single pixel so the amount of overlap between adjacent structures diminishes and the image is better defined The usual number of chosen data points is 128 or 256 A smaller number results in insufficient resolution and can also cause artifacts created by truncation of the time domain VNMR 6 1C User Guide Imaging 01 999163 00 A0800 2 7 Spatial Frame of Reference signal A larger number of points along the phase encode dimension ni or nv significantly increases the data acquisition times More points along the readout dimension increase the acquisition therefore the echo times are increased which leads to loss of signal caused by the T effect The number of data points is usually set to a power of 2 as required by the Fourier transform Sometimes image presentation can be improved by zero filling that is by increasing the number of image points along the phase and readout dimensions However this method does not improve the inherent resolution of the image 2 7 Spatial Frame of Reference The section Image Resolution page 35 described the NMR method for
324. gradient P Pilot Automatic sequence calculation P Slice selection gradient level Predefined parameters for specifying gradient levels for different slice selection events in an imaging pulse sequence gss Slice selection gradient strength P Control phase encoding gradient in EPI experiments P Systems with echo planar imaging EPI capabilities Turns on and off the phase encoding gradient in EPI experiments image also specifies the number of EPI images to collect in an arrayed experiment 0 specifies that the phase encoding gradient is turned off 1 specifies that the phase encoding gradient is turned on image 0 1 1 1 collects a set of four EPI images The first dataset refers to the reference scan Localized Voxel Spectroscopy Gradient Parameters gvoxl gvox3 Description 01 999163 00 A0800 Gradient strength for voxel selection Voxel select gradient levels for the first second and third dimensions of a voxel in a localized spectroscopy experiment For example imprep sets gvox1 based on the corresponding voxel dimension vox1 and rf pulse bandwidth For nonoblique voxels the orientation of gvox1 lies along one of the three main gradient axes X Y or Z Oblique angle voxel orientation is also available and for this reason the name gvox1 is used instead of gx for example 313 VNMR 6 1C User Guide Imaging Appendix A Commands Macros and Parameters Values Related Special gcrush Descriptio
325. gradient coils The gradient calibration information or file corresponding to each coil must exist in the vnmr imaging gradtables directory Use the creategtable macro to create the gradient calibration file Gradient Amplifier On The gradient amplifier must be turned on and enabled before proceeding with the initial setup procedure Be aware that x y and z shimming is done via the gradient coils and that the amplifiers can generate a small dc offset current that must be corrected by shimming Eddy Current Compensation Files Loaded If you have a microimaging system with the computer controlled analog eddy current compensation use the program ecctool to load the appropriate file For systems equipped with digital eddy current compensation DECC use the decctool program described in Chapter 8 Digital Eddy Current Compensation to load the appropriate file Shim Power Supply Turned On The shim power supply must be turned on for shimming purposes during experiments If the shim currents are high they can generate excessive heat in the bore of the magnet Air or water cooling is employed to remove the excess heat buildup in the magnet If the system is not being used for extensive periods or if the air or water cooling is turned off turn off the shim power supply 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 43 Chapter 3 Imaging Pulse Sequences Pulse Calibration Done Imaging sequences expect the rf calibration inform
326. he Load option is clicked Saving Files Select the File then Save to open a FileBrowser tool for saving files CSI saves data from the global buffers except for spectrum data which it saves from the currently selected Gframe Because data is saved from the Gframe when a file name is entered or selected into the top line of the FileBrowser and Save is clicked a Save Tool window opens VNMR 6 1C User Guide Imaging 01 999163 00 A0800 6 5 Files and Other Items Figure 78 shows an example of a Save Tool window The file name can be changed after the window Sre Dst Save Tool has appeared pen pata Localized FID gt gt gt gt ols csi DATA heart mys The type of data to be saved must MYS Data be selected If Spectrum or MVS Curve Fit Data Save Cancel Single FID is selected the data Image must be in a selected Gframe Metabolic Map Spectrum Single FID If Metabolic Map gt Image is selected the appropriate metabolic map number must also be selected A metabolic map is created and saved to the specified Figure 78 FileBrowser Save Tool Window Metabolic Map gt Image file The metabolic map is created with the Matrix Size and Interpolation as specified in the CSI Metabolic Map Display window For the Matrix Size and Interpolation to be set a metabolic map must be displayed after the desired fields are selected otherwise the FileBrowser saves the metabolic map according to the spe
327. he QRS complex The P wave is the electrical event associated with the beginning of atrial contraction The mechanical motion associated with atrial contraction takes place in the time interval between the P and R waves This time is called the PR interval when referring to the electrical events and atrial systole when referring to the mechanical events The period between the QRS complex and the P wave of the next cardiac cycle is known as atrial diastole and refers to the relaxation of the atria prior to their next contraction VNMR 6 1C User Guide Imaging 01 999163 00 A0800 9 2 Hardware Description Figure 100 ECG Interpretation The QRS complex is the electrical event associated with the beginning of ventricular contraction The motion associated with ventricular contraction takes place in the time interval between the QRS complex and the end of the T wave The interval measured for the electrical events is the QT interval and this time period is known as ventricular systole or simply systole when referring to the mechanical events The ventricles are typically in the fully contracted state at the end of the QT interval The heart is said to be fully systolic The period following the T wave up to the next QRS complex is called ventricular diastole or diastole and refers to the mechanical events associated with the ventricles relaxing to the resting state before the advent of the next cardiac cycle The heart becomes fully relaxed or diastoli
328. he cursor draws a rectangle on the graph 3 Drag the cursor to the opposite comer of the desired expansion area and click again To cancel the operation second click the right mouse button 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 205 Chapter 8 Digital Eddy Current Compensation Close Window button Scale buttons eccGraph 1 2 exp t 2 13 2 3 exp t 2 13 1 exp 1 47 3 3 exp t 2 13 1 5 exp t 47 0 5 exp t 138 Text input fields Legend pS SSE E 2 1E 1 1E0 1E1 1E2 1E3 Time ms linear log a m in Left click on corners of area Zoom out Right click Figure 98 eccGraph Window You can magnify a very small area by repeatedly zooming in on the region Zooming out of a Region To zoom out of a region click the right mouse button anywhere on the graph You can zoom out of an region in successive zoom stages by repeatedly clicking the right mouse button Note that with a logarithmic time axis zoom areas are forced to end on an even decade so a linear scale must be used to zoom in on a very short time interval Closing decctool To close decctool double click on the frame button in the top left corner of the decctool 8 4 Exercising decctool Using an Oscilloscope The decctool interface and the hardware can be exercised without resorting to an actual NMR experiment You might do this for example to become acquainted with the operation
329. he intersection of the cursors label is a string argument for the label color specifies the color of the label imark Spectrum 1 imark Spectrum 1 yellow write Write formatted text to a device C Arithmetic amp other manipulations on 2D images phasefiles M UNIX From VNMR imcalc optype phf1 lt phf2 outphf args gt From UNIX imcalc optype phfl lt phf2 outphf args gt Performs arithmetic and spatial manipulations on 2D images on a pixel by pixel basis The operands used by imcalc are phasefiles that must have been previously saved with the VNMR command svphf imcalc can be accessed with the imcalci macro or in one of the following three modes e Direct execution of the UNIX program from a UNIX shell not recommended e Executed from VNMR with the appropriate arguments recommended only for macro controlled repetitive operations e Executed from VNMR with no arguments recommended mode Limitation on imcalc The t race parameter must be set to 1 when saving phasefiles for use with imcalc and when displaying phasefiles resulting from calculations Trying to display an absolute value phasefile in an experiment in which ph mode is selected or vice versa does not work See the following subsection Helpful Hints for a solution to this problem If a nonsquare image is rotated 90 degrees the result is not displayed with the correct aspect ratio because the 1 ro and 1 pe parameters are not alte
330. he most common problem with monitor adjustment is that the black level is set too dark making everything near the bottom end of the intensity scale appear black Set the brightness control labeled X on some monitors just low enough so that the blackest level at the left of the grayscale ramps pixel value 0 is indistinguishable from the unscanned black background at the edge of the monitor screen To accomplish this adjustment it might be convenient to move the Gamma Correction window slightly off the bottom of the screen so that the bottom row of steps directly merges with the unscanned margin Once monitor brightness has been adjusted correctly the perceived prominence of the intensity steps in the Gamma Correction window should be roughly equal with no gamma correction Gamma Correction The gamma correction described in the following paragraph is still effective on a poorly adjusted monitor although if the brightness is set too high there is no way that the lowest gray level can be made entirely black Two forms of gamma correction are available When the Gamma and Log switches are both set to ON ImageBrowser attempts to make each step in the colormap index an equal step in the log of the screen intensity which assumes that the screen intensity is described by a function of the form I I V Eq 32 where is the intensity V is the voltage proportional to the pixel value y is a characteristic of the monitor equal
331. he reference scan data 0 phase encoding off 1 phase encoding on 2 Do the following procedure to store the reference scan as the first dataset so that it can be used for subsequent data analysis The reference scan is used to generate the phasemap file which is used to phase correct EPI datasets Enter go to acquire the data b Enter svf file to save the data where file is the name of the file to be to save the data Enter epiph to generate the phasemap file from the reference scan d Enter epift index to process and display the image in array number index Displaying and Manipulating Images You can display and interactively manipulate the image by using dconi Viewing Images You can view the data with the ImageBrowser To run ImageBrowser enter browser on a UNIX command line Before you can view image data first convert the data with the episvib macro episvib expects the first image to be the reference scan 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 61 Chapter 3 Imaging Pulse Sequences Zero Frequency Spike EPI data is usually collected using nt 1 Therefore any imbalance dc offset between the real and imaginary quadrature signals after Fourier transformation generates a zero frequency spike in the resulting image To remove this artifact enter dermv y If nt is set to a multiple of 2 the phase cycling schemes in the pulse sequence eliminate the artifact In this case enter dermv n 3
332. he window All intensities below the value at the cursor are unused or zeroed in any of the segmentation functions Press the left mouse button again to draw another cursor All voxels with intensities outside the intensity region delimited by the two cursors are segmented out of the image Define the segmentation range by entering the desired ranges into the Image segmentation keep range Min and Max fields Note that these values also change as the cursors are moved around in the histogram Move the cursors by holding down the left mouse button and dragging the cursors Delete the segmentation cursors by clicking on them with the middle mouse button Select the Show segmented region box to interactively adjust the segmented region This option updates the color map and places blue pixels wherever a pixel lies below the desired intensity range and places orange pixels wherever a pixel lies above the desired intensity range These colors can be changed in the colormap init file Because this option is changing the color map all the images in the graphics region are affected not just the image containing the ROI However the segmentation display is only correct for images with the same vertical scale as the image with the selected ROI Once the desired intensity ranges have been picked the image can be segmented by zeroing all the pixels in the image outside the selected intensity range Alternatively the ROI can be segmented within the i
333. hen the stack of slices correctly overlays the scout image click on Exit select the target experiment from the list and transfer the image prescription by clicking on the appropriate menu button To exit from the planning process without making any changes to a target experiment press Return on the keyboard VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Appendix A Commands Macros and Parameters Sections in this appendix e A 1 Setting the Path to Imaging Macros this page e A 2 Macros for Setting Up Experiments page 256 e A 3 Macros for Planning Experiments page 273 e A 4 Commands and Macros for Processing and Display page 278 e A 5 Parameters page 306 e A 6 Image Browser Commands Not in VNMR page 345 This appendix summarizes commands macros and parameters necessary or at least particularly useful for imaging experiments For a list of entries refer to the table of contents at the front of this manual In the section Commands and Macros for Processing and Display page 278 commands are identified by the code C at the end of header line and macros are identified by the code M All commands and macros are entered on the VNMR command line The code letter U at the end of the header line e g U or M U means the command can be entered on a UNIX command line Note that the UNIX syntax is always different from VNMR syntax There is an important di
334. hest between the forelegs of most animal subjects 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 207 Chapter 9 Physiological Gating Module 208 The upper chambers of the heart are called atria and are respectively referred to as the left and right atria The lower chambers of the heart are called ventricles and are referred to as the left and right ventricles The function of the atria is to receive blood from the vena cava great vein and pulmonary vein to contract and pump blood into the respective ventricles The vena cava supplies deoxygenated blood from the Inferior body to the right atrium and the Vena Cava pulmonary vein supplies oxygenated blood from the lungs to the left atrium Aorta Pulmonary Right Left Ventricle Ventricle Figure 99 Cardiac Anatomy After atrial contraction the ventricles contract and pump blood into the pulmonary artery and the aorta great artery The right ventricle supplies blood to the pulmonary artery and the left ventricle supplies blood to the aorta The heart chambers and associated blood vessels are all visible in cardiac gated NMR images The assignment of the ventricles from their appearance in images is quite simple The left ventricle is usually the largest chamber of the heart and a substantial thickening of the heart wall is observed as it contracts The right ventricle is the next largest chamber and possesses a thinner wall than the left ventricle Both ventricles can be
335. hich then manages the entire experiment through real time loops and pulse sequence elements All data that is accumulated in the real time loops is retained in the acquisition data memory until the experiment or array element is complete at which time it is sent back to the host There is no timing overhead associated with a real time loop and extremely short timing intervals can therefore be achieved with the compressed mode Compressed data acquisition is controlled by the parameter n f following the single rule that the number of points acquired must be nf np Experiments can be run completely in arrayed acquisition mode or completely in compressed acquisition mode or in a combination of the two set loop uses the seqcon parameter to determine which acquisition loops if present are arrayed and which are compressed It then computes nf as the product of all compressed loop counts and sets ni appropriately as either nv in the case of uncompressed phase encode or zero in the case of compressed phase encode Each of the parameters ne ns nv nv2 and nv3 have corresponding underscore macros that execute setloop for example _ne set Loop is thus a lower level 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 267 Appendix A Commands Macros and Parameters setof Description Related Syntax Related setorient Description setgpe 268 Syntax Related Syntax management macro that is automatical
336. i spsi stheta Euler angles for saturation band orientation P vorient Voxel orientation P 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 329 Appendix A Commands Macros and Parameters sphi spsi stheta Euler angles for saturation band orientation Description Euler angle parameters used to define saturation band orientation Descriptions and definitions are equivalent to vphi vpsi and vtheta Related sorient Saturation band orientation P vphi vpsi vtheta Euler angles for voxel orientation P Frequency Offsets and Spectral Widths Predefined frequency offset parameters are provided to cover the majority of common applications such as water suppression magnetization transfer or chemical shift selection All of these frequency parameters have units of Hz and are created in VNMR as frequency type parameters Most vertical bore microimaging systems have frequency resolution of 0 1 Hz while most horizontal imaging systems have frequency resolution of 1 Hz Some pulse sequences may use certain frequency offsets differently than others that is in some cases a frequency offset parameter may be an absolute offset from the base spectrometer frequency and in other cases it may be a delta or relative offset from some other reference frequency Frequency Parameters chessfrq Chemical shift selective pulse frequency Description Frequency offset parameter for use in specifying the frequency for a chemical resto shift s
337. ich is normal Enter make depend whenever you change include directives ina file or change the makefile itself 4 Enter make fit to create the new version of the fit program You do not need to exit Image Browser to define new functions Whenever you click on the Execute button in the Image Browser Math Panel the current version of fit is loaded and executed Function Definition Files By convention your fitting files should be named xxxfit c where xxx is the type of fit For example the file t 1 it c is divided into two sections with preprocessor directives ifdef FUNCSELECTION first section else second section endif The first section contains a fragment of C code that selects the type of fit several macros are defined to make the job easier Macros are indicated by ALL CAPITAL letters The following example is taken from t1fit c IF_FITCODE t1 N_PARAMETERS 3 FIT_TYPE NONLINEAR FUNCTION exp_function JACOBIAN exp_jacobian GUESS exp_guess 122 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 PARFIX return TRUE 5 4 The Fit Program tl_parfix These macros are defined in the following table IF_FITCODE E N_PARAMETE RIT_WTYPE FUNCTION JACOBIAN 01 999163 00 A0800 RS Compares your fit type string to a given string and executes the following lines enclosed by braces if the
338. ics to the Info Messages window stat_print filepath orstat_print filepath w writes the statistics directly to the file rather than to the Info Messages window The format is similar to format used in the window except that the printed file is not truncated This command deletes any previous contents of the file If i 1epath is not an absolute path the contents of the Info Messages window are saved in the directory that was open when Image Browser was started stat_print filepath a issimilarto stat_print filepath except that output is appended to the previous file contents stat_update Updates statistics in the Statistics panel stat_xcoord roi z area volume integrated mean median min max sdv Suser Sets the x coordinate of statistics display for multiple ROIs stat_ycoord area volume integrated mean median min max sdv Sets the y coordinate of statistics display for multiple ROIs rotate 90 180 270 flip flipO f 1ip45 flip90 f 1ip135 Rotates or reflects images in selected Gframes The first three arguments rotate an image counterclockwise by specified amount in degrees flip number arguments reflect an image through an axis perpendicular to a specified direction A number specifies the direction of the corresponding double headed arrow in the Rotation panel The argument flip is equivalent to flip0 Startup Macro When Image Brows
339. ies either double click on a directory selection or click on a selection to put the directory name onto the top line and then press the Return key The full directory name also can be typed followed by pressing Return The identifier operates the same as the in the C Shell CSI loads VNMR data files differently than ImageBrowser To load a phasefile in ImageBrowser select the directory containing the phasefile then select LOAD e To load raw data In CSI move to the directory where the fid file is located select the file named fid then select LOAD To load FDF files select the file with the data then select LOAD See Files and Other Items page 104 fora more complete description of the FileBrowser Using Command Panel Menus Figure 54 shows the command panel with its set of basic command options Figure 54 CSI Command Panel Options with an arrow V have menus that are activated by the right mouse button or the left mouse button can be used to select the default choice The action of these submenus can process data open a window etc depending on the functional operation Most functions are self explanatory and are explained in this section or later in other sections of this manual Creating and Manipulating Graphics Frames Graphics frames are a variety of graphics objects Perform the following steps to create and manipulate frames 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 135 Chapter 6 CS
340. ieving Gframes Gframe files are stored into and retrieved from the directory BROWSERDIR gframe or a subdirectory of gf rame Gframes are retrieved with the same size and positions with which they were stored They are not adjusted to fit the size of the graphics window If any of frames are entirely outside the current graphics region or overlap with existing frames those frames are not loaded To store Gframes e Select the Save menu in the Frame Properties menu To retrieve Gframes e Select the Load menu in the Frame Properties menu Deleting Gframes To delete graphics frames on the screen e Select the Delete option in the Frame Properties menu to delete all the frames on the screen You can also delete all of the selected frames all the unselected frames or all the frames without images Clearing Gframes To clear images out of the Gframes VNMR 6 1C User Guide Imaging 01 999163 00 A0800 4 2 Getting Started e Select the Clear command in the Frame Properties menu The Clear command has several options it clears all frames clears selected frames or clears unselected frames Using File Browser Many functions that read or write user selected files use the File Browser tool The initial File Browser directory is the directory in which Image Browser started Changing Directories To change directories do one of the following actions e Double click on a directory selection e Click on a select
341. ifted Note that reconstruction artifacts might appear if the spin echo appears too left shifted 5 Set the recovery time parameter t r to the value you want In the case of pure T weighting as well as for sr and ir T weighting setting tr is a compromise between total measurement time and full T relaxation For T weighting using aps tr can be set to the time value currently measured because the aps sequence completely dephases the magnetization on its own Starting the Measurement Enter go to start the measurement Other Excitation Schemes The remainder of this section shows the use of pulse sequences for the different excitation schemes Where applicable further parameters to control the operation are described Volume Based BP Acquisition As indicated in Figure 117 each pulse sequence consists of a preparation phase indicated by A and the image acquisition phase indicated by B VNMR 6 1C User Guide Imaging 01 999163 00 A0800 10 4 Routine Usage se ms ie Figure 117 Phases A Preparation and B Acquisition The preparation phase A takes the recovery time t r and any NMR weighting applied with sr ir and aps The acquisition phase B starts with a period of time t rise covering the switching of the gradients It continues with two rf pulses usually a 90 dx 180 sequence selective or nonselective according to the selection bp2ds or bp2d and bp3d The spin echo time te is determined by dy an
342. ilarly nvars is not used because exp_function only deals with one independent variable JACOBIAN is the second routine Given vectors of parameter values and x values JACOBIAN calculates the partial derivative dy dp at each x value for each parameter Note that it returns what looks like the transpose of the Jacobian as it is usually defined 01 999163 00 A0800 125 VNMR 6 1C User Guide Imaging Chapter 5 Image Browser Math Processing This transposition is the result of the underlying fitting routines which are derived from Fortran routines Compared to C Fortran stores arrays in transposed order Figure 50 shows the definition of a JACOBIAN routine static void exp_jacobian int npoints Nbr of data points int nparams Nbr of parameters float params nparams parameter values int nvars float x Number of indep variables npoints nvars values of indep vars float dydp Derivative values OUT int i for i 0 i lt npoints itt dydp 0 i 1 dydp 1 i exp x i params 2 dydp 2 i dydp 1 i x i params 1 Figure 50 JACOBIAN Definition The third routine is the GUESS function which is required for nonlinear fits and is usually the most difficult routine to define Accurate first guesses will usually speed up the fit considerably as well as ensure that it does not converge to a spurious local minimum Since the guess algorithm is idiosync
343. ile can be generated by simply calculating the absolute value without the need for any phase correction An echo signal can be generated by first VNMR 6 1C User Guide Imaging 01 999163 00 A0800 2 4 Frequency Encoding dephasing the excited spins by using a readout gradient pulse and then rephasing the spins by reversing the sign of the gradient When the area of the rephasing gradient equals the area of the dephasing gradient a gradient echo is formed as shown in Figure 10 lt i tr _ JdToH _ A te p te AN VA gss Refocusing gradient lt _ at gt ta ts gro tig tg ty toti a gt ADC Dephasing gradient i A NIV A y v Gradient echo Figure 10 Readout Gradient and Gradient Echo The readout gradient is applied during the acquisition time at so that the echo appears at the center of the acquisition window a condition that is assured if the shaded areas in Figure 10 are equal as shown in the following equation t4 te Eq 11 gro dt gro dt a l5 The Fourier transform of the echo signal gives the profile along the readout direction only the signal from the selected slice contributes to the profile The sequence shown in Figure 10 is commonly used to observe the profile during the initial setup of imaging experiments The profile can be very useful in doing the following procedures e Positioning the sample along the readout direction e Checking or
344. iltering tool Weighting and Filtering Tool The Weighting and Filtering tool allows weighting functions to be interactively set and applied to individually selected spectra This tool is used in conjunction with the spatial and spectral reconstruction processes When the Weighting and Filtering tool is selected three windows open in the selected frame The top window contains the transformed data the middle the filtering weighting function and the bottom the untransformed data Use the mouse buttons to control the shape and position of the filtering functions SELECT in the weighting function window Adjusts the Time Const field ADJUST in the weighting function window Adjusts the Shift Const field This tool works on two types of data e Raw Data Spatial Filtering If no data exists in the currently selected frame spatial filtering is selected when the tool is entered The spatial filtering tool is quite limited regarding the data that is used Only the voxels making up the midpoint of the data in the x fast direction are selected After data has been selected filtering functions in the Spatial Reconstruction window Point f1 Filter Type Time Const Shift Const Delay can all be interactively selected to adjust the filter applied to the data e Localized FID Data Spectral Filtering For processing localized FID data into spectral data a spectrum must exist in the selected graphics frame This is the default
345. imation Image Browser provides an option to sequentially display images in a single Gframe This option allows images to be browsed or an animated image to be produced similar to a movie Macros Image Browser incorporates the MAGICAL II macro programming language MAGICAL can greatly speed up work that involves repetitive tasks Display Control Various image display parameters can be manipulated with some of the graphics tools For example the vertical scale tool controls the intensity and contrast of the display and the zooming tool allows part of an image to be seen in more detail Data Formats Image Browser supports two input data types VNMR phasefile format and Flexible Data Format FDF Because of limitations in the phasefile format using FDF is preferred A number of data formats are supported for output 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 67 Chapter 4 Image Browser 4 2 Getting Started This section describes the process of verifying the correct user environment starting Image Browser and performing some of the basic functions User Environment Image Browser has been designed to run in an X Window System environment This means that any X terminal can be used as the user interface as long as it supports the 8 bit graphics However for Image Browser version 5 3 the host system that runs Image Browser must be a Sun SPARC workstation running Solaris 2 3 or higher If your X Windows manager does not
346. imple check to prevent it from being executed more than once in an experiment on the same data set The check looks for the parameter flash_converted created by flashc when it is run In order to rerun flashc you must remove the parameter with the following commands destroy flash_converted destroy flash_converted processed 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 45 Chapter 3 Imaging Pulse Sequences 46 Arrayed or Multislice Compressed Data In previous versions of VNMR arrayed or multislice compressed images seqcon nscnn had to be reformatted to a standard 2D format and f lashc had to be used before the t 2d routine could be performed on the data Now this method is no longer necessary By using the command ft 2d nf lt index gt you can improve processing time by reformatting data from the standard format to the compressed format However for compressed compressed 2D data seqcon nccnn you must run flashc orflashc nf 3D Data Sets flashc is not needed for 3D data sets Use the ft 3d routine on standard compressed data seqcon nncsn or compressed compressed 3D data seqcon nnecn Compressed compressed or Standard to Compressed Format When ft2d nf lt index gt is used you need to use flashc only when converting a compressed compressed multislice multiecho or multi image sequence However for a large standard multislice experiment seqcon ncsnn converting
347. in the VNMR graphics window The single or multislice data is also reconstructed into Flexible Data Format FDF files for viewing by ImageBrowser These files are put in expn datdir with the names bp2d000 fdf bp2d001 fdf bp2dnnn fdf 10 4 Routine Usage This section describes the functionality provided by the BP imaging package and includes an overview of the NMR excitation schemes implemented with the package NMR Excitation Schemes The BP package provides a variety of different NMR excitation schemes slice and volume and weighting of the signal obtained with NMR parameters T2 T1 or T1 p etc Table 20 lists the schemes implemented Table 20 Implemented NMR Excitation Schemes NMR Weighting Parameters Probe Excitation Sequence Preparation Imaging BP Imaging Result slice bp2d T2 one or more image slices volume slice bp_image T sr ir aps T2 one image slice volume slice bp_image Tlrho T2 one image slice volume bp3d T2 one image slice volume bp_image T sr ir aps T2 one image slice volume bp_image Tlrho T2 one image slice volume bp3d T2 volume volume bp_image T sr ir aps T2 volume volume bp_image Tlrho T2 volume T gt weighting of the NMR signal a spin echo in the imaging case is achieved by setting the echo time te in the imaging phase T and T p weighting are performed in a preparation phase prior to the imaging phase In the case of T weighting three different excitations
348. in the sagittal plane orient zyx along the center plane of the magnet This plane should correspond to the central plane through the subject In order to obtain this image in the gated mode set the value of the parameter ticks as ticks 1 Set the delays rcvry and hold to zero Choose the value of d1 so that it is greater than one heart period Choose all other parameters as appropriate for a single slice scout image Once the sagittal scout image has been obtained slice positions for coronal or transverse images can be selected The scout image should show a diastolic heart located in the chest cavity above the liver The position of the ventricles should be readily apparent Target images can be obtained in the desired plane by adjusting the parameters in the normal way Images of the heart in the diastolic phase can be obtained with value of the hold delay equal to zero or slightly less than one heart period Using a setting of the heart period minus the P to R wave interval for the parameter ho1d allows images with the both the atria and the ventricles in the diastolic state to be obtained Images of the heart in the systolic phase can be obtained by using a value of the hold delay equal to the R to T wave interval in the ECG signal Images of the heart throughout the cardiac cycle can be collected by acquiring images separately rather than by arraying the hold parameter Multislice Spin Echo Imaging Multislice images can be obtained
349. incorrectly referenced resto parameter which in turn could result in positional errors in images homo Enables time shared homonuclear decoupling and should generally be set to n for imaging experiments 1 2 Using the Scout Image to Plan a New Target Image 22 Now that you have acquired the first scout image let s use it to locate a new target image that it includes whatever features you are interested in observing You can skip many of the steps we had to go through to get the scout such as rf calibration determination of resto etc because these do not change from the scout to the new target image Moving the Parameters to New Experiment You need to copy the parameter set you have been working with to another experiment the target experiment You do not have to do this as the first step but you need do it eventually so let s get it out of the way It is possible to both plan and acquire the target image in the same experiment but then the scout image is lost which we might want to use again to plan a different target To make the copy enter mp new_exp This moves the entire imaging parameter set to the designated experiment For purposes of this example and the rest of this chapter VNMR 6 1C User Guide Imaging 01 999163 00 A0800 1 2 Using the Scout Image to Plan a New Target Image assume that you have been working in experiment 2 to acquire the scout image and wish to use experiment 6 to acquire the targ
350. indows 6 5 Files and Other Items This section describes file input and output and the error and information displays FileBrowser The FileBrowser is a standard interface used for storing and retrieving files It is always used when saving files It is also always used when retrieving image files The Gframe ROI and Filter interfaces use the FileBrowser for saving files but do not use it for retrieving files because the Load interfaces are built for quick access and always assume a specified directory For more information about the particular directory for these interfaces see Tools page 147 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 167 Chapter 6 CSI Data Processing 168 Figure 77 is an example of a FileBrowser window for loading images The basic window is the same for most operations The title of the window in this case FileBrowser Data describes the use Ss export gauss chris ib RABBIT of the current File Browser window pe File Browser Data Load File From Load Load All image0002 fdf uf In the case of loading movie images image0001 fdf the title is Movie Frame Loader for image0002 fdf ROIs it is FileBrowser ROI When SBER p imageooo4 files are saved Load is replaced by image0oos fdf Save Load All does not change image0006 fdf because there is no corre sponding image0007 fdf Save All command image0008 fdf imageooos fdf The FileBrowser displays the image0010 fdf
351. ine involves extra work but the routine might be an advantage over having to specify different functions for fits that are equivalent but use different parameters return TRUE Must be entered before the closing brace Additional information can be included before the return TRUE statement as shown in a fragment of the shamesfit c file in Figure 48 In this fragment FIT_TYPE is made to depend on the number of image vectors passed and additional numerical parameters on the command line after the threshold value are used to set values of variables used in calculating the function Note that the nbr_params variable is set to the number of numerical values on the command line after the threshold value User variables are defined in the second section as static local to the current file However on compilation all your xfit c files are combined with fit c into one file so names should be unique among all fitting functions The second section in an xxxfit c file contains the user supplied functions that are mentioned in the first section First there is FUNCTION which calculates the values of your fitting function FUNCTION is the only routine needed for any of the varieties of linear fits It calculates a vector of y values given a vector of x values and a vector of parameter values Figure 49 is an example Note that the nparams variable is not used in this routine because exp_ function is only used for three parameter f
352. ing attributes Local Peak Picking Local Peak Picking is performed the same way as for the Peak Sampling mode in baseline correction It works on a selected spectrum in a selected Gframe One and only one Gframe can be selected The following list describes the functions of the attributes that appear in the Local Peak Picking portion of the Mmap calculation window e Sampling Mode Manual Automatic If Manual is selected use the Picking tool otherwise select Automatic e Prior Knowledge If Use is selected the correct PK File must be selected e PK File selects a set of predefined peaks These files are located in the CSI initialization directory under PEAK Standard files have been set up but additional peak files can be defined the user e Sampling Go finds the peaks in the spectrum and displays markers at each peak e Edit OK registers the peak information from the picking markers in the selected spectrum These markers might have be added moved or deleted after the Sampling Go process was performed To perform automatic peak picking 1 Click the Sampling Go option 2 Load a voxel spectrum into a selected Gframe 3 Use the Picking tool to modify selected peaks and then click Edit OK to register these peaks Alternatively desired peaks can be selected by using the Picking tool without using any automatic peak picking Peaks must be selected for the curve fitting routines to work Local Specification Local Sp
353. ing choices used to define new slice or voxel targets for imaging and localized spectroscopy experiments The menu allows graphical selection of new target slice or voxel positions and orientations from a scout imaging experiment and transfer of this information to the target imaging or localized spectroscopy experiment transfer Move field of view information to a target experiment M Store marked positions for planning target imaging planes slicemark lt reset gt Stores the locations of points selected during the planning of new imaging plane positions and orientations in the parameter t_mark slicemark is called by the Mark button in the Slice planning menu and is not normally executed from the command line reset is a keyword to clear any previously marked positions by zeroing t_mark Target Parameters page 341 plan Interactive slice and voxel selection M Reorder slice position list sliceorder lt a d i gt 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 275 Appendix A Commands Macros and Parameters Description Arguments Examples Related sliceplan Syntax Description See also Related transfer Syntax Description Arguments Reorders the list of physical slice positions pss in ascending descending or alternating odd and even order Alternating order is often used for multislice excitation to separate physically adjacent slices in time to reduce sat
354. ing dy to a minimal value In this case the acquisition starts directly after the refocusing rf pulse Because of this time constraint the signal typically shows a small FID on the left side which results from the imperfections of the pulse In the Fourier transform this FID originating from the leftmost part of the signal is transformed to a high frequency modulation of the profile Since the FID is similar for all projection angles the modulation is similar as well After reconstruction a 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 245 Chapter 10 2D and 3D Backprojection 246 Figure 127 Saturation in First Projection circular or spherical modulation is obvious in the slice or volume Figure 128 shows an example ae Figure 128 Circular or Spherical Modulation To solve the problem perform the following corrective actions e Increase the spin echo time te and move the spin echo to later time regimes to the right The loss in signal to noise must be compensated by a longer measurement time e If anew acquisition of the data is not possible use a weighted FT which reduces the effect of the residual FID Image Intensity Modulation The image intensity gets modulated as shown by the example in Figure 129 if several projections are faulty The following conditions might cause modulation e Gradient switch off during acquisition because of an overrange situation detected during the acquisition in th
355. ing parameters 59 interleaved sequences 58 limitations 52 56 phase coherence lost 52 phase correction 57 pulse sequence 53 54 sequence variations 58 time course experiments 58 waveform shapes 58 EPI experiments acquisition delay time 317 control phase encoding gradient 313 data collecting 283 echoes centering 317 effective echo position 283 EPI data displaying and processing 283 image displaying 283 image processing 283 images in FDF saving 284 number of EPI images to collect 313 parameters setting up 284 phase file generating 283 readout dephasing gradient adjuster 312 readout gradient adjuster 311 readout gradient dephaser 283 reverse spectral data 283 VNMR 6 1C User Guide Imaging 349 Index slice gradient calculating 300 slice selection parameters calculating 300 EPS file format 107 equilibrium magnetization 40 Error Messages option 171 Euler angles 24 parameters 20 set imaging orientation 268 excitation pulse length calculating 63 shape specifying 63 excitation schemes pulse sequences 236 exp xpan file 197 exparray macro 51 62 257 experiment control parameters 333 experiments acquire and Fourier transform 290 animal preparation 217 counters 333 hardware preparation 216 macros and parameters 32 obtain cardiac gated images 221 repetition time 318 retrieve FIDs from a file 264 retrieve parameters from file 264 save FIDs 301 save parameters 302 set
356. ingly Offset frequency is saved in the global frequency file SHOME vnmrsys Hloffset by the setof macro movetof Sets tof parameter to that specified by cursor offset Sets frequency offset corresponding to cursor location plan Defines slice parameters using a reference image pulsecal Loads rf pulse power calibration parameters rt Retrieves FIDs from filename fid directory rtp Retrieves parameters from filename par directory s2pul Loads default single pulse sequence parameters setarray Sets an array of values for a given parameter 62 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 3 6 Commands Macros and Parameters Table 5 Imaging Pulse Sequence Commands Macros and Parameters continued setgn Sets receiver gain setof Sets spatial reference position spuls Loads default single pulse sequence parameters relevant for imaging svf Saves current parameters and FID data in filename fid directory svp Saves current parameters in filename par directory Parameter Function d1 Sets first delay length in standard two pulse sequence and other pulse sequences fliplist Contains a list of pulse flip angles in degrees fn Selects Fourier number in read dimension fnl Selects Fourier number in phase dimension gcoil Specifies physical gradient set currently installed and allows updating of gradient characteristics gcoil is a database file containing gradient calibration values from the vnmr imaging gradtables di
357. initial system installation so first check in the gradtables directory for an entry appropriate for your system Because a gradient calibration file is a text file containing the maximum gradient strength rise time and usable bore size for the gradient coil a new file can be created manually with any text editor or most easily with the macro creategtable as follows 1 Onthe VNMR command line enter the command creategtable The following prompt appears Are all gradient axis calibrated to the same maximum value y n 2 Ifyou respond y you are asked to give a name to the file Respond with The letter m for a main gradient coil file name e The letter h for an hpag file name The letter o if you want to define another name If you respond with o you are asked to enter a name 3 Enter a brief description of the gradient coil to help in identifying this gradtables entry in the future for example Main Actively Shielded Gradient 4 Enter the usable bore size in cm for this gradient set This value is used only as an internal check of reasonableness for the field of view 5 Enter the maximum gradient strength in gauss cm for the gradient set 6 Enter the rise time in us Remember that Varian gradient hardware is installed with a linear slew rate limitation that is dependent on the gradient set The new gradient calibration is now ready to use but first the configuration parameter sysgcoil must
358. inversion time delay results in varying signal intensities depending on the t i of the spins Notice that the signal is negative at short inversion times and gradually becomes positive at longer inversion times When ti 0 69 T the signal is zero as shown in Figure 16 If the sign of the intensities is to be retained in the images it is necessary to phase correct the images instead of taking the absolute value mode ti ir imaging experiments can be inefficient because of the long recycle time required to allow the spins to return to equilibrium VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Chapter 3 Imaging Pulse Sequences Sections in this chapter e 3 1 Initial Setup this page e 3 2 Conditions for Use page 42 e 3 3 GEMS Multislice Imaging page 44 e 3 4 Obtaining a GEMS Image page 49 e 3 5 Echo Planar Imaging and Phase Correction Map Files page 51 e 3 6 Commands Macros and Parameters page 62 This chapter describes some pulse sequences for imaging available on Varian NMR spectrometers You should be familiar with basic operations of the spectrometer therefore explanations of operations such as shimming and tuning are not included in this chapter Refer to the manual Getting Started and the VNMR User Guides for more information on various spectrometer operations More detailed descriptions of all commands macros and parameters are in the appendix Commands Macros and Parameters of
359. ion to put the directory name onto the top line and then press the Return key Enter a full directory name followed by a Return You can use the identifier in the same manner as in the C shell to represent your home directory Saving Images from VNMR for Image Browser Images can be saved from VNMR by joining an experiment in VNMR with image data and then running a macro that saves an image or multiple images to disk For current imaging pulse sequences SEMS MEMS SEDIFF FLASH etc the macro is svib directory For example entering svib mydata on the VNMR command line creates the directory mydata dat in the current VNMR directory One or more images can then be saved in mydata dat Images are named image0001 fdf image0002 fdf image0003 fdf etc For older SIS imaging pulse sequences and microimaging pulse sequences IMAGE SHORTE SSFP etc the macro for saving images is svsis directory Thus entering svsis mydata on the VNMR command line creates the mydata dat directory in the current VNMR directory Images can then be saved in mydata data as image0001 fdf image0002 fdf image0003 fdf etc If svsis does not know about the pulse sequence edit the macro to define the sequence name and type 3D image data sets can be transformed and saved in FDF format with the ft 3d macro If no image data is available on the system a file named image 4T fid in the directory vnmr fidlib can be retrieved You can then sav
360. irectly found as an argument to the pulse sequence statement delay Instead te is used to determine smaller delays and events whose sum results in the requested te However there is no general rule regarding which parameter is directly used and which is indirectly used in internal calculations dl First delay Description Length of the first delay in the standard two pulse sequence and most other pulse sequences This delay is used to allow recovery of magnetization back to equilibrium if such a delay is desired Values On MERCURY systems 0 0 2 us to 150 000 sec On GEMINI 2000 systems 0 to 4095 sec smallest value possible is 0 2 us finest increment possible is 0 1 us On systems with a Data Acquisition Controller board 0 to 8190 sec smallest value possible is 0 1 us finest increment possible is 12 5 ns On systems with a Pulse Sequence Controller or Acquisition Controller board 0 to 8190 sec smallest value possible is 0 2 us finest increment possible is 25 ns On systems with an Output board 0 to 8190 sec smallest value possible is 0 2 us finest increment possible is 0 1 us Refer to acquire statement in the manual VNMR User Programming for a description of these boards Related alfa Set alfa delay before acquisition P d2 Incremented delay in 1st indirectly detected dimension P d3 Incremented delay in 2nd indirectly detected dimension P pad Preacquisition delay P hold Post trigger delay Description Delay parameter
361. is database file has the same name as the macro pul secal1 is used for automated setup of rf pulse powers in imaging and localized spectroscopy experiments The desired entry in the pulsecal file is selected with r coil and provides the automated setup routines with information about the 90 pulse power performance This information is used to compute the power levels required by all pulses found in plist Each user has a private pul seca file found in the vnmrsys directory If a pulsecal file does not already exist pulsecal creates it when the first entry is made Some form of pulse length or power calibration data is required to provide the information necessary to create a new entry in pulsecal This could be a simple 90 pulse length array using s2pul an array of pulse power levels or a more advanced calibration using an imaging or localized spectroscopy experiment tpwrcal for example Once an entry is made it is used to determine pulse powers for a wide range of pulse lengths and shapes in all imaging and localized spectroscopy experiments As long as the computed power levels remain within the linear performance range of the system typically below tpwr of about 60 these power levels should be as accurate as could be determined through individual optimization 262 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Arguments Examples Related rescal Syntax Description Arguments Related A 2 Macros fo
362. is selected the filtered image overwrites the source image VNMR 6 1C User Guide Imaging 01 999163 00 A0800 4 4 Data Processing Histogram Enhancement Images can be enhanced using histogram methods Select the Image Histogram Enhancement option from the Process menu to open a Histogram Enhancement window as shown in Figure 41 The histogram function performs equalization low intensity Figure 41 Histogram Window enhancement high intensity enhancement and hyperbolization The function works by looking at a histogram of the intensities and enhancing the intensity histogram according to the selection Cursor and Line Functions Click the right mouse button on Cursor Data in the Process menu to obtain cursor distance and intensity information The popup window is blank until a point ROI is drawn Cursor Data Cursor Data uses the point ROIs when obtaining information and provides point intensities coordinates and the distance between the just selected or drawn point and the last selected point The cursor function is most useful for searching for distances between slices in a multislice experiment or between slices in two different experiments as long as the location information is present in the header of both images Figure 42 shows a Cursor Data window Coordinates provide the ee et absolute position of the cursor in Intensity 0 01023 the magnet reference frame Coordinates 1 445 4 366 2 133 cm Projected
363. is the most general form for specifying an image vector image_list image_list is a list of frame numbers separated by commas and optionally including ranges of frame numbers denoted by hyphens For example the statement 11 maxof 1 3 8 10 6 returns the maximum of images 1 3 8 9 10 and 6 The simple 3 notation as used in Image Browser Math Expressions specifies a vector with one element and is equivalent to 3 If the vector only contains one range of consecutive frame numbers it can be abbreviated as 1 10 Be aware that a construction like 1 3 8 9 10 6 does not specify a vector of images but rather six vectors each containing one image Some programs such as maxof can treat the two cases identically but others such as fit discussed on page 120 do not Image Browser Math Functions can also produce more than one output image In such cases the output images must be specified as an image vector 11 12 maxof 1 10 In this example maxof writes the maximum intensity image to frame 11 and writes a map of which image had the maximum intensity for each pixel in frame 12 Note that the following construction produces only one output image the 12 frame is ignored 11 12 maxof 1 10 In summary a vector of images can be specified three ways e 1 specifies a vector with one element e 1 10 specifies a vector with a single range of image numbers e 1 10
364. istogram display appearance 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 91 Chapter 4 Image Browser 92 Match Segmentation Uses the Image segmentation keep range defined by histogram Limits cursors whose values are displayed by the Min and Max entries see Figure 34 The default range limits infinity infinity are the same as those in Span ROI Intensities In this mode statistics values depend on segmentation limits because the only pixels being used to generate statistics are pixels whose intensity values lie within the image segmentation keep range Narrowing the segmentation limits decreases the calculated area when statistics are updated Specifying the Intensity Range Select the User Specified option to enter limits for the intensity range of the pixels selected for statistics and histogram display To get greater resolution in the histogram modify the Histogram bins entry A region with finer resolution can expanded and a search for intensity patterns within a large grouping of intensities can be run To update the histogram and the statistics after the limits have been changed or the number of bins has been changed select the Update option Segmenting Images You can perform simple image segmentation functions by using the histogram display in the Statistics window After a histogram is displayed position the cursor within the Histogram window and press the left mouse button to draw the min cursor in t
365. ition to define the frequency This provides a convenient method of moving the transmitter frequency outside the current spectral window cr Cursor position in directly detected dimension P minsw Reduce spectral width to minimum required M movesw Move spectral window according to cursors M tof Frequency offset for observe transmitter P Move imaging readout position movepro Sets the readout position for an image or image projection to a point defined by the position of the cursor the cr parameter movepro works with either a 1D display a projection or trace along F2 or 2D display in either single cursor or box modes only the position of the cursor in the F2 readout dimension is used the position of the cursor in the F1 phase encode dimension does not matter movepro determines the position of the cursor relative to the gradient origin and sets the parameter pro to this value independent of image orientation Because pro is measured in dimensional units like mm or cm and cursor position is stored internally in hertz movepro works in Hz taking into account any spectral referencing that might have been set and converts to cm or mm to assign the value of pro To use movepro 1 Display an image image projection or trace 2 Move the cursor to the position along the readout axis you desire to be at the center of the next image acquisition and 3 Enter movepro 260 VNMR 6 1C User Guide Imaging 01 999163 00 A0800
366. its If you were fitting an nth VNMR 6 1C User Guide Imaging 01 999163 00 A0800 5 4 The Fit Program ifdef FUNCSELECTION IF_FITCODE Shames2 N_PARAMETERS 2 FUNCTION shames_function switch nbr_image_vecs case 1 FIT_TYPE LINEAR FIXED break case 2 FIT_TYPE LINEAR_RECALC_OFFSET break default FIT_TYPE LINEAR_RECALC break if nbr_params gt 0 alpha in_params 0 if nbr_params gt 1 sbv0 in_params 1 if nbr_params gt 2 hct in_params 2 return TRUE else not FUNCSELECTION Constants static float static float static float alpha 0 136 sbv0 0 13 het 0 37 for Shames model Time Const for Initial value of Hematocrit CA plasma signal decay CA plasma signal Figure 48 Fragment of shamesfit c File static void exp_function int npoints int nparams float params int nvars float x float y gt int i for i 0 i lt npoints itt yli params 0 params 1 Nbr of data points Nbr of parameters NOT USED nparams parameter values Number of indep variables NOT USED npoints nvars values of indep vars Function values OUT exp x i params 2 Figure 49 FUNCTION Specifications order polynomial for example npa rams would specify the order Sim
367. ive 2D data display C dcrmv Remove dc offsets from FIDs in special cases P fpmult First point multiplier for np FID data P fpmult1 First point multiplier for ni interferogram data P 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 289 Appendix A Commands Macros and Parameters ftnf ga 290 Syntax Description Examples Related Syntax Description Arguments ftid Fourier transform along f dimension C lsfid Number of complex points to left shift np FID P lsfid1 Number of complex points to left shift ni interferogram P lsfid2 Number of complex points to left shift ni2 interferogram P lsfrq Frequency shift of the fn spectrum P lsfrql Frequency shift of the n1 spectrum P lsfrq2 Frequency shift of the n2 spectrum P parfidss Create parameters for time domain solvent subtraction M phfid Zero order phasing constant for np FID P phfidl Zero order phasing constant for ni interferogram P phfid2 Zero order phasing constant for ni2 interferogram P proc Type of processing on np FID P procl Type of processing on ni interferogram P proc2 Type of processing on ni2 interferogram P pmode Processing mode for 2D data P ssorder Order of polynomial to fit digitally filtered FID P ssfilter Full bandwidth of digital filter to yield a filtered FID P wftld Weight and Fourier transform f for 2D data C wft2d Weight and Fourier transform 2D data C Fourier transform data acquire
368. ively shielded gradients and additional eddy current compensation hardware are essential to minimize the residual eddy current fields Operating at high fields also has its disadvantages spurious gradient fields inhomogeneity susceptibility and eddy current related effects are enhanced at high field strengths which make experiments such as EPI more difficult Any spurious field gradients tend to distort the EPI k space data in unpredictable ways as shown in Figure 21 resulting in severely distorted images Therefore shimming and eddy current compensation often become the more dominant factors in getting good EPI images Conventional FID shimming using a single pulse sequence often leads to misleading results because the FID is an integrated signal from the whole sample within the rf coil For example if the signal from outside the slice region contains large susceptibility or inhomogeneity field gradients the shim current values are biased by those regions Therefore the imaging slice region might not be optimally shimmed To obtain the best results slice shimming is recommended The region corresponding to the imaging slice is selectively excited and the resulting FID is optimized in the usual way Low Resolution Because of gradient strength and acquisition time limitations the matrix size for single shot EPI is limited to about 64x64 or 128x128 which means that EPI images are usually low resolution Higher resolution images can be ob
369. justed to fill the screen from left to right with the entire array The parameter cut of f if it exists and is active defines the distance above and below the current vertical position vp at which peaks are truncated By arraying cutoff to have two different values the truncation limits above and below the current vertical position may be controlled independently For example cutoff 50 truncates peaks at vp 50 mm and vp 50 mm and cutoff 50 10 truncates peaks at vp 50 mm and vp 10 mm start is the index of the first spectra when displaying multiple spectra It is also the index number of a particular trace to be viewed when displaying arrayed 1D spectra or 2D spectra finish is the index of the last spectra when displaying multiple spectra step is the increment for the spectral index when displaying multiple spectra The default is 1 options can be any of the following e all isa keyword to display all of the spectra e int isa keyword to only display the integral independently of the value of the parameter intmod e dodc is a keyword that causes all spectra to be drift corrected independently dssh 1 3 User Guide Liquids NMR cutoff Data truncation limit P dss Display stacked spectra C dssa Display stacked spectra automatically C dssan Display stacked spectra automatically without erasing C dsshn Display stacked spectra horizontally without erasing C dssn Display stacked spectra without screen erase C
370. l parameters nf and ni which are used during pulse sequence execution to determine the mode of data acquisition set Loop manages the values of nf and ni as required to be consistent with the experiment parameters ne nv etc Two modes of data acquisition are supported in VNMR arrayed and compressed The difference is mainly in the timing of the flow of data between host and acquisition computers Arrayed data acquisition involves continuous communications between host and acquisition as pulse sequence instructions are sent to the acquisition CPU and data returned to the host Sun for each element in the arrayed experiment All explicitly arrayed experiments for example pw 10 20 30 run in this manner 2D experiments including most high resolution liquids and many imaging experiments also run as implicit arrays with the array size set by ni Although the communications between acquisition and host computers are quite fast a small delay typically a few msec is required to accommodate the communications and reinitialization between array elements Certain fast imaging experiments such as turboflash echo planar imaging EPI or even conventional multislice often require loop timing that is on the order of this interelement delay These experiments use a second mode of data acquisition the compressed mode In compressed data acquisition a single pulse sequence instruction set is sent to the acquisition computer w
371. l gating module See PGM pi parameter 237 238 241 242 Picking tool 155 PICT file format 107 pilot parameter 20 pixel interpolation 75 81 replication 75 81 resolution 235 Pj parameter 243 pulse 238 242 plan macro 23 32 62 63 275 plane orientation extracting 102 345 plane_decode macro 275 01 999163 00 A0800 playlist definition of a 77 generating a 78 PNG file format 107 point intensities 97 point ROI drawing tool 74 88 polygon ROI drawing tool 74 89 polyline ROI tool 89 posl pos2 pos3 parameters 327 post trigger delay 315 power amplifiers 190 level 18 PGM 223 preacquisition delay 63 316 preamplifier signal level 63 344 preemphasis function 191 theory 199 prep parameter 244 presig parameter 42 63 Print Stats button 94 printing statistics 103 pro parameter 21 326 probe diameter 235 preparation 248 vibration 194 processing EPI data 61 284 functions 131 156 profile degradation 247 file 250 file parameters 251 magnitude calculation of 249 storing data 251 profile file parameters 251 projection reconstruction 225 properties button 80 prospective gating 207 prosthetic parts warning 11 protection circuitry 49 proton resonance offset frequency 18 PS file format 107 PS2 file format 107 psi parameter 24 pss parameter 21 23 24 32 44 63 puls shape 322 pulse calibration 18 63 computing powers 42 conditions for sequences 42 control 238
372. l of the HPAG gradient are as follows e Parameter gcoil has been created to allow the following five gradient coil dependent parameters to be rapidly set to values appropriate for the active gradient coil boresize griserate gxcal gycal gzcal The value of gcoil is a string that identifies a text file in the directory Svnmrsystem gradtables The contents of the text file are the values of the five coil parameters Altering the value of gcoil automatically updates the values of all five parameters to the values specified in the corresponding text file If desired values for any of the gradient coil dependent parameters can be entered manually without forcing an automatic update of the other parameters e Gradient calibration parameters gxcal gycal and gzcal have been moved from the global file vnmrsys global to the curpar and procpar files of parameter sets FIDs and experiment directories The parameters now have the status of local acquisition parameters rather than global configuration constants They are transferred by the svf and svp commands the same way as other acquisition parameters The rt and rtp commands create these parameters if they do not exist when older parameter sets are recalled The values of these parameters are in units of G em DAC unit i e the value of the gradient strength per unit step of the output DAC used to drive the gradients e Parameter boresize has been moved from vnmrsys glob
373. l or injure exist inside the instrument Before working inside a cabinet turn off the main system power switch located on the back of the console then disconnect the ac power cord WARNING Do not substitute parts or modify the instrument Any unauthorized modification could injure personnel or damage equipment and potentially terminate the warranty agreements and or service contract Written authorization approved by a Varian Inc product manager is required to implement any changes to the hardware of a Varian NMR spectrometer Maintain safety features by referring system service to a Varian service office WARNING Do not operate in the presence of flammable gases or fumes Operation with flammable gases or fumes present creates the risk of injury or death from toxic fumes explosion or fire WARNING Leave area immediately in the event of a magnet quench If the magnet dewar should quench sudden appearance of gasses from the top of the dewar leave the area immediately Sudden release of helium or nitrogen gases can rapidly displace oxygen in an enclosed space creating a possibility of asphyxiation Do not return until the oxygen level returns to normal WARNING Avoid liquid helium or nitrogen contact with any part of the body In contact with the body liquid helium and nitrogen can cause an injury similar to a burn Never place your head over the helium and nitrogen exit tubes on top of the magnet If liquid helium or nitrogen c
374. l planning Mark button are properly handled by voxp1an resulting in an array of voxel positions and dimensions voxplan is called by the Compute Target button in the Voxel planning menu and is not normally executed from the command line voxplan stores its computed results in the target planning parameters t_posl t_pos2 t_pos3 t_voxl t_vox2 t_vphi t_vpsi and t_vtheta for later transfer to a new target experiment The out of plane voxel dimension t_vox3 must be selected separately with the Set vox3 button in the Voxel planning menu Target Parameters page 341 plan Interactive slice and voxel selection M sliceplan Compute slice position and orientation for target imaging plane M voxmark Store marked positions for planning target voxels M 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 2 7 Appendix A Commands Macros and Parameters A 4 Commands and Macros for Processing and Display Use the macros in this section to process and display data and graphics dconi 278 Syntax Description Arguments Interactive 2D data display C dconix lt options gt Interactively adjusts various 2D data displays The dconi program can accommodate any data set that can be displayed by dcon dpcon and ds2d including 2D FIDs interferograms 2D spectra planes from 3D data sets and images These data sets are generated by the commands df 2d ft 1d ft2d and ft3d options can be any of the following note th
375. l width setgro lt x readout_gradient level gt In imaging experiments automatically computes and sets the readout gradient strength gro and spectral width sw for the readout dimension consistent with the field of view lro The relationship between gradient strength field of view and spectral width is governed by the principle that the spins at the edges of the field of view must undergo a phase shift of 180 during the dwell time between successive sampling of points Nyquist sampling frequency following the expression sw y lro gro In its automatic mode set gro attempts to balance two opposing factors in choosing the readout gradient strength too low a value of gro results in large chemical shift displacement artifacts in the resulting image Too high a value of gro requires a large spectral width and therefore a large audio filter bandwidth resulting in increased noise and reduced signal to noise in the resulting image In both manual and automatic modes set gro uses the current values for number of points np and field of view 1ro np can be subsequently altered without the need to re run set gro or imprep but any change of 1ro must be followed by execution of set gro or imprep to recompute other dependent parameters The comprehensive setup macro imprep incorporates the functions of set gro so set gro is not normally directly executed by the operator except to override the value of gro selected by imprep 01 99
376. le If you have been running the IMAGE MSLICER or SHORTE sequences this is a direct replacement We assume that a probe and sample are in place the probe is tuned properly and that the system is otherwise ready to run If you are running the system for the first time and need instructions on setting up or turning on any of the hardware you should refer to the manual Getting Started Most of the macros used for imaging are located in the subdirectory maclib imaging of vnmr mac1lib Similarly menus used for imaging are placed in the subdirectory menulib imaging of vnmr menulib The system knows that you want access to these imaging subdirectories through the value of the parameter appmode a global parameter that each user can set To set the value of appmode for imaging e Enter appmode imaging on the VNMR command line Alternatively you can select Setup from the Main menu select App Mode and then select Imaging This sets global parameters sysmaclibpath and sysmenulibpath to the path of the following imaging directories so that these directories are searched each time you enter a command e sysmaclibpath is setto vnmr maclib maclib imaging e sysmenulibpath is set to vnmr menulib menulib imaging For more information about the commands parameters and procedures used refer to the appropriate chapters elsewhere in this manual and to the VNMR Command and Parameter Reference 1 1 Making an Initial Scout Image The
377. le is drawn When the left mouse button is released the completed rectangle appears in the selected ROI color 6 3 Tools This section describes the graphics tools listed in the Tools menu Graphics Tools Figure 66 shows a Graphics Tools G Tools window This window contains a set of tools to create and manipulate objects or an image inside an object and to annotate text on images Choose a tool with the left mouse button Only one graphics tool can be active at a time In addition to graphics tools the Frame Properties option activates a pulldown menu listing several options such as split save and load frames The properties menu changes according to the individual function of the selected graphics tool Figure 66 Graphics Tools Window The following sections describe the functions of graphics tools Mouse use to select create move or resize graphic frames or text is not described here See the OpenWindow Version 2 User s Guide for mouse use related to graphics Graphics Frame Tools This section describes the functions of graphics tools for creating zooming and scaling graphics frames Frame Tool The Frame tool creates a graphics frame A graphics frame is used to indicate the position and size of an image on the screen An image can only be displayed inside graphics frame The number of graphics frames is limited only by computer memory When selected frames can be created and resized in the graphic
378. lected by pressing the right mouse button on the Format Type field Besides FDF Table 7 lists the other available formats The data type in the output file Integer or Float as well as the data size 8 16 or 32 bits is purportedly set independently However almost all of the types support only 8 bit integer data and all except FITS and FDF are converted to 8 bit integers during the dumping process For all integer formats the data is scaled to match the currently displayed Vertical Scale of the image That is pixels that are saturated set to the maximum value in the current display are set to the maximum integer value in the output file and other pixels are scaled proportionally For scaling to properly work the data type in the Output File Format window must be set to integer otherwise the data is scaled to map the brightest pixel to the maximum integer value This problem is caused by the convert routine when a floating point FITS file is converted to an integer format The available formats are specified in the file SBROWSERDIR fileformats init This file lists the format names and specifies a shell command that converts a FITS file into that format If a non FDF format is selected Image Browser dumps the data in the FITS format and then calls another program to convert it to the requested format All the supplied formats use the convert program from the ImageMagick display package see ImageMagick Packa
379. lists the macros described in this section Table 14 Eddy Current Interface Commands and Parameters Commands eccsend Create eddy current setup file ecctool Open the eccTool window eddysend lt file gt Update acquisition eddy current settings Parameter curecc string Name of eddy current compensation file Gradient Compensation Board Each gradient compensation board controls one channel only Each board has five exponential pre emphasis functions a duty cycle limiter a slew rate control and an overall channel gain control see Figure 91 and Figure 92 The pre emphasis function adds up to five exponential waveforms to the input demand signal The controls are the values of the time constants themselves and the percent response amplitude The circuitry then drives the gradient current to compensate for the loss in gradient field from induced eddy currents The overall adjustment process is not detailed here The time constants are absolute values in milliseconds and the response amplitude from 0 to 100 referenced to the amplitude of the input signal The gain control sets the overall channel gain effectively establishing what current will be produced for a given demand input This control allows the resolution in the experimenter s demand voltage to remain independent of the range of gradient currents The gain control is linear with 100 giving the maximum current when the input voltage is full scale This control ch
380. lit Select the option Frame Properties Select the option Split Selected Frames Choose the desired split 1x2 1x3 1x4 etc A e p S Storing and Retrieving Gframes You can store and retrieve Gframes by clicking on the Save Frame Layout and Load Frame Layout options in the Frame Props menu shown in Figure 56 The files are stored into and retrieved from the CSIDIR gframe directory or a subdirectory Gframes are retrieved with the same size and positions with which they were stored They are not adjusted to fit the size of the graphics window Frames that are entirely outside the current graphics region or overlap with existing frames are not loaded The Save Frame Layout menu selection saves all currently selected Gframes It switches the FileBrowser to graphics frame save mode Use the FileBrowser to change to the desired directory and save the frames Clearing Gframes Use the Clear command in the Frame Props menu shown in Figure 56 to erase the contents of all frames selected frames or unselected frames Loading Data To load data select the File option The window CSI File Handling Tool opens in data load mode Directories and data files can be browsed and the desired data set can be loaded CSI accepts two types of data formats Flexible Data Format FDF and VNMR raw data FID format Simulated data can also be generated Data simulation allows processing and graphics functions to be tried without having to acquire da
381. lity Syntax Description Related explib2 Syntax Description Related 284 VNMR 6 1C User Guide Imaging Collects process and displays EPI data It is used to obtain a single EPI image The phasemap file must be present in the current experiment directory epiph Generate phasemap file in EPI experiments M episet Set up parameters for EPI experiments M Set up parameters for EPI experiments M Systems with echo planar imaging EPI capabilities episet Collects an EPI dataset with the phase encode gradient turned off image 0 It optimizes parameters for EPI collects a reference scan and allows you to adjust the gradient parameters groa and grora and the timing parameter t ep The phasemap file is generated in the current experiment directory epiph Generate phasemap file in EPI experiments M groa Readout gradient adjuster in EPI experiments P grora Readout dephasing gradient adjuster in EPI experiments P image Control phase encoding gradient in EPI experiments P tep Post acquisition delay in EPI experiment P Load default parameters Systems with echo planar imaging EPI capabilities episs Loads the default parameters for single shot EPI from the default parameter directory Save EPI images in FDF for Image Browser M Systems with echo planar imaging EPI capabilities episvib Saves images in Flexible Data Format FDF for viewing with Image Browser The first image in an arrayed
382. ls of the PGM 1000 receiver so that the high pass frequency is 0 5 Hz and the low pass frequency is 160 Hz At this point the hardware is prepared but the oscilloscope does not register useful signals Animal Preparation Anesthetize the subject using an established method Longer acting injectable anesthetics or controlled inhalant anesthetics are to be preferred for gated experiments because extra 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 217 Chapter 9 Physiological Gating Module 218 preparation time is required to establish ECG gating requirements For initial trial experiments about 45 minutes extra time is probably required to investigate the use of the PGM 1000 receiver controls In practical situations persons who are familiar with the PGM 1000 require only 10 to 15 minutes extra time 1 If the subject s feet are unsuitable for electrode attachment make an attachment area by shaving sites on the animal s right limbs and left foreleg Place the subject into the animal bed in the supine position ventral surface upper most Place the center of the thorax as close as possible to the center of both the magnet and rf coil Attach the electrodes to the forelegs and the right hind leg of the animal Connect these electrodes to the cardiac electrode leads It is important to connect the ground green lead to the hind leg of the animal Figure 106 on page 215 shows the proper electrode connection pattern The polarity
383. lt sqrt image 1 image2 addc Add a constant value to each pixel in an image multc Multiply each pixel in an image by a constant value abs Absolute value log Logarithm result log10 abs image exp Antilog result 10 image pow Exponentiation result image constant reverse Linear inversion of pixel intensities reverse contrast clipmax Set pixel values above a user supplied maximum to zero clipmin Set pixel values below a user supplied minimum to zero thresh Compress pixel values above a selected threshold thresh to 1 and below a threshold to 0 thresh2 Compress all pixel values above a user supplied minimum and below a user supplied maximum to 1 all others to 0 flroll Wrap image in F1 direction a selected number of pixels f2rol Wrap image in F2 direction a selected number of pixels flip _horiz Flip image about central horizontal axis flip_vert Flip image about central vertical axis flip_diag Flip image about x y diagonal only square images rotate_90 Rotate image clockwise 90 degrees only square images rotate_180 Rotate image 180 degrees viine Replace a selected vertical trace by average of two adjacent traces hline Replace a selected horizontal trace by average of two adjacent traces From UNIX imcalc add phfl phf2 outphf 0 5 From VNMR imcalc add phf1 phf2 imcalc Interactive prompt for imcalc M rtphf Return a stored phasefile into the current VNMR experiment M svphf Sa
384. ltidimensional experiments are acquired in either standard also called arrayed mode or compressed mode ni is used to control standard acquisitions and nf to control compressed acquisitions For more information refer to the parameter seqcon Experiment Counters Current FID Description Specifies which FID to operate on when working with multi FID compressed data All subsequent operations such as Fourier transformation are applied to the selected data block Individual images from a compressed multislice acquisition for example are selected through the cf parameter Setting cf 3 selects slice number 3 in the order acquired not necessarily in position order Refer to the manual VVMR Command and Parameter Reference for information about the additional use of cf in nonimaging applications Values Number through the value of parameter nf Related flashc Convert compressed 2D data to standard 2D format C ne Number of echoes to be acquired P nE Number of FIDs P ns Number of slices to be acquired P Number of echoes to be acquired Description The number of echoes in a multiecho experiment 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 333 Appendix A Commands Macros and Parameters nf ni ns 334 Values Related Description Values Related Description See also Related Description All multiecho acquisitions must be in compressed mode ne is then used as the limit f
385. lumns frame_delete selected unselected empty all Deletes Gframes of a specified type VNMR 6 1C User Guide Imaging 01 999163 00 A0800 4 5 Macros frame_clear selected unselected all Clears remove images from Gframes of a specified type frame_select all none n lt m gt Selects or deselects all Gframes or selects specific Gframes by number For example frame_select none 1 2 3 selects only frames 1 2 and 3 frame_load file Loads Gframes in file into the graphics region frame_save file fullpath Saves selected Gframes in file into the graphics region If a file does not begin with it is taken to be relative to the SBROWSERDIR gframe directory Display and Intensity Commands display_vs_bind on off Turns on off V scale binding property display_vs max Rescales images in all selected Gframes so that the data value max is at the top of the intensity scale display_vs x y lt nframe gt Rescales images If nf rame is not given this command rescales images in all selected Gframes as if you clicked the V scale tool at the data coordinate x y in the image If nframe is given this command rescales only the image in the Gframe number nf rame display_contrast Shows Gamma Correction tool display_contrast slope Sets display contrast to a specified slope with 50 gray in center of colormap ramp slope 1 corresponds to the default display
386. ly run each time one of these parameters is entered and is not normally and explicitly run by the user The comprehensive setup macro imprep also performs the set loop function so if imprep has been executed there is no need to run set loop do Overhead delay between FIDs P flashc Convert compressed 2D data to standard 2D format M imprep Set up rf pulses imaging and voxel selection gradients M ne Number of echoes to be acquired P nf Number of FIDs P ni Number of increments in first indirectly detected dimension P ns Number of slices to be acquired P nv Number of phase encode steps for 1st indirectly detected dimension P seqcon Acquisition loop control P Measure and save resonance transmitter offset frequency setof Collects a spectrum and determines the resonance frequency of the tallest peak in a spectrum The corresponding transmitter frequency tof is then saved in the file SHOME vnmrsys Hloffset for use in imaging experiments H1 refers to the value of the current nucleus parameter tn If the s2pul sequence is used to collect data then set of sets the transmitter on the tallest peak and collects a dataset and displays the result which shows the tallest peak appearing in the center of the spectrum ldof Load resonance offset frequency P tn Nucleus for observe transmitter P tof Frequency offset for observe transmitter P Set imaging orientation Euler angles to match orient setorient Sets the i
387. m EPI because it not only monitors the dynamic changes it also minimizes flow induced and motion induced artifacts in images Table 3 shows a list of commands and macros used by EPI routines Pulse Sequence Figure 18 shows the gradient echo version and Figure 19 shows the spin echo version of the EPI pulse sequence The rf pulses are slice selective pulses very similar to those used in conventional spin warp sequences GEMS SEMS etc The major difference between the EPI sequence and the conventional spin echo sequence is that in EPI the signal is frequency encoded multiple times by generating a series of gradient echoes The readout gradient is rapidly switched to generate a train of gradient echoes The echo amplitudes eventually drop off because of T and T decay In the case of the spin echo EPI sequence the echo amplitude initially increases because the T effects are refocused at the center of the echo train by the refocusing 180 pulse Each of the collected echoes is phase encoded by the application of a phase encoding blipped gradient as shown in Figure 18 and Figure 19 The main advantage of the EPI sequence is obvious an entire time domain imaging dataset is obtained in a single shot 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 51 Chapter 3 Imaging Pulse Sequences 52 Table 3 EPI Related Commands and Parameters Commands dconi Displays noninteractive color intensity map epift index Processes displ
388. m vent tubes Air that enters the magnet contains moisture that can freeze causing blockage of the vent tubes and possibly extensive damage to the magnet It could also cause a sudden dangerous release of nitrogen and helium gases from the dewar Except when transferring nitrogen or helium be certain that the relief valves are secured on the vent tubes WARNING On magnets with removable quench tubes keep the tubes in place except during helium servicing On Varian 200 and 300 MHz 54 mm magnets only the dewar includes removable helium vent tubes If the magnet dewar should quench sudden appearance of gases from the top of the dewar and the vent tubes are not in place the helium gas would be partially vented sideways possibly injuring the skin and eyes of personnel beside the magnet During helium servicing when the tubes must be removed carefully follow the instructions and safety precautions given in the manual supplied with the magnet Caution Notices Observe the following precautions during installation operation maintenance and repair of the instrument Failure to comply with these cautions or with specific cautions elsewhere in Varian manuals violates safety standards of design manufacturing and intended use of the instrument Varian assumes no liability for customer failure to comply with these precautions CAUTION Keep magnetic media ATM and credit cards and watches outside the 5 gauss perimeter from the centerline o
389. mage by zeroing all the pixels outside the ROI and zeroing all the pixels outside the selected intensity range within the ROI The first or second action can be taken by selecting Segment Image or Segment ROIs respectively When Segment ROIs is selected all selected ROIs are segmented Once an image has been segmented it cannot be restored except by reading it back in from its original file So if permanent segmentation of an image is not wanted and only statistics from the defined segmented region are instead desired choose Match Segmentation Limits in the Statistics Histogram limits field VNMR 6 1C User Guide Imaging 01 999163 00 A0800 4 4 Data Processing Making Volume Measurements Use the Image Segmentation features to make volume measurements over one image or over a number of multislice images The volume field in the Statistics window is calculated as the image area within the ROI times the slice thickness of the image When using the Match Segmentation Limits only the voxels with intensities within the segmented intensity region are used in the volume calculations which is also true for the area and other calculated statistics Graphical Display When more than pop Statisties SO one ROI is Min 5 116e 05 Statistics Histogram limits 7 Span ROI intensities selected and Max 0 03354 Histogram bins 100 statistics are Mean 0 01778 Image segmentation keep range Stdv 0 006198 Min infinity
390. mage par directory Load the parameters by entering bp_image Figure 114 shows a typical display of reference parameters 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 233 Chapter 10 2D and 3D Backprojection BACKPROJECTION bptype noslice ACYULSITION 402 174 H1 23000 0 u RE_PULSES 1 20 Sd 2 40 od 4095 GRADIENTS orient kyz qcal 0 o02Z000 Iro 1 00 gro 3405 r par lib bp_imape solvent none OLELYLO cu 29991 U Figure 114 Parameters for Sequence dp_image Setting System Specific Parameters Some reference parameters differ depending on the system configuration Perform the following steps to make sure these parameters are correct for your system 1 Check that s frq has the correct spectrometer frequency 300 400 etc for your system 2 For slice selective imaging use a shaped pulse For volume imaging use a square or hard pulse 3 Check that tpwr1 is set to an appropriate transmitter power for a 90 pulse and that p1 is set to the duration of the 90 pulse 4 Check that t pwr is set to an appropriate transmitter power for a 180 pulse and that pw is set to the duration of the 180 pulse 5 Check that the gradient strength is calibrated See the appendix Commands Macros and Parameters for guidelines for using the macro set gcal to check gradient strength calibration Setting On Resonance BP imaging requires the on resonance condition to ensure an identical center in all proj
391. maging 01 999163 00 A0800 6 4 Processing Functions Processing Attributes The following list describes the functions of Metabolic Map Display processing attributes Interpolation Selects No Interpolation or Interpolation No Interpolation displays a metabolic map grayscale image of the voxels in the MVS data set Interpolation allows a selection of the matrix size greater than the number of voxels in the MVS data set and it interpolates between the different intensities Matrix Size Number of discrete voxels to use metabolic map display Peak No Peak number to form a metabolic map Display Take selected peak and display its map Image Reconstruction The Image Reconstruction window shown in Figure 75 transforms a standard 2D field of view reference image Figure 75 Image Reconstruction Window Processing Attributes The following list describes the processing attributes in the Image Reconstruction window Filter Types Weighting functions applicable to the raw data Not implemented Time Const Property of the weighting functions that can adjust the functions to the data Shift Const Property of the weighting functions that can adjust the functions to the data Rotation number Allows rotating images in 90 increments The raw data can also be transposed by using the Transposed Image selections before transforming The matrix values are selected by the number of points in the data file but can be adjusted to allow f
392. maging orientation Euler angles to match the orient parameter This is a lower level macro that is not normally directly executed by the operator Imaging plane orientation is normally selected through orient or through interactive graphical planning However oblique gradient pulse sequence elements use a set of three Euler angle parameters phi psi and theta to determine the exact angular orientation Each of the three major imaging plane orientations trans sag and cor require a unique set of Euler angles setorient is automatically executed upon entry of orient and sets the three Euler angles to the appropriate values for the specified orientation orient Slice plane orientation P phi Euler angle for defining imaging plane orientation P psi Euler angle for defining imaging plane orientation P theta Euler angle for defining imaging plane orientation P Set phase encode gradient levels and timing setgpe VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Description Related setgro Syntax Description A 2 Macros for Setting Up Experiments In imaging experiments automatically computes and sets the phase encode increment and timing and the indirect dimension spectral width associated with each phase encode dimension present The gradient t ime integral for the increment between phase encode levels is governed by the requirement that the spins at the edges of the field of view undergo a phase shift of 180
393. make new gradtables entries If the parameter gcoil does not exist in a parameter set and a user wants to create it the protection bit that causes the macro __gcoil to be executed when the value for gcoil is changed must be set There are two ways to create gcoil e Use the macro updtgcoil which will create the gcoil parameter if it does not exist and set the protection bits e Enter the following commands create gcoil string setprotect gcoil set 9 gcoil and the associated gradient calibration parameters Variable Name Value boresize gmax andtrise are updated with the values listed boresize 22 50 cm in the table on the right each time a gmax 5 00 gauss em parameter set is retrieved or when teise 0 000500 sec an experiment is joined In the rare case that a gradtables file is modified but the value of gcoil is not changed manually force an update of the calibration parameters Updating may be accomplished either by setting gcoil to itself for example gcoil gcoil or by using the macro_gcoil Be aware that if an old dataset is returned and processed gradient parameters associated with that dataset will replace any new gcoil parameters The table above is a gradient table gradient coil name asg33 for a Variable Name Value as rie system with all bores 5 10 cm t ee axes set to the same maximum EE 0 000200 sec gradient strength gxmax 29 00 gauss cm On the right is a gradient table 27 0
394. mands and options The choices of these menus can be an action to save load process popup another window etc depending on the individual function of the tool selected Frame Properties Menu The frame properties menus can be pinned to the screen desktop by selecting the pushpin icon in the top left hand corner of the menu Pushpins allow a group of functions to be easily accessed without first selecting the corresponding graphics tool For example with the Zoom Properties menu pinned the Pixel Interpolation button can be toggled at any time without having to go into zoom mode Be aware that when pinned menus are used some menu choices display a list of file names used to retrieve ROIs filters etc These submenus are not updated if for example a new ROl is stored The submenus list the files that existed when the menu was pinned To update the menu close it by selecting the pushpin and then pin a new menu Graphics Frame Tools The following sections describe the functionality of tools Use of the mouse to select create move or resize is not discussed here see the OpenWindows User s Guide for mouse use related to graphics Frame Tool The Frame tool is used to create a graphics frame Gframe A Gframe is used to indicate the position and size of an image on the screen An image can only be displayed inside a Gframe The number of Gframes is limited only by computer memory When this tool is selected frames can be cr
395. me object but they show variations in the amplitudes Since this problem is independent from gradient settling times it can only be related to a shift of the Bo field This shift is caused by gradient switching and has a long time constant Experience has shown that the resulting images can be improved by not only taking a 180 angular view but a full 360 view which includes doubling the number of projections However this problem needs further investigation 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 247 Chapter 10 2D and 3D Backprojection Figure 131 B Field Shift Sample Probe Preparation To obtain the first BP image you might want to use a phantom setup such as the one shown in Figure 132 two cylinders of silicon hoses slid over an inner silicon to fit in 5mm NMR tube 4mm 5 32 1 8 Figure 132 Phantom Setup for BP Imaging 248 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 10 6 BP Macros and Programs Details The phantom is based on two silicone hoses with different diameters constructed as follows 1 From the hose with the smaller diameter cut one piece 10 mm 13 32 inches long 2 From the hose with the larger diameter cut two pieces 3 mm 1 8 inches and 4 mm 5 32 inches long 3 Slide the larger diameter pieces onto the smaller diameter piece as shown in Figure 132 Friction should hold the pieces in place 4 Put the phantom in a cylinder of an NMR tube The cylinder
396. meter 191 gcoil parameter 20 50 63 308 GEMS data processing compressed 50 limitations 48 requirements for using 44 gems macro 62 258 getting and Fourier transforming data 62 Gframes 66 69 70 81 134 136 148 clearing 72 81 creating and manipulating 70 deleting 72 81 100 directory 69 layout loading and saving 81 loading 81 101 manipulation tool 74 mathematical expressions 87 moving 71 137 operations 135 refreshing and redisplaying 108 related commands 71 removing images from 101 resizing 72 saving 81 101 105 selected splitting 80 selecting 71 81 selecting deselecting 101 01 999163 00 A0800 Index splitting 72 splitting into rows and columns 100 splitting selected frames 80 tools 80 GIF file format 107 GIF87 file format 107 gmax parameter 309 Go button 292 go macro 22 24 50 51 62 291 Go Wft button 291 gpe parameter 21 gradient 2nd phase encode increment 310 3rd phase encode increment 311 amplifier 43 calibration constant 265 calibration file creating 43 calibration files 19 calibration parameters 307 coil 189 191 308 310 compensation 191 194 197 control system cabinet 190 echo 33 34 echo imaging sequence 45 echo sequence EPI 58 field display 195 fields spurious 56 junction unit 191 parameters 314 phase encode dephasing 311 phase encode increment 310 power amplifiers 191 recalled echo multi slice imaging sequence 44 rise
397. meter does not exist and the deccgo macro by default executes a go command If the parameter is created in an experiment with the command string deccgo whatever string value the parameter contains is executed as a command by the deccgo macro instead of go deccgo ga deccgo Perform an action for decctool P decctool Open decctool window M U string Create a string variable C Open decctool window M U decctool Systems with digital eddy current compensation DECC Starts the decctool program to adjust eddy current compensation parameters and sets gradient gain slew rate and duty cycle Array a numeric parameter exparray lt parameter start end number gt Arrays any numeric parameter in exponentially increasing steps exparray provides a convenient method of arraying a numeric parameter when an exponentially changing increment between arrayed values is desired such as in T or T experiments It works with any arrayable parameter and generates arrayed values in ascending or descending order When other parameters are already arrayed the parameter array is updated If more advanced array capabilities such a simultaneous arrays were specified through array the value of a parameter might need to be corrected after use of exparray parameter is the name of parameter to be arrayed The default is an interactive mode in which you are prompted for the parameter Only numeric parameters can be arrayed start is the
398. meters seqcon Acquisition loop control Description Controls the status of various possible looping processes in most inna gene sequences Position Loop Values 5 character string The table on the First Multiecho right shows how each character Second Multislice position has place value and affects Third Ist Phase Encode 2D a different looping operation Fourth 2nd Phase Encode 3D The value of each character controls Fifth 3rd Phase Encode 4D the type of loop used during pulse sequence execution for the corresponding sequence function not all looping functions are present in most sequences e n specifies that this particular looping operation is not used in the sequence e s sets the looping operation to occur during the execution of pulse sequence generation in the host computer as a standard arrayed acquisition Each pass through the loop generates a new acode set for execution in the acquisition computer in turn returning a new data block in the FID file A standard loop therefore lies outside the signal averaging transient counter loop Parameter arrays and the implicit 2D loop are standard loops The multiecho loop cannot be a standard loop because of the rapid timing restrictions normally associated with multiecho data acquisition e c sets the looping operation to occur dynamically in the acquisition computer controlled by real time pulse sequence variables Each pass through a compressed loop gener
399. meters You can save on calculation time by asking for fewer output images In this example images that you do not ask for are not calculated In practice residuals take negligible time to calculate and parameter sigmas increase the calculation time by less than a factor of two e The first field to the right of the equal sign in this case fit is the name of the program to run Since fit exists in BROWSERDIR math functions bin Image Browser does not try to parse the name as an Image Browser Math Expression The remaining fields are passed to the fit program e 1 8 is the list of input images e t1 is the type of fit required t 1 does not need to be the first string parameter Rather the first string that names a known fit type is taken as the fit type specification e tiis the independent variable of the fit whose value is found in the header of the input images Often the desired independent variable values are put in the header when the image files are created with svib because any arrayed parameters will have their values put in Otherwise new header values can be set with the data_header_set command described on page 102 If the header parameter name happens to be the same as the fit type enter the same string twice e Parameter 01 is the threshold value Pixels that have values in all the images with absolute value less than the threshold return zeroes in the output images The default is 0 Other string argum
400. mits are specified during the initial system configuration process see the command config and depend on the system hardware Power levels are integer values on a logarithmic dB scale on VXR and UNITY generation SISCO systems a unit change in a power level parameter corresponds to a 0 5 dB change in output power Pulse power levels are controlled by 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 319 Appendix A Commands Macros and Parameters selecting a variable level of attenuation at the output of the transmitter The minimum power level not necessarily zero on all systems does not result in zero transmitter output but simply minimum output which depends on the attenuator range Pulse shape parameters are string parameters that may be used to hold the name of an rf pattern file found in a local or system shapelib Pulse sequences are generally written using these shape parameters instead of hard coding the shape names to allow the pulse shapes to be changed conveniently in the parameter set from the command line or a macro Pulse Length Parameters pw p1 p5 Description Values Related pi Description Related pmt Description Related psat Description Related Pulse length General purpose rf pulse length parameters used to specify pulse durations where a descriptive name is not required Definition and usage will vary from sequence to sequence Standard Varian imaging sequences us
401. modes e trace is a keyword to draw a trace above the spectrum e expand is a keyword to toggle between the expand and full views of the spectrum e plot is a keyword to plot a projection or a trace e hproj_max isa keyword to do a horizontal projection of the maximum trace e hproj_sum isa keyword to do a horizontal projection of the sum of all traces e vproj_max is a keyword to do a vertical projection of the maximum trace e vproj_sum is a keyword to do a vertical projection of the sum of all traces VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Examples dgm Syntax Description Related disp3d Syntax Description Arguments Related A 4 Commands and Macros for Processing and Display dconi dconi dcon gray linear dconi dpcon Display dg parameter groups menu M dgm Displays a menu that allows selection of all dg parameter groups in an experiment The primary parameters of any imaging experiment can be displayed in the text window with the dg command Most secondary parameter groups such as dg1 and dgs are found in each imaging experiment along with several other specialized parameter groups These additional parameter groups allow the display for example of all predefined gradient parameters or all predefined rf pulse parameters etc although some of the displayed parameters are unused in any given experiment and have values set to zero or null strin
402. modifying the display s color map When you release the middle button the original color map is restored and all the selected frames are rescaled All images will change while you are dragging the mouse but only the selected images will be permanently changed Also the preview feature only works well if the V scale mapping function is nearly linear e Open a popup window to enter the desired vertical scale value The Vs Prop vertical scale properties menu has three choices as shown in Figure 30 e V scale changes the mapping of data values to the colormap index e Gamma changes the pixel values in the colormap itself Gamma correction is to be used only to correct the image display of a particular monitor e Unbind or Bind sets whether only one image or all selected images are rescaled For details see VsProp Menu Unbind or Bind page 87 Figure 30 Vertical Scale Properties Window V scale adjustment is to be used to emphasize particular intensity ranges in an image Because gamma corrections are made in the common Image Browser colormap they apply to all images being displayed the V scale adjustments might be different for each image The V scale choice is described in the next section gamma is covered starting in VsProp Menu Gamma Correction page 85 82 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 4 3 Graphics Tools Vs Prop Menu Vertical Scaling The V scale choice on the Vs Prop men
403. mouse button and slowly drag the cursor along the edge of the region of interest area As the cursor is being dragged a line is drawn in the active ROI color following the movement of the cursor 3 Release the left button and move the mouse to connect the cursor to the last defined point a straight line appears 4 Press the left button to define the next point Be careful about moving the cursor before the line is closed because that cursor location is included as part of the closing position however this shouldn t cause much concern because each freehand or polygon segment can be adjusted after it has been created To draw a polygon ROI do the following procedure 1 Move the cursor to each desired vertex and click the left button After the first click a straight line follows the cursor and at each cursor location where the mouse eft button is clicked a vertex is placed 2 Click the middle button to close a freehand or polygon ROI A straight line is drawn between the last and first vertices and the completed ROI appears in the selected color Polyline ROI Tool The Polyline ROI tool functions the same way as the Polygon ROI tool except that the last line segment closing the polygon is not drawn It can be used in the Statistics processing function in which case it defines the union of all the 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 89 Chapter 4 Image Browser line segments in the polyline It ca
404. mplifier Battery Powerdex VP 6 1400 Disposable Electrodes package of 500 00 967573 00 1 PGM Receiver 00 967572 00 1 Cardiac Preamplifier battery included 00 967646 00 1 Cardiac Electrode Leads 67 405203 00 1 Fiber Optic Cable 00 958298 10 2 Coax Cable short 00 958298 20 1 Coax Cable long 1 1 Component Functions Electrical signals generated during the cardiac cycle are detected using three disposable electrodes attached to the limbs of the animal subject These signals are conducted to the cardiac preamplifier module 00 967572 00 via the cardiac electrode leads 00 967646 00 The cardiac preamplifier module is usually located in the magnet bore during normal operation Inside the preamplifier the cardiac signals are amplified and encoded for optical transmission through the optical fiber link 67 405203 00 to the PGM 1000 receiver module 00 967573 00 Inside the PGM 1000 receiver the optical signals are reconverted and filtered The QRS complex in the ECG is detected using either an automatic or manual voltage threshold Trigger pulses for gating the spectrometer are generated as each QRS complex is detected in the incoming electrocardiogram signal A controlled number of trigger pulses can be suppressed through the use of the inhibit feature of the PGM 1000 receiver if desired Trigger pulses are conducted to the spectrometer port J 8120 located on the system patch panel and labeled Biological Gate through coax cable
405. mponent consists of a set of terms which decay according to Equation 33 The BO terms are independent of spatial position and therefore influence the NMR signal at sample I and II equally However the linear or gradient terms influence the NMR signal differently depending on the magnitude of the gradient field at I and II In this case we assumed that the samples are along the z axis and that the Z gradient is pulsed so these terms are more specifically known as the Z gt Z main terms Also for this example the terms that cause the BO shift are known as the Z gt B0 terms When the gradient is applied along one of the other axes instead of along the z axis there quite often also arise gradients in the z axis or cross terms For sample I and sample II 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 201 Chapter 8 Digital Eddy Current Compensation oriented along z the effect of an applied pulse along the x axis is caused by the X gt Z cross terms and the effect of an applied pulse along the y axis is caused by the Y gt Z cross terms In summary a variety of main terms cross terms and BO terms make up the eddy current effects These effects can be corrected with DECC 8 3 Using the decctool Interface This section describes how to use the decctool interface Table 16 lists commands macros and parameters related to the program Table 16 decctool Macros and Parameters Macro deccgo Perform an action for
406. mt mtpat and mtpwr y means turn on magnetization transfer n means turn it off mtpat Magnetization transfer pulse rf shape P mtpwr Magnetization transfer pulse power level P pmt Magnetization pulse length P Automatic sequence calculation Specifies automatic or manual calculation of gradient refocusing levels in imaging pulse sequences The automatic mode pulse sequence calculations are generally quite reliable but it may sometimes be of interest to verify these calculations by arraying the parameters with pilot set to the manual mode Operating at the extreme limits of the pulse sequence such as ultra short echo times may also require some fine adjustment of refocusing gradient levels 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 337 Appendix A Commands Macros and Parameters Values Related presat Description Values Related rfspoil ws 338 Description Values Related Description Values Related y sets the automatic mode that uses internally computed refocusing levels n sets the manual mode that bypasses internal calculations and directly uses the values found in the parameters gssr and gror gror Read out dephasing gradient P gssf Slice selection fractional refocusing P gssr Slice selection refocusing gradient P Presaturation pulse execution on off Sets whether to turn on or off execution of a presaturation pulse in sequences that include this capa
407. n Related gdiff Description Related gflow Description Related gpat gpat3 Description gpepat Description gropat Description gspoil Description Related gsspat Description 314 VNMR 6 1C User Guide Imaging Number in gauss cm less than t gmax gmax Maximum gradient strength P gss Slice selection gradient strength P gx Gradient strength for X Y and Z gradients P voxl vox3 Voxel dimension P Purpose Gradient Parameters Crusher gradient level Predefined parameter available for use in setting a crusher gradient level often paired with the timing parameter t crush gspoil Spoiler gradient level P terus Crusher gradient control P tspoil Gradient spoiling time P Diffusion gradient level Predefined parameter available for use in setting a diffusion gradient level often paired with the timing parameters tdiff ortdelta tdelta Control diffusion sensitizing gradient pulse length P tDELTA Control separation of two diffusion sensitizing gradient pulses P tda t Diffusion sensitizing gradient pulse length control P Flow encoding gradient level Predefined parameter available for use in setting a flow encoding gradient level often paired with the timing parameter t f Low tflow Pulse length control P Gradient shape Predefined string parameters available to specify gradient shapes Phase encode gradient shape Predefined string parameter to
408. n The left button can also be used to select the default choice The action of submenus processes data opens a window etc depending on the functional operation A button with three dots following an item s name e g Macro opens a popup window rather than immediately performing the selected action The Cancel button at the right end of the control panel is normally faded and cannot be selected However performing a potentially lengthy operation such as loading all the images from a directory activates the Cancel button Selecting the activated Cancel button aborts the current operation See Graphics Tools page 80 for more information about the control panel menu option Tools Creating and Manipulating Graphics Frames The Frame button must be selected when performing any of the Gframe functions other than selecting a Gframe To select the Frame button 1 Position the mouse pointer on the Tools button in the control panel and press the left mouse button The Tools popup window opens 2 Select the Frame button rae to activate the Frame tool and display Frame Properties in the Tools menu 70 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 4 2 Getting Started 3 Position the pointer over the Frame Properties button and hold down the right mouse button until the menu shown in Figure 27 appears You can now work with Gframes To select a Frame Properties command 1 Hold down the right mouse button an
409. n Pi and PCr and a b pK2 are constants In the pH map processing function the correct peaks must be specified The constants are set to default values but can be changed Figure 76 shows the window for the pH map process The pH map process can also generate frequency difference maps between any peaks in the CSI spectra and acid and alkali variations of the pH map The box ROI can be used to select a region of interest when applying a global map by using the Prior Knowledge or Confirm Peak definitions Figure 76 pH Map Control Window The following list describes the functions of pH Map Control processing attributes Map Type Type of map to generate Freq Diff pH Acid or Alkali Peak Define Source of information to define the peaks Current Prior Knowledge Confirm or Mmap Current is for a selected spectrum cannot be used for global apply 166 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 6 5 Files and Other Items Prior Knowledge and Confirm use previously registered prior knowledge or confirmed peak picking information with the MVS data buffer to determine the peaks for a local or global mapping Mmap uses already curve fitted metabolic map information to determine the peaks for a local or global mapping Peak A B Peaks in spectrum to obtain the difference in frequency Check Performs a check of the frequency difference or pH in currently selected spectrum and displays result in the Info Message
410. n VNMR data_header_set Syntax Description Arguments Examples See also vol_extract Syntax Description Arguments Related vol_mip Syntax 01 999163 00 A0800 Create and set float header variables C not in VNMR data_header_set parname command Provides a way of creating and setting new float type header variables in images that have already been loaded in to Image Browser parname is the header parameter name that is created if it does not exist in all selected images command is the command line sent to the UNIX shell by data_header_set The standard input of command is a list of names of the selected images in the order that the images were selected none 1 2 3 myparm cat data frame_select data_header_set In the previous example the frame_select command selects frames 1 2 and 3 Then data_header_set sets the header myparm in the first three images to the respective values of the three numbers in the data file Chapter 4 Image Browser Extract one plane orientation C not in VNMR vol_extract xt yz xz first_slice last_slice incr Extracts one orientation of planes as selected by xy the default xz or yz used to process 3D data first__slice extracts only that plane number last__slice extracts planes gt first_slice and lt last_slice incr is the increment between successive slices it should be po
411. n also be used in the Line Data processing function It also provides a way of drawing arbitrary lines on the image for annotation Annotation Tool The Annotation tool is used for text annotation After selecting the tool position the cursor at the desired spot and click the left mouse button An underscore cursor appears at the marked location indicating that the label is selected and ready to accept typed input Typed characters are always added to the end of the annotation field they cannot be inserted into the middle of a string The label can be selected and moved to other locations at any time If more than one label is selected typed input is appended to all of the selected labels 4 4 Data Processing 90 Image Browser can process multiple images Some operations can be simultaneously applied to several images and some can only be applied to one image and then repeated on other images For example image rotation can be applied to several images at once but it is not suitable to simultaneously add several sets of two images Therefore the decision to simultaneously apply a specific operation to several images depends on the nature of the operation To simultaneously apply an operation to several images select several graphics frames that contain images to be processed Of the processing functions only image rotation can be done simultaneously on multiple images Some operations such as adding two images might need more th
412. n field characters cannot be inserted into the middle of a string The label can be selected and moved to other locations at any time If more than one label is selected any typed input is appended to all of the selected labels Spectrum Tool The Spectrum tool is used for manual phasing and vertical scaling of a spectrum After a spectrum has been selected by the Voxel Select tool this tool can be selected to do phasing and scaling The Marker Properties menu contains phase adjustment types To phase a spectrum place the cursor on the selected spectrum and drag the left mouse button Scaling is done with the middle mouse button When the middle mouse button is clicked the spectrum scale is proportionately increased or decreased depending on the distance of the cursor from the baseline origin of the spectrum If the cursor is placed at the left hand side of the spectrum click the middle mouse button to move the origin of the spectrum to the location of the cursor Const amp Linear phasing is not currently implemented Voxel Select Tool The Voxel Select tool allows a very quick way to look at selected spectra within a CSI data set This tool can be used on localized FID data MVS data or curve fit MVS data This tool allows a voxel to be selected out of a CSI grid and displayed in its own frame After it has been activated when a Gframe is selected without CSI data displayed in it the frame is selected When CSI data is dis
413. n occur to both gradient and shim supply if the supplies are powered up as connections are being modified Shim Connector Port The shim connector port J5912 receives power from the system shim power supply via the shim power cable P59X2 Power is supplied to all shims except to X Y and Z which obtain power through the gradient connector cable CAUTION Do not disconnect the shim power cable from the shim connector port of the gradient coil unless the system shim supply has been switched off Severe damage to the shim supply can occur if it is powered up as connections are being modified Thermocouple Connector The thermocouple connector J5913 mates with the thermocouple sensor cable P59X3 from the system gradient supply to complete the sensor circuits needed to protect the gradient coil from thermal overload CAUTION Ensure that the thermocouple sensor cable is connected to the gradient coil you are about to use If the sensor cable is connected to the main gradient coil when the HPAG auxiliary coil is in use or if the cable remains disconnected the thermal overload protection circuits of the system gradient supply will not function correctly Experiments requiring high gradient duty cycle could then lead to damage of the gradient coil Water Connectors and Hoses Water hoses supply cooling water to the 183 mm gradient coil when the hoses are connected to the water fittings located on the HPAG quick disconnect box The
414. n of each panel e X selects x channel parameter entry with four subpanels e Y selects y channel parameter entry with four subpanels e Z selects z channel parameter entry with four subpanels e Limits selects the panel where duty cycle and rise time are set e Scale selects the panel where various gains are set Changing Time Constants and Amplitude Values The X Y and Z parameter entry panels are essentially the same If you click on the tabs to select the various subpanels you will see that there are six main compensation terms X gt X three in each of the two cross terms Y gt X and Z gt X and four BO compensation terms X gt BO To change the time constant and amplitude value for a term do the following steps 1 Select the text field in which you want to make the change 2 Type in a number or click on the up or down arrows to the right of the text field 3 Press Return After you have pressed Return notice that the message at the bottom of the decctool window has changed from Unmodified to Modified Values displayed in the various text fields that are the same as the master file are Unmodified Values that have changed from the master file are Modified Selecting or Deselecting Values Note that if you enter a nonzero value for amplitude the Enable button next to the field in which you just made the change now becomes a highlighted color if you had not previously selected the
415. n readout dimension cm Slice position offset cm NMR reference frequency Hz set to resonance frequency offset RF coil calibration entry in pulsecal database 1 spin echo O gradient echo method Spectral bandwidth Hz Slice thickness mm Recycle time sec Crusher or spoiler gradient time sec Enter ssprep to calculate the slice selection parameters Slice gradient gss and pulse power levels tpwr1 tpwr2 are calculated by ssprep You must enter ssprep whenever slice selection parameters such as pulse width pulse shape or slice thickness are modified ssprep is very similar to the imprep macro except that ssprep does not calculate readout and phase encode gradient parameters Readout gradients and phase encode gradients are explicitly calculated within the pulse sequence ssprep unlike imprep allows you to manually set the at and sw parameters Do NOT use imprep when running the episs sequence Align echoes and generate the phase map from the reference scan a The echo maxima in EPI ideally should appear at t2 0 However because of nonideal conditions the echoes appear shifted from this position To view the echo train and adjust some parameters to shift the echo position towards 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 59 Chapter 3 Imaging Pulse Sequences 12 0 use the episet macro episet optimizes parameters for EPI collects a reference scan and allows you to adjust the gradient
416. n the CSI Metabolic Map Calculation window see Figure 61 At this point the peaks must be specified for curve fitting This must be done on a local spectrum so as in the previous processing steps select a spectrum from the CSI display 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 143 Chapter 6 CSI Data Processing 144 Local Peak Picking The CSI tool works best when Prior Knowledge is used Select Prior Knowledge Use and PK File 31P in vivo standard and select Sampling Go A marker should appear on each peak If they do not it may be necessary to select the Picking Tool from the G Tools window to manually specify any missed peaks If there are markers on each peak you can move on to the Local Specification The peak information is displayed in the Info Messages window Local Mmap Specification To define the Mmap peaks and curve fitting parameters select the Specify CurveFit and Mmap button which opens the Interactive Curve Fitting window Figure 61 Metabolic Map Calculation Interactive Curve Fitting When the interactive Curve Fitting window opens a curve fit of the first peak is overlaid on the spectrum in the selected Gframe along with cross hair markers on each peak The curve fit parameters for the first peaks are displayed in the window Step through the peaks on the panel Each time a new peak is selected its curve fit is overlaid on the spectrum If all the curve fits look okay register the
417. n the selective gradient and the rf flip angle pulse length and shape The list parameters must be present with appropriate entries and the specified rf shape file must exist in shapelib with the proper header information Gradient strength for a slice or voxel selective event is determined from the relationship gss BW y thk where gss is the gradient strength BW is the rf pulse bandwidth and thk is the slice or voxel thickness setgss uses the rf pulse bandwidth extracted from the rf shape file in shapelib together with the slice or voxel thickness to compute and assign the required gradient strength in G cm If more than one rf pulse is used during a sequence for a slice selection operation on a given axis such as in a spin echo imaging sequence where both the 90 and 180 pulses are slice selective on a single axis with slice gradient level specified by gss the effective bandwidth of each is determined and the smallest bandwidth is used to compute gss If the rf pulse or pulses found in plist are not frequency selective setgss issues an error message and exits If the slice or voxel thickness found in the designated thickness parameter is too small for the maximum gradient strength of the system the thickness value is reset to its minimum possible value consistent with gmax gradient_parameter is the gradient strength parameter thickness_parameter is the slice or voxel thickness parameter 270 VNMR 6 1C User Guide Ima
418. nal acquisition ni is not normally directly entered in imaging experiments Instead nv to control the number of 2D increments Refer to the VNMR Command and Parameter Reference for information about the use of ni in 2D spectroscopy experiments User Guide Liquids imprep Set up rf pulses imaging and voxel selection gradients M nf Number of FIDs P nv Number of phase encode steps for 1st indirectly detected dim P seqcon Acquisition loop control P setloop Control arrayed and real time looping M Number of slices to be acquired Number of slices in a compressed multislice experiment The number of slices is determined by the number of arrayed elements in pss and is displayed in ns which cannot be directly entered and reflects only the number of values found in the pss array VNMR 6 1C User Guide Imaging 01 999163 00 A0800 np nt nv Values Related Description Values Related Description Values Description A 5 Parameters To increase or decrease the number of slices pss must be changed or re entered after which ns is automatically updated When the multislice control character in seqcon is s indicating a standard arrayed mode of data acquisition for multiple slices ns is set to 1 The number of slices can then be determined directly from the pss array Number to desired number in integer steps ef Current FID P ne Number of echoes to be acquired P nt Number of FIDs
419. nce for imaging orientation is the magnet bore with the Z axis lying along the bore For a horizontal bore magnet the X and Z axes are parallel to the floor with Y in the vertical direction For a vertical bore magnet Z lies along the bore in the vertical direction with X and Y parallel to the floor X and Y orientation in a vertical system depends on the rotational position of the gradient set orient is a convenient way to specify imaging plane orientation but underlying orient are three additional parameters that explicitly control the orientation These are the Euler angle parameters psi phi and theta which are used to precisely set the imaging plane to any arbitrary major or oblique orientation and to communicate this information to the pulse sequence Two of these Euler angle parameters psi and theta determine the orientation of a vector that is perpendicular to the desired imaging plane the slice position pss specifies the distance from the origin to the imaging plane along this vector theta is the angle between this vector and the magnet Z axis psi is the angle between the projection of this vector onto the magnet XY plane and the magnet 324 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 phi Values Related Description Values Related A 5 Parameters Y axis The third angle phi determines the rotational orientation of the imaging plane about the psi theta vector The table on the right lists the
420. nd diffusion flow can be significantly improved by modifying the basic EPI sequence e Pseudo real time images can be continuously obtained which makes EPI ideal for time course studies Variations of the EPI Sequence This section describes four variations of the EPI sequence 1 Gradient Echo or Spin Echo Sequence The EPI sequence can be either gradient echo based or spin echo based In a spin echo sequence inhomogeneity effects are minimized because of the refocusing 180 pulse However scan time is slightly increased by approximately 50 multiplied by the echo train duration 2 Time Course EPI Experiments Time course experiments can be set up by arraying the parameter pad 3 Interleaved Sequences The limitations of gradient strengths resolution and long acquisition times can be overcome by implementing interleaved EPI sequences In such an experiment multiple EPI echo trains are collected Each of the echoes represents segments of k space data They are then combined to generate the complete k space dataset during the post processing stage However this type of experiment is no longer a single shot method The total scan time for interleaved EPI sequences is increased by TR n in which n refers to the number of interleaved experiments 4 Waveform Shapes Readout gradients do not need to be rectangular or constant pulses as shown in Figure 18 and Figure 19 For example the pulses can be trapezoidal or sinusoidal wavef
421. nd display the first image then adjust chart position and retrieve the second image with imconn name2 where name2 is the name of the second phasefile Images in two different experiments can be simultaneously displayed by using jexp with the desired experiment number as an argument in the first experiment adjust the display parameters for example left to display the image on the left side of the screen then use jexp 6 to join experiment 6 without erasing the screen followed by right and imconn to position and display the image in second experiment on the right side of the screen without erasing the first image file is the image phasefile name imconn imconn imagel dconi Interactive 2D contour display C dmi Transform and display multiple images in graphics window M jexp Join existing experiment C etpnE Return a stored phasefile into the current VNMR experiment M imconi Display 2D data in interactive grayscale mode M svphf Save currently displayed phasefile to planes directory M Process arrayed 2D imaging data and fit to T1 or T2 map M UNIX From VNMR imfit t1 t2 basename min_threshold From UNIX imfit t1 t2 basename min_threshold timel time2 timeN Fits an arrayed set of 2D image data and computes a pixel by pixel T or T gt map The imfit macro provides a convenient link to the fitting program by automatically constructing and passing the required arguments to the UNIX 01 999163 00 A0800 VN
422. nding target parameter with a name that is formed by adding the prefix t_ For example slice positions that are planned for a new target experiment are held in the parameter t__pss orientations for a new target slice plane are held in the parameters t_phi t_psi and t_theta ete Miscellaneous Parameters This section lists miscellaneous parameters that do not belong in the previous categories appmode Application mode Applicability All systems except GEMINI 2000 Description Allows selection of specialized system applications modes such as imaging by setting the global parameters sysmaclibpath sysmenulibpath and syshelppath For example in vnmr maclib is a subdirectory maclib imaging that contains macros used primarily with imaging applications Similarly in vnmr menulib is a subdirectory menulib imaging for imaging related menus By separating the imaging macros and menus into subdirectories access to imaging specific macros and menus is more convenient This separation also allows minor modifications to some macros and menus while retaining the names that are in common use or required by other VNMR commands The dconi menu illustrates how appmode works In normal 2D spectroscopy operation defined by setting appmode standard the dconi menu displays a button labeled Peak that provides access to interactive 2D peak picking With appmode imaging however this button is labeled Mark instead and now performs the 1D or 2D ma
423. ndow Calctool and Figure 65 shows the Save Check window Note that the 8 as a result in the expression was optional and nothing needed to be placed to the right of the sign When Save is selected a window allowing the map number and a comment field to be specified opens Enter something in the comment field that allows you to later recognize the Figure 65 Save Check Window map pH Map Calculate pH maps and frequency difference maps from the MVS data or the metabolic map data by performing the following steps 1 Select pH Map from the Process option with the right mouse button 2 Select a Gframe 3 As an example create a default pHmap Select Mmap in the Peak Define field 4 Select the Mapping Apply option to display a pH map in the selected Gframe VNMR 6 1C User Guide Imaging 01 999163 00 A0800 6 3 Tools Nothing is registered or saved until Save Map is selected which opens a save window that again allows the map number and a comment field to be specified See pH Map Control page 166 for more information on pH and frequency difference maps Box ROI Tool The Box ROI tool draws a rectangular ROI It is used in the statistics processing function To draw a rectangular ROI after the tool is selected position the cursor at one of the desired corner coordinates press the left mouse button and drag the cursor over the desired region of interest area As the cursor is being dragged an XORed rectang
424. nect the shim power cable from the shim connector port of the gradient coil unless the system shim supply has been switched off Severe damage to the shim supply can occur if it is powered up as connections are being modified Thermocouple Connector The thermocouple connector J5903 mates with the thermocouple sensor cable P59X3 from the system gradient supply to complete the sensor circuits needed to protect the gradient coil from thermal overload CAUTION Make sure that the thermocouple sensor cable is connected to the gradient coil you are about to use If the sensor cable remains disconnected the thermal overload protection circuits of the system gradient supply will not function correctly Experiments requiring high gradient duty cycle could then lead to damage of the gradient coil Water Connectors and Hoses When connected to the water fittings located on the HPAG quick disconnect box the water hoses supply cooling water to the main gradient coil The quick disconnect fittings provide automatic water shut off through spring loaded valves located in the fittings This allows the water connections to the gradient coil to be broken with minimal spillage of cooling water from the coil Locking Mechanism The rear plate of the rf shield for the main gradient coil has threaded holes to accept the locking screws for the auxiliary gradient coil Eddy Current Compensation Boards The system gradient power supply GPS 2239 operates
425. nel screws and then flip down the control panel Figure 87 shows the internal card cage which holds the power supply control boards Security Board PSU Board 1 2 3 4 5 6 7 8 9 10 11 12 jf Exchange X Y and Z Compensation ba Figure 87 Gradient Supply Internal Card Cage WARNING Do not proceed with the following steps unless the gradient supply is fully powered off CAUTION The compensation boards are individually keyed to the internal card cage slots Do not use force if the board does not fit into the slot You could damage the boards by doing so To exchange eddy current compensation boards take the following steps 182 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 7 7 2 Experimental Setup Power off the system gradient supply by first pressing the Stop button and then turning the main power switch to the off position Remove the two retaining screws from the top of the gradient supply control panel and flip it down to expose the internal card cage that contains the power supply control boards Refer to Figure 87 and locate the positions of the three eddy current compensation boards If we label the slots of the internal card cage through 12 starting on the left hand side with the security board then the eddy current compensation boards are located in slots 3 6 and 9 The bonds are typically labeled X Compen
426. ngle Gframe is created that fills the entire graphics region and the image is loaded into it To load all the files in the current directory click the Load All button Loading Images Load FDF files by selecting the FDF file and clicking the Load button For VNMR phasefiles the directory that contains the phasefile must be selected when the Load button is clicked Loading 3D Images Image Browser can load 3D data sets that are in FDF format These are identified by having a rank of 3 and a spatial_rank or subrank of 3dfov specified in the header When a 3D data set is loaded into Image Browser the Slice Extraction window shown in Figure 46 opens This window has a File menu where the _ xz top 0 name of the current 3D data set _ yz side is selected and displayed To i extract slices first make sure Extract Slices Extract MIPs Unload that an appropriate Gframe is File usr25 chrisp sw ib DATADIRS 3D cube fdf selected to load into Also make sure that the desired data Figure 46 Slice Extraction Window set is selected in the File menu Then in the extractor window check off the slice orientations desired and the range of slice numbers The increment Incr may be set to some n greater than one to load only every nth slice Press the Extract Slices button to actually load the selected slices If there is only one Gframe it will be split into enough frames to hold all the slices
427. ns in any experiment by searching for all parameter names that begin with the two letters dg and presents a menu of all such names To display any of these parameter groups select the button with the desired description Once a parameter group is displayed use the Print button to print it Gradient Parameters A predefined group of gradient parameters is present in all imaging parameter sets covering the range of most imaging applications All of these gradient parameters have units of gauss cm and are created in VNMR as type real Because the maximum gradient strength is dependent on the gradient hardware in use there is no automatic over range checking of gradient parameters While a value larger than the maximum possible gradient may be assigned to a parameter there is no risk of physical damage to the gradients because the pulse sequence functions that control gradients do check for values exceeding the allowed physical maximum Gradient Calibration Parameters BO Magnet main static field Description Field strength of the main magnetic field This value is used by planning setup macros in their calculations Values Number in units of gauss Nominal value is 234 9 h1l freq For example a 4 7T 200 MHz system has a value of approximately 47 000 Related hlfreq Proton frequency of spectrometer P boresize Magnet bore size Description The internal usable diameter of the gradient set This parameter is used by various p
428. nsion P nv2 Number of phase encode steps for 2nd indirectly detected dim P ny3 Number of phase encode steps for 3rd indirectly detected dim P seqcon Acquisition loop control P setloop Control arrayed and real time looping M Number of phase encode steps for 2nd indirectly detected dimension The number of phase encode steps for the second indirectly detected dimension in a multidimensional imaging or CSI experiment In a 3D image nv2 controls the resolution in the third spatial dimension lpe2 In a 2D or higher CSI experiment nv2 controls the second spatial dimension 1pe2 The lower level parameters ni and nf are automatically set each time a value of nv is entered through the macro set loop which uses the seqcon parameter to determine if the acquisition is standard or compressed in the dimension controlled by nv2 and appropriately sets either ni or nf Because nv2 is explicitly used in most imaging pulse sequences to specify the number of phase encode steps the user should never directly set ni or nf but instead set nv2 and let the software automatically assign ni and nf flashe Convert compressed 2D data to standard 2D format C imprep Set up rf pulses imaging and voxel selection gradients M lpe2 Field of view size for 2nd phase encode axis P nE Number of FIDs P ni Number of increments in 1st indirectly detected dimension P nv Number of phase encode steps for 1st indirectly detected dim P nv3 Number o
429. nsity which assumes that the screen intensity is described by a function of the form I 1 V Eq 26 where is the intensity V is the voltage proportional to the pixel value y is a characteristic of the monitor equal to about 2 5 and J is the background intensity due to room illumination or poor adjustment of the monitor The Value field next to the Gamma switch controls the value of y used in the above equation The Contrast field next to the Log switch specifies the value of the ratio of maximum to minimum displayable intensities in effect J in the previous equation Normal values for a properly adjusted monitor are 50 to 100 for 7 and about 2 5 for gamma If the monitor brightness is not properly adjusted it is still usually possible to get a good fit by adjusting y the function is relatively insensitive to the Contrast value When the Gamma switch is on a control point is displayed near the middle of the gamma correction curve This control point can be dragged with the left mouse button to adjust the Gamma value The Contrast value can only be changed by typing a new value in the text field If the Gamma switch is ON and the Log switch is OFF correction is made for equal steps in intensity according to the formula J V This correction is not ideal but it might be useful for emphasizing the contrast in some region of the colormap which could normally be done with the V scale function instead Saturation
430. nsmitter semicircle in the center of oneresonance off resonance the spectrum The spatial frequency spectrum Figure 3 Frequency Ranges shown in Figure 3 is also referred to as a profile or projection of the sample along the y direction The projection resolves the spatial frequency components along a single direction But an imaging sample is three dimensional so more imaging must be done to visualize our sample in 3D space Many experiments have been designed in the past to uniquely identify and map the spin distribution in the sample Each experiment has its own advantages and limitations Experiments based on the spin warp techniques are the most commonly used in MRI Therefore it is useful to understand how these experiments resolve the spatial frequency components of a 3D sample The 2D spin warp experiment contains the following three parts which correspond to the preparation evolution and detection steps in a conventional 2D NMR experiment e Slice selection e Phase encoding e Readout 28 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 2 3 Slice Selection 2 3 Slice Selection Magnetic resonance images are displayed as 2D pictures in either grayscale or color scale for further analysis The 2D images represent the NMR signals taken from a slice in the sample as shown in Figure 4 It is possible to selectively obtain signals from a slice by using a slice selection process During the preparation phase of the experim
431. nt which must always be supplied ranges from to n it specifies the desired correction map block within the file pcmapapply 1 pemapclose Close phase correction map file C pcmapgen Generate phase correction map C pcmapopen Open phase correction map file C Close Phase Correction Map C Systems with echo planar imaging capabilities pcmapclose Closes a phase correction map file that was explicitly opened with the pcmapopen command pcmapclose pcmapapply Apply phase correction map to data C pcmapgen Generate phase correction map C pcmapopen Open phase correction map file C Generate Phase Correction Map C Systems with echo planar imaging capabilities pemapgen lt file gt lt index gt Generates pixel by pixel complex phase correction values from the current data file and stores them into the lt index gt block in the phase correction map file Svnmruser expN datdir lt file gt file must reside in your Svnmruser expN datdir directory where N is the current experiment number One or more phase correction maps can be generated In the case of a multislice echo planar imaging experiment there can be one phase correction map for each slice 298 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Arguments Examples Related pcmapopen Applicability Syntax Description Arguments Examples Related rtphf Syntax Description A 4 Commands and Macros for Processing and Di
432. nt reflections of the image about an axis perpendicular to the arrow The operation is applied to all selected frames Note that the header information is also Figure 38 Rotation Panel transformed on rotation or reflection in order to keep track of the actual orientation and position of the slice in the magnet Image Arithmetic Image Arithmetic is another processing function in Image Browser Select the Image Arithmetic option from the Process menu in the control panel to open the Arithmetic window This window allows addition subtraction multiplication and division of two images or of an image and a scalar value The operands can be selected first or the images can be selected first Images are selected by selecting the Gframe where the image resides The first Gframe is always selected with 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 95 Chapter 4 Image Browser 96 the left button and the following Gframes are selected with the middle button The Operands field offers two options Image lt op gt Image If this field is selected two or three Gframes can be selected and the operation is executed according to the order given If two Gframes are selected the second one selected is also used to store the result If three Gframes are selected the third Gframe gets the result Image lt op gt Constant If this choice is selected a field for entering a constant is displayed in the Arithmetic window One or two images c
433. ntrol points changing the control points in one mode also changes them in the other The spline function used here interpolates between control points with cubic polynomials arranging that the slopes match at the control points The final curve is continuous up to the second derivative At the endpoints second derivative is forced to zero the defining condition for the so called natural cubic spline Underflow and Overflow The Underflow and Overflow menus control how data values outside of the domain of the mapping function are displayed The default is Off meaning that data values less than the minimum data value x lt d are displayed the same as x d and that data values x gt D are displayed the same as if x D The menus offer a number of alternative color choices for such values VsProp Menu Gamma Correction The Gamma choice in the Vs Prop menu opens the Gamma Correction Show Saturation _ Gamma Correction window shown in Figure 33 The primary purpose of gamma correction is to make optimal use of the limited number of grayscale steps in Image Browser s colormap A secondary purpose is to compensate for any unusual nonlinearities in the monitor s displayed intensities Compensation allows images to appear the same with identical scaling on any monitor once gamma correction has been done For a properly Figure 33 Gamma Correction Window adjusted monitor minimal gamma correction should be
434. ocated on the front panel The input output jacks and unit s power cord are located on the back panel Receiver Front Panel Figure 104 shows the front panel of the receiver SIS PHYSIOLOGICAL GATING MODULE INHIBIT TIME SEC ECG PREAMP FILTERS m THRESHOLD V can POLARITY ON AUTO 6 fo PGM 1000 Figure 104 Front Panel of PGM 1000 Receiver The front panel contains the following controls and indicators e ON OFF activates the unit when plugged into a source of ac current at 115 V 50 60 Hz e POWER ON lights to indicate that the PGM 1000 receiver is powered up e PREAMP ON lights to indicate that the cardiac preamplifier is powered up and that the optical link between the modules is functional 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 213 Chapter 9 Physiological Gating Module e PREAMP LOW BAT lights to indicate that the power of the cardiac preamplifier battery is low Replace the battery The PGM 1000 units will continue to operate once the low battery condition is indicated until the PREAMP ON LED dims indicating failure of the optical link e GAIN X10 X1 boosts the gain of the PGM 1000 receiver amplifier to increase the level of the decoded ECG signal The switch has X1 and X10 positions e POLARITY POS NEG inverts the polarity of the ECG signal The PGM 1000 receiver detection circuits only provide trigger pulses for positive signals upward deflections on oscilloscope trace The polarity swi
435. ods 209 vertical line marker tool 155 projection of trace 278 01 999163 00 A0800 vertical scale V scale binding turning on and off 101 property 82 vertical scaling 75 78 adjusting image 51 bind unbind 153 gamma correction 151 properties 149 tool 67 74 82 148 window 82 83 149 VIFF file format 107 VNMR files 108 phasefile format 67 74 raw data format 133 137 VnmrIMAGE pulse sequence 17 vol_ commands 102 345 vol_extract command 345 volume calculation 93 measurements 93 volume based BP acquisition 236 vox1 vox2 vox3 parameters 328 voxel dimensions 328 select tool 154 selection 313 setting up selection 62 voxmark macro 277 Vs Props window 148 VT experiment warning 12 Ww warnings defined 11 waveform shapes EPI 58 weighted Fourier transform 232 weighting function 231 wit2d command 51 wildcards 106 window init file 69 133 wti command 231 X XBM file format 107 X coord list 94 XPM file format 107 XWD file format 107 Y Y coord list 94 Z zero phase encode projection 21 zero filling 343 zooming 78 _factor command 100 factor setting 100 function 75 81 magnification 79 01 999163 00 A0800 Index tool 67 74 148 VNMR 6 1C User Guide Imaging 359 Index 360 VNMR 6 1C User Guide Imaging 01 999163 00 A0800
436. of Preemphasis This section is a brief theoretical description of preemphasis also known as eddy current compensation and is provided to orient you to the function of the module and the software and give you a description of a few key terms It is not intended to be a full description of 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 199 Chapter 8 Digital Eddy Current Compensation X WFG 5 X to amp coil Y WFG a T to amp coil WFG Z Z to amp coil G G G Bo SDAR to amp or coil BO DSP ECC 50 y DSP ECC BO DSP ECC DECC HJHQG gt Amplifier QO Summing junction WEG Gradient waveform generator gt Digital to analog Converter DSP Digital Signal Processor G Gain block Figure 95 DECC Module Block Diagram the issue and you are referred to other NMR and MRI literature for more background Also this chapter does not provide any descriptions of methods for measuring eddy current effects 200 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 8 2 Theory of Preemphasis Measuring Two Samples Consider a configuration that consists of two samples one sample I located at the center of the gradients center of X Y an
437. om Magnification You can change zoom magnification with the Image Browser command zoom_factor As an example to change magnification by a factor of 1 414 do the following steps 1 Click on the Macro button 2 Click the On button in the Record field to record the change 3 Enter zoom_factor 1 414 on the Name line 4 Click on the Execute button You can also change zoom magnification by doing the following steps 1 Select the Zoom button in the Tools window 2 Click on the Zoom Properties button with the right mouse button and select the Zoom factor option 3 Inthe Zoom magnification factor window enter the desired magnification factor as shown in Figure 28 Figure 28 Zoom Magnification Factor Window 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 79 Chapter 4 Image Browser 4 3 Graphics Tools 80 This section is a reference about the Tools window displayed when the Tools button in the Image Browser control panel is selected Figure 29 shows the Tools popup window Only one graphics tool can be active at a time to prevent confusion over mouse button use The Tools window contains a set of graphics tools to create objects manipulate objects or an image inside an object and draw annotation on images Choose a tool by clicking the left mouse button for the desired tool Figure 29 Tools Window In addition to the buttons for tools there is a Properties button that activates a menu listing several com
438. ometric center with the center of the field of view Make sure that the probe under investigation fits into the given boundaries If the probe exceeds the given boundaries the profile will suffer from folding aliasing artifacts and exhibit nonzero values on the left and right edges as depicted in Figure 126 In the reconstruction process these effects are interpreted like a step function with unlimited slope The reconstruction itself uses the derivative and therefore its result will be imposed To prevent distortion increase the field of view readjust the probe alignment with regard to the center of the field of view or take both actions Dynamic Range Limitations In a simple approach BP image reconstruction can be viewed as adding each profile onto the slice or volume taking its particular orientation angle phi and theta into account In reality a filter or convolution process is involved together with a linear interpolation Therefore the center points of all profiles are added to the center point of the slice or volume On the other hand the center point of a profile corresponds to the dc offset of the VNMR 6 1C User Guide Imaging 01 999163 00 A0800 10 5 Artifacts in BP Imaging Figure 126 Distorted Images acquired magnetic resonance signal Any imperfections in dc offset correction result in a small additional intensity in the center of the profile These imperfections are added up in the reconstruction process
439. ompatible FDF files M svib directory lt f m gt Generates images from the current experiment and saves them into the specified directory as Flexible Data Format FDF files suitable for display in the Image Browser image processing program svib saves a single image or a number of images from a multislice multiecho or arrayed imaging experiment The VNMR command svdat is used to write the binary image file directory specifies the name of the directory to save the FDF files svib creates the directory in the current working VNMR directory and appends it with the extension dat FDF image files are created in this directory as image0001 fdf image0002 fdf etc A copy of the procpar file from the current experiment is also saved in this directory f is a keyword to save the output data in 32 bit floating point format This is the default m is a keyword to save the output data scaled to 12 bit integer and saved as 16 bit words historical Siemens Magnetom data format svib phantom svib rodent images m makephf Transform arrayed imaging data and save as phasefiles M svdat Save data C svphf Save currently displayed phasefile to planes directory M Save parameters from current experiment M svp file Saves parameters from current experiment to a file The parameter set can be retrieved with the rtp and rt macros svp reflects any changes made in parameters up to the moment of entering svp including acqui
440. on in 2D data sets the f3 dimension in 3D data sets etc n or a number equal to a power of 2 minimum is 32 If fn is not entered exactly as a power of 2 it is automatically rounded to the nearest higher power of 2 e g setting fn 32000 gives fn 32768 fn can be less than equal to or greater than np the number of directly detected data points e If fn is less than np only fn points are transformed e If fn is greater than np fn minus np zeros are added to the data table zero filling e If fn n fn is automatically set to the power of 2 greater than or equal to np Enl Fourier number in 1st indirectly detected dimension P fn2 Fourier number in 2nd indirectly detected dimension P np Number of data points P Fourier number in 1st indirectly detected dimension Selects the Fourier number for the Fourier transformation along the first indirectly detected dimension This dimension is often referred to as the f1 dimension of a multi dimensional data set The number of increments along this dimension is controlled by the parameter ni fn1 is setin a manner analogous to the parameter n with np being substituted by 2 ni fn Fourier number in directly detected dimension P fn2 Fourier number in 2nd indirectly detected dimension P ni Number of increments in 1st indirectly detected dimension P np Number of data points P Homodecoupling control for first decoupler All systems except MERCURY and GEMINI 20
441. once the ROIs have been created When ROI binding is on all ROI modifications moving resizing or adding or deleting polygon vertices are applied to all ROIs in a group While a group of ROIs are being created or modified they might not appear exactly identical because integer arithmetic is used to translate mouse actions in one graphics frame to roughly equivalent mouse actions in another frame This effect can be particularly noticeable when the master frame is much larger than the slave frames Polygons in particular can have fewer vertices in smaller frames However when the creation or modification is completed all the slave ROIs are replaced with copies of the master ROI Controls the real time updating of the slave ROIs when ROI binding is enabled The maximum number of tracking ROIs is set by the user If set to 0 only the ROI on which the mouse operates directly changes in real time but when the mouse button is released all the ROIs in all the group snap to the new configuration In general if set to a number n less than the number of selected ROIs only the ROIs in the first n Gframes track in real time the cursor is being dragged the line is drawn in the active ROI color purple by default When the eft button is released the completed line appears in the selected ROI color The Line ROI tool has the same ROI Properties menu choices as the ROI Selector tool Point ROI Tool The Point ROI tool
442. ons to acquire for 2D Also set nv2 for 3D Set phi2 and also thet a2 for 3D These values select between a 180 or a 360 angular span of the projections taken Usually the 180 span is taken because the projections obtained at 0 are identical to the centrally mirrored projections from 230 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 10 4 Routine Usage 180 However in slice selective excitations and cases of Bo shift due to gradient switching the image quality can be improved by taking projections from the full 360 span 10 Enter imprep which calculates rf strengths gradient strengths and timing Starting the Measurement The following steps perform the measurement for sequences dp2d and dp3d 1 Enter go to start the acquisition 2 Check the spin echo signal by displaying it with df If the signal amplitude is too high decrease the gain with gain lower_value You can also look at projections during acquisition by entering ft and then ds Performing the Fourier Transform To obtain profiles from the projections taken perform a Fourier transform You may use an unweighted or weighted transform e For an unweighted transform enter ft e Fora weighted transform weighting is determined by the desired pixel resolution and the available signal to noise To set the weighting enter wti and then wft Figure 112 shows a typical display If the center of your spin echo is left shifted move the center of the weightin
443. ontacts the body seek immediate medical attention especially if the skin is blistered or the eyes are affected WARNING Do not look down the upper barrel Unless the probe is removed from the magnet never look down the upper barrel You could be injured by the sample tube as it ejects pneumatically from the probe WARNING Do not exceed the boiling or freezing point of a sample during variable temperature experiments A sample tube subjected to a change in temperature can build up excessive pressure which can break the sample tube glass and cause injury by flying glass and toxic materials To avoid this hazard establish the freezing and boiling point of a sample before doing a variable temperature experiment VNMR 6 1C User Guide Imaging 01 999163 00 A0800 SAFETY PRECAUTIONS Warning Notices continued WARNING Support the magnet and prevent it from tipping over The magnet dewar has a high center of gravity and could tip over in an earthquake or after being struck by a large object injuring personnel and causing sudden dangerous release of nitrogen and helium gasses from the dewar Therefore the magnet must be supported by at least one of two methods with ropes suspended from the ceiling or with the antivibration legs bolted to the floor Refer to the Installation Planning Manual for details WARNING Do not remove the relief valves on the vent tubes The relief valves prevent air from entering the nitrogen and heliu
444. ontrol panel The movie is played in the currently selected Graphics frame Note that when the vertical scaling or image size is changed the movie runs more slowly the next time through the loop The slower speed occurs because the program is taking advantage of the pixel buffering capabilities of the X Window System and generating pixel files for display The movie can be stopped at any time and another graphics frame can be selected and the movie can be started in the new Gframe Changing the Frames sec entry alters movie speed To change movie speed stop the movie enter a new frame speed number and restart the movie Frame speed is also monitored so that it can be determined whether or not the current environment can support the requested speed While running over the network the Speed indicator does not always clearly indicate problems but any kind of erratic movement of the indicator should signal that there is a problem A subsection of the playlist can be played by using Start and Stop Pictures can be stepped through one at a time by using Current Zooming and Vertical Scaling Zooming and vertical scaling can be performed on images Images can be zoomed and the zoomed region animated by stopping the movie and selecting Zoom in the Tools window Interpolation can be used when zooming but it makes the startup time much longer because each image has to be interpolated to generate the pixel image to display Vertical scaling can also be
445. ool draws a line ROI This tool is used in the Line Data processing function It is also possible to obtain statistics from a line ROI although this might not generally be useful The points included in the statistics are the points along the line To draw a line after the tool is selected position the cursor at one of the desired endpoints press the left mouse button and drag the cursor to the other end point As the cursor is being dragged an XORed line is drawn Release the left mouse button and the line appears in the selected ROI color 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 153 Chapter 6 CSI Data Processing 154 Box ROI Tool The Box ROI tool draws a rectangular ROI It is used in the statistics processing function To draw a rectangular ROI after the tool is selected position the cursor at one of the desired corner coordinates press the left mouse button and drag the cursor over the desired region of interest area As the cursor is being dragged an XORed rectangle is drawn When the left mouse button is released the completed rectangle appears in the selected ROI color Annotation Tool The Annotation tool annotates text After it has been selected position the cursor at the desired spot and click the left mouse button An underscore cursor appears at the marked location indicating that the label is selected and ready to accept typed input Typed characters are always added to the end of the annotatio
446. open the program 1 Select the Image Browser Math choice from the Process menu in the Image Browser control panel The Image Math window shown in Figure 47 is displayed Figure 47 Image Browser Math Panel 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 111 Chapter 5 Image Browser Math Processing 2 Type an expression or function into the scrolling window at the bottom of the panel You can use the Expression button to automatically enter a previously compiled expression 3 For either expressions or functions you need to specify which images are to be operated on Images are specified by their graphic frame Gframe numbers using symbols such as n in which n is the number of a Gframe containing an image To automatically enter Gframe numbers do the following procedure Select the Image Browser Math process b Click the mouse cursor inside a Gframe The number of that frame is entered in the Image Browser Math equation area at the current cursor location If the cursor is positioned just after a only the Gframe number is entered and any preexisting number is deleted otherwise a and the Gframe number are inserted 5 2 Image Browser Math Expressions Legal expressions are in the form of standard C expressions with the image specifiers n treated like float type C variables in evaluating the expression For example the following expression calculates the average of the images in Gfram
447. or the echo loop counter in pulse sequences with this capability 1 to desired number in integer steps ee Current FID P nt Number of FIDs P ns Number of slices to be acquired P seqcon Acquisition loop control P te Echo time P setloop Control arrayed and real time looping M Number of FIDs The number of compressed acquisitions in a compressed multidimensional multislice or multiecho experiment nf is not normally entered directly but is set automatically when required through other parameters such as ne ns or nv The parameter nf together with np governs the total number of points that are acquired during one pass through the pulse sequence code including all loops The single requirement is that this number of points be equal to the product nf np Refer to the manual VVMR Command and Parameter Reference for information about the additional use of nf in nonimaging applications Positive integer imprep Set up rf pulses imaging and voxel selection gradients M ne Number of echoes to be acquired P sala Number of increments in 1st indirectly detected dim P ns Number of slices to be acquired P nv Number of phase encode steps for 1st indirectly detected dim P seqcon Acquisition loop control P setloop Control arrayed and real time looping M Number of increments in 1st indirectly detected dimension The number of standard increments in the first indirectly detected dimension of a multidimensio
448. or zero filling 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 165 Chapter 6 CSI Data Processing It is generally easier and better to read in the images In the future Image Reconstruction may be made obsolete as a processing function Metabolic Image Calctool The metabolic Image Calctool is a calculation tool for spectral peaks from the MVS data It can add subtract multiply and divide peaks Set the result equal to a new value to create new peaks Click Save to save the created peak to the metabolic map data buffer Figure 64 on page 146 shows the Image Calctool and an example calculation The calculation adds peaks and 2 together and multiplies them by a constant 2 0 Peaks are specified by integers constants are specified by real numbers A peak number might or might not be specified as a result In this example a peak number is specified as a result To execute this calculation click on the aj button Even though a peak number has been specified as the result the storage of this calculation is not performed until the Save option is selected If no peak has been specified in the result a peak map number can be entered in the Save Check window shown in Figure 65 on page 146 Select Save to activate this window pH Map Control The pH Map process can create pH maps or frequency difference maps pH maps are generated with the calculation ph pK2 In s b a s where s is the chemical shift difference betwee
449. origin to the desired imaging slice along the imaging plane orientation vector It can be arrayed to specify a list of slice positions for a multislice imaging experiment Most multislice sequences acquire data following the order of slice positions found in pss A monotonic list of positions for example pss 1 2 3 4 5 6 results in multislice excitation in that order To get interleaved slice excitation order e g 1 3 5 2 4 6 pss should be arrayed exactly as desired for example pss 1 3 5 2 4 6 The number of slices in a multislice experiment is determined by the number of arrayed elements in pss and is displayed in the parameter ns which cannot be directly entered and only reflects the number of values found in the pss array To increase or decrease the number of slices pss must be changed or reentered after which ns is automatically updated Although pss is an acquisition parameter arraying it does not normally result in a conventional arrayed experiment When seqcon is set to specify multislice acquisition in compressed mode pss protection bit 8 is turned on turning off the automatic arrayed experiment feature In this case the values of pss are read into the pulse sequence and used in the poffset_list or position_offset_list pulse sequence VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Values Related theta Description Related thk Description Values Related A 5 Parameters statements
450. orms There are two advantages of such pulses e They are less demanding on the gradient hardware because of the reduced slew rate VNMR 6 1C User Guide Imaging 01 999163 00 A0800 3 5 Echo Planar Imaging and Phase Correction Map Files e Eddy current effects are minimized Eddy current effects are a function of the rate of change of the gradient fields Note that the gradient fields vary during the acquisition period If the collected data is not rectangular it must be corrected either by post processing or by nonlinear sampling so that the final k space data is regenerated onto a rectangular grid before further image processing The usual data processing algorithms such as ft expect the data to collected in a linear fashion Experimental Procedure The following steps perform an EPI experiment 1 Enter the episs macro to load the default parameters for single shot EPI from the default parameter directory Initialize the imaging parameters The common parameters are listed in Table 4 Table 4 Imaging Parameters Parameters at gcoil ir lpe lro np nv orient pro pss resto rfcoil spinecho sw thk cE tspoil Acquisition time per echo Gradient calibration file Inversion recovery flag 0 off 1 on Length in phase encode direction cm Length in readout direction cm Number of points in read dimension real and imaginary Number of phase encode values Image orientation Position offset i
451. ors for Gframes ROIs and text annotations can be personally defined The number of grayscale levels can also be reduced if colormap flashing is a problem levels can also be increased if more intensity resolution is desired Machines with 24 bit frame buffers should not exhibit flashing problems with Image Browser For those machines set the number of gray levels to 200 by changing the 64 to 200 in the line gray color 64 DEFAULT_GRAY_COLOR The number of colors available for ROIs and labels can also be increased by changing the 12 in the line mark color 1 to whatever is desired and adding lines specifying RGB values to the list that follows that line macro Directory containing user macros and in particular the macro startup which is executed when Image Browser starts startup might load a set of Gframes and set various options such as the gamma correction settings 68 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 4 2 Getting Started window init File containing the default positions for the main Image Browser window and various popup windows gframe Directory containing the supplied Gframes The file default in gframe is the set of Gframes that are loaded at startup In this directory or a subdirectory sets of Gframes can be saved A personal default set of Gframes can be created by overwriting the current default file roi Directory possibly with subdirectories in which any created ROIs for loading onto a set of
452. ors from the front and back of the main gradient coil and any samples or bore equipment present in the magnet Set aside for future use 6 Load the auxiliary gradient coil into the magnet through the rear entrance The auxiliary coil is heavy use at least two people to lift and manipulate it into position 7 Align the locking mechanism brackets on the auxiliary coil with the threaded holes in the main coil rf shield and lock in place with the locking screws 8 Disconnect the thermocouple sensor cable P59X3 from the main gradient coil J5903 Connect it to the auxiliary coil J5913 9 Disconnect the shim power cable P59X2 from the main gradient coil J5902 Connect it to the auxiliary coil J5912 184 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 7 2 Experimental Setup 10 Disconnect the main gradient power cable P5901 from the HPAG quick disconnect box J59X1 Connect the gradient power cable P5911 from the auxiliary coil in its place 11 Disconnect the water hoses from the main coil Connect the water hoses from the auxiliary coil to the water quick disconnect fittings at the HPAG quick disconnect box 12 Restore the water supply to the gradient coil at the main water shut off valve Check the HPAG quick disconnect box for potential leaks 13 Exchange the eddy current compensation boards in the system gradient supply for the set calibrated for the auxiliary gradient coil 14 Verify that system connections a
453. ositioning of at least one of the chemical species due to the chemical shift difference The VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Related satfirg Description Related wsfrq Sw Description Related A 5 Parameters chemical shift specified by resto therefore is most accurately positioned in an image or localized spectroscopy voxel Users of vertical bore microimaging system may choose to adjust Z0 to bring the reference chemical shift on resonance and set rest o 0 Most horizontal bore imaging systems do not have a ZO shim adjustment so this is not an option gss Slice selection gradient strength P offset Calculate and display absolute frequency offset at cursor M pss Slice position P Presaturation frequency Frequency offset parameter for use in specifying the frequency for presaturation offset Calculate and display absolute frequency offset at cursor M presat Presaturation pulse execution on off P resto NMR resonance offset frequency P Water suppression frequency Frequency offset parameter for use in specifying the frequency for water suppression offset Calculate and display absolute frequency offset at cursor M resto NMR resonance offset frequency P ws Water suppression P Spectral Width Parameters The spectral width parameters sw swl sw2 and sw3 are used somewhat differently in imaging than in analytical high resolution spectroscopy because of the addition of g
454. ot already exist This procedure can also be used to set sysmenulibpath and syshelppath A 2 Macros for Setting Up Experiments Many macros are available for setting up NMR experiments This section summarizes the most useful macros for imaging experiments creategtable Create gradient calibration file Syntax creategtable file Description Generates a new gradient calibration file for gradient sets with nonisotropic strengths Gradient calibration constants such as gmax maximum gradient strength and t rise rise time of a gradient from 0 to gmax are stored in the directory vnmr imaging gradtables Each gradient set installed with the system should have a corresponding file in this directory describing its gradient strength and rise time These gradt ables text files can be manually copied and edited to add or modify gradient calibrations creategtable is supplied as a convenient method of generating a new file through a series of prompted responses It should be used to make gradtables entries for gradient sets that have isotropic strengths i e strength on X Y and Z axes and nonisotropic gradient strengths Arguments file is the new gradient calibration file name Examples creategtable asg33 Related createpfgtable Create gradient calibration file nonisotropic strengths M gmax Maximum gradient strength P trise Gradient rise time P createpfgtable Create new gradient calibration file nonisotropic strengths S
455. out axis dimensions when the axis parameter is set to positional units of cm or mm To change 1 ro enter the desired value through the VNMR command line and then run the macro imprep to update other dependent parameters 1 ro sw and gro are related by the expression sw y lro gro Values Number in cm Related axis Axis label for displays and plots P dconi Interactive 2D contour display C gro Readout gradient strength P imconi Display 2D data in interactive gray scale mode M imprep Set up rf pulses imaging and voxel selection gradients M lpe Field of view size for phase encode axis P setgro Set readout gradient M sw Spectrum width P orient Slice plane orientation Description The orientation of an imaging plane volume or projection in the magnet reference frame The allowed settings of orient are trans cor sag and oblique corresponding to transverse Z slice plane coronal Y slice plane and sagittal X slice plane trans cor and sag are the three major orientations that is they have readout phase encode and slice selection axes that are combinations of the three major X Y and Z laboratory frame axes The table on the right lists the complete descriptions of the three Orientation Readout major orientations Phase Slice Encode Select An oblique orientation is trans Y X Z angled so that it does not cor Z x Y correspond to one of the sag Z Y x three major planes The frame of refere
456. out your rf coil the slice thickness and field of view you have selected and computes and sets the parameters gro gpe gss tpwrl tpwr2 and sw 2 Ifthe parameter nv was zero a warning is issued otherwise nv is left alone so if you want just a projection first set nv to zero nv controls the number of phase encode steps and is described in more detail on page 335 and ignore the warning 3 You should get the message setup complete if all went well If not you should get an error message that gives you some hint of what could be wrong Checking the Readout Projection It is a good idea to get a zero phase encode projection to check proper operation and to center the image in the readout direction 1 Enter nv 0 to specify just the projection then enter ga to run the experiment 2 Ifthe resulting projection is off center put the cursor where you want the new center to be and enter movepro which computes a new value for the pro readout position parameter pro sets the proper frequency during data acquisition 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 21 Chapter 1 First Steps Making an Image Entering the go Command The final step is to complete the image and see the end product 1 If you are making a projection with nv 0 enter ga otherwise for the complete image set nv to the number of phase encode increments you want typically 128 or 256 and enter go the difference is that ga automatically does a
457. outines use this information together with the pulse calibration database to compute the required power level SEMS is a spin echo imaging sequence which typically uses 90 and 180 pulses giving fliplist 90 180 imprep Set up rf pulses imaging and voxel selection gradients M patlist Pulse shape parameter list P plist Pulse length parameter list P pwrlist Pulse power level parameter list P sslist Gradient parameter names list P First pulse width Length of first pulse in the standard two pulse sequence On MERCURY systems 0 0 2 us to 4095 us On GEMINI 2000 systems 0 0 2 to 4095 us in 100 ns steps On systems with a Data Acquisition Controller board 0 0 1 to 8190 us in 12 5 ns steps On systems with Pulse Sequence Controller or Acquisition Controller boards 0 0 2 to 8190 us in 25 ns steps On systems with Output boards 0 0 2 to 8190 us in 0 1 us steps Refer to the acquire statement in the manual VVMR User Programming for a description of these boards pl Enter pulse width p in degrees C Pulse shape parameter list Contains a list of the parameters that define the rf shapes used for each rf pulse in the sequence The SEMS sequence uses two parameters to define the shapes used by the first and second rf pulses p1 and p2 These parameters are plpat and p2pat with patlist plpat p2pat VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Related plist Description Related pwrlist Des
458. ow iisiii tess cihet aaeecivaeves das s E EER E E ROI EES E EES eaaa 195 Figure 94 ecc Tool Files Window siceieniei nosci iire niiae ee ea EE rE E E ES Siea 196 Figure 95 DECC Module Block Diagram sssscsecsriressiecspiseierossir essre esiisa inene te seers pierin eroista 200 Fipure 96 RF Pulse Acquire Sequence ss cisersrsccseisriueriprseer ereer keste EE EPERE E R NEEE EEE E SEE ESS 201 Fig re 97 decctool Window sscssiscesssesaahesvascevteet sancencsesaasesitonsseseassSdhacosesavehoes sancspccenvasvanhseancvesteiys 202 Fipure 98 eccGrapl Widow cissscsccsessacsssastenscsssastonscdssceeunesbescneasessiaseensessaeesonsdapteebvantannstuneedsieeys 206 Figure 99 Cardiac Anatomy ecne innear n a A EAE E E r E E 208 Figure 100 Figure 101 Figure 102 Figure 103 Figure 104 Figure 105 Figure 106 Figure 107 Figure 108 Figure 109 Figure 110 Figure 111 Figure 112 Figure 113 Figure 114 Figure 115 Figure 116 Figure 117 Figure 118 Figure 119 Figure 120 Figure 121 Figure 122 Figure 123 Figure 124 Figure 125 Figure 126 Figure 127 Figure 128 Figure 129 Figure 130 Figure 131 Figure 132 Figure 133 01 ECG Interpretation sonerien enio aeei E EE EER Eea Rr EERE 209 Front Panel of Cardiac Preamplifier seseeeseeeseeeeseeeeresersreersesereesssrsrerersrerrerersreeeesse 211 Rear Panel of Cardiac Preamplifier eseseeeseeeeseeseseseereersreerersrrressstsreretsreerererseeererse 211 Battery Replacem
459. ower If you have not already made an entry in pulsecal this message appears pulsecal file does not exist 2 Enter pulsecal again this time supplying values for the arguments e For name choose a name that makes sense for the probe and or sample you are using if this is the cube phantom in the large imaging coil for example liccube might make it easier to select the best entry again if you use this combination at a later date For pattern unless you used a shaped pulse enter square If you used a shaped pulse enter its name instead For length enter the pulse length in us For flip if it is a 90 pulse enter 90 if it is a 180 pulse enter 180 or whatever value is appropriate For power enter a value in tpwr units used to measure this pulse length For example if you measured a 180 pulse length of 800 us with a tpwr of 80 your entry is probably pulsecal lic square 800 180 80 A listing of the new or updated pulsecal file is displayed in the text window The current date month day year is also included Determining the Reference Offset Frequency You must provide the proton resonance offset frequency for an imaging experiment You can do this easily now while you have a proton spectrum readily available 1 Display one of the spectra in the array for example ds 1 2 Set the cursor on the resonance probably water 3 Enter the command offset Record the number that appears in the mes
460. p of a system cabinet Plug the power cord of the PGM 1000 receiver into one of the spare power sockets available on the rear of this system cabinet 216 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 9 3 Experimental Setup Cardiac fad preamplifier LA optic Gate out Cardiac filtered Channel 1 Channel 2 Patch panel J8120 Figure 107 Unit Interconnection Diagram 5 Connect the optical fiber cable to the FIBER OPTIC input jack located on the rear of the PGM 1000 receiver Power on both the PGM 1000 receiver and cardiac preamplifier The PREAMP ON LED of the PGM 1000 receiver should be lit indicating that the optical link between the cardiac preamplifier and PGM 1000 receiver has been properly established 6 Connect the GATE OUT jack of the PGM 1000 receiver to the input port on the spectrometer patch panel marked Biological Gate J8120 for an external trigger 7 Connect the CARDIAC OUT FILTERED jack to channel 1 of an oscilloscope Adjust the channel amplitude to 0 5 V per division and select dc input 8 Connect the INHIBIT OUT jack to channel 2 of the oscilloscope and adjust the channel amplitude to 2 V per division Select dc input and normal polarity 9 Adjust the oscilloscope to dual channel mode 10 Adjust the oscilloscope time base control to 0 1 or 0 2 s per division Select channel 1 as the trigger source with normal triggering mode and ac coupling 11 Adjust the bandpass filter contro
461. parameters are stored with the phasefile file specifies the name to be used for the stored file svphf fleming rtph Return a stored phasefile into the current VNMR experiment M svib Generate and save images as Image Browser compatible FDF files M Compute a pixel by pixel T4 map M tlimage Computes a pixel by pixel T map from arrayed inversion recovery imaging data t limage performs all of the pre processing required for fitting inversion recovery T data It prompts for the base phasefile name and lower limit noise threshold transforms and saves all of the images and calls imfit to complete the fitting process and display the computed T map The values at each pixel in the 7 map represent the computed T in seconds imfit Process arrayed 2D imaging data and fit to T4 or T map M Convert data in table order to linear order M tabc lt dimension gt Converts arbitrarily ordered data obtained under control of an external AP table to linear monotonic order suitable for processing in VNMR The data must have been acquired according to a table in the tab1lib directory Imaging and other 2D experiments are normally acquired so that the order of the incremented acquisition parameter such as the phase encode gradient is linear and monotonic For a standard imaging experiment this linear order means that the phase encode gradient progresses from a starting negative value monotonically up through zero to a positive value e
462. part of the initial setup procedure Now the center frequency in the spatial frequency domain refers to the origin or the center of the gradient frame of reference In addition to the standard equipment in NMR spectrometers imaging systems are equipped with X Y and Z field gradient coils that are designed to produce linear field gradients along the x y and z directions respectively In MRI these field gradients are used to get the spatial information from the sample The x y and z gradient fields are orthogonal to each other and their origins lie at the center of the gradient system The field produced in each direction is linear and ranges from a negative value to a positive value the field at the origin is zero Consider the water sample shown in Figure 1 and apply a linear field gradient along the y direction ranging from a negative value to a positive as shown in Figure 2 rf FT i b J karis jy Gy 4 p 0 Vo 3 i y g x Sample in a field gradient Magnetic frame of reference Figure 2 Effect of a Field Gradient Along Direction y In Figure 2 the field along the y direction is no longer constant but varies linearly depending on the position y The field at a particular location y is defined by y Gy in which Gy in gauss cm refers to the field gradient along y direction Therefore the spins along the y direction experience a unique field depending on the location of the y direction 01 999163
463. periodic fashion as each QRS complex is detected 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 219 Chapter 9 Physiological Gating Module 220 The response of the inhibit output should be identical to the previously described response for the automatic threshold when cardiac triggering is obtained This is the minimum setting for the ECG detection threshold Note the position of the threshold voltage control Continue to increase the threshold voltage until the inhibit output just ceases to respond to the presence of QRS waves in the ECG The threshold is now set to the maximum point of the R wave signal Note the position of the threshold voltage control Now reset the control midway between the minimum setting to obtain proper cardiac triggering and the maximum point of the R wave The periodic response of the inhibit output signal should resume Proper cardiac triggering has been obtained e Voltage Threshold The manual threshold voltage level can also be adjusted by observing the voltage threshold output in a what you see is what you get fashion First reduce the inhibit delay and threshold voltage levels to their minimum values Adjust the oscilloscope so that the baseline traces of channels 1 and 2 are coincident with zero external input Adjust the gain control of both channels to the same value either 0 5 V or 1 0 V per division It is important to adjust the oscilloscope channels to the same gain or else this procedure in
464. perpendicular to the gradient direction To obtain a 2D image of the object the direction of the gradient is changed case B C and D In comparing case A and D it is obvious that the position of the cube and the cylinder in the profile have changed By taking a series of angular projections over a range from 0 to 180 the two dimensions of the object are mapped to the one dimension of the profile and the angular dependency VNMR 6 1C User Guide Imaging 01 999163 00 A0800 10 3 Getting Started A mathematical algorithm named projection reconstruction allows reconstruction of the 2D object from this series of angular projections The BP package relies on an efficient implementation of this algorithm to provide short reconstruction times Image generation can be performed not only in 2D but also in 3D 10 3 Getting Started This section describes the steps for setting up acquiring and reconstructing an image by using BP A simple 2D slice select experiment is used in the example Retrieving a Parameter Set Start with the following steps 1 Verify that there is a sample in the probe and that the probe has been tuned shimmed and ready for experiments 2 When you are ready to take a measurement retrieve the parameter set by entering the name of the pulse sequence In this example to use the bp2d pulse sequence enter bp2d to load the parameters Figure 110 shows a typical display of bp2d parameters NUCLEUS RF PULSES GR
465. played in the Gframe the voxel that the cursor is in when the left mouse button is clicked is copied into the selected Gframe If more than one Gframe has been selected an error results To scale the selected spectrum select the View option from the command panel Select Display Properties In the Display Control window choose Auto Normalized or Fixed scaling Select an axis to be displayed in Hz or ppm axis is not yet implemented This tool can be used in conjunction with the processing functions when selecting individual spectrum for processing VNMR 6 1C User Guide Imaging 01 999163 00 A0800 6 3 Tools Marker Tools This section describes the functions of graphics tools for marking points on spectra and spectra data and tools for curve fitting and voxel shifting Picking Tool The Picking tool allows points to be marked on a spectrum for peak and baseline processing It is used in the baseline correction and curve fitting processing functions To mark a point after the tool is selected position the cursor at the desired point and click the left mouse button A marker appears and is selected Whenever this function is used the Edit OK option must be selected afterwards in order for these user defined points to be put into the peak or baseline lists The properties menus of the Picking tool consists of the following Delete Deletes all selected points Frequency Difference Display the frequency difference between
466. ple parameters such as lock spin and temp are initialized to n s2pul Set up parameters for standard two pulse sequence Calculate slice gradient and slice selection parameters M Systems with echo planar imaging EPI capabilities ssprep Calculates the slice gradient parameter gs s and the slice selection parameters tpwrl and tpwr2 for use in the EPI experiment Unlike imprep readout and phase encode related parameters are not modified by ssprep gss Slice selection gradient strength P imprep Calculate gradient and rf parameters for imaging M tpwrl Intensity of an excitation pulse P tpwr2 Intensity of an inversion pulse P Calculate statistics of points specified by cursor position M stats Computes the mean range and standard deviation of the set of points defined by the cursor position in a set of arrayed 1D spectra This function is useful in measuring the stability or reproducibility of data acquisition 01 999163 00 A0800 svdat svf Syntax Arguments Examples Related Syntax Description Arguments A 4 Commands and Macros for Processing and Display Save data C svdat file lt f m i b gt Outputs current data from the current experiment to a file Integer data is scaled when it is written note that svdat replaces the former command svsdfd Floating point data is not scaled when written but integer data is scaled when written A data value x is scaled as ax b whe
467. plifier Back Panel CARDIAC IN The back panel of the preamplifier shown in Figure 102 is fitted O O O with three jacks that interface with corresponding colored plugs on LA RL RA the cardiac electrode leads Table 18 lists the color and connection for each jack and Figure 102 Rear Panel of Cardiac Preamplifier plug Table 18 Cardiac Preamplifier Electrode Connections Jack Color Electrode Plug Limb Electrode LA Black Black left foreleg arm RL Green Green right hind leg leg RA White White right foreleg arm Internal Battery The cardiac preamplifier is battery powered so that it can be mounted in the animal cradle during experiments Before any attempt to replace the battery be sure the preamplifier is removed from the vicinity of the magnet beyond the 5 gauss line CAUTION The battery used inside the cardiac preamplifier is weakly magnetic As a result the unit is subject to a small magnetic force when placed close to the magnet If the preamplifier is located at least 12 cm away from the image plane the battery used to power the unit which is weakly magnetic should create minimal disturbance in the homogeneity of the main magnetic field From time to time the internal battery in the cardiac preamplifier needs to be replaced Symptoms that indicate battery replacement is needed include e LOW BAT indicator on preamplifier front panel blinks when the module is powered up Battery power is low Replace the
468. ply table conversion reformatting to data C tcapply lt file gt Rearranges the spectra in a 2D data set that resides in the current data file You must apply t 1d to the data before you can use this command Using values from an AP table t capp1ly arranges the spectra corresponding to the value in the AP table from low value to high value The values might have already been read in by the t copen command If you provide file the values are read in from vnmruser tablib lt file gt As an example for a standard imaging experiment phase encode gradients monotonically progress from a starting negative value up through zero to a positive value 64 7 603 02 ada pols OF Lys ac 62 63 It is possible to acquire the equivalent data in nonmonotonic order either by explicitly coding the desired progression into a pulse sequence or by using an 304 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Arguments Examples Related tcclose Syntax Description Examples Related tcopen Syntax Description Arguments Examples Related title Syntax Description Arguments Examples Related 01 999163 00 A0800 A 4 Commands and Macros for Processing and Display external AP table to control the order In either method t 2d is not able to properly process the resulting data until t capply and t abc are applied to the data t capply and t abc are functions that reconstruct a properly ordered dat
469. pply Main Supply Figure 84 HPAG Quick Disconnect Box Gradient Connector Port The gradient connector port J59X1 mates with the gradient power cable from either the main system gradient coil P5901 or the auxiliary gradient coil P5911 to provide power for the X Y and Z shims and gradients WARNING Do not connect or disconnect the gradient power cable to or from the HPAG quick disconnect box unless both the system gradient and shim supply have been switched off Gradient connector port J59X1 of the HPAG quick disconnect box presents a risk of electrocution if the gradient power cable is disconnected while the system gradient supply is switched on CAUTION Do not connect or disconnect the gradient power cable to or from the HPAG quick disconnect box unless both the system gradient and system shim supply have been switched off Severe damage can occur to the gradient and shim supply if these are powered on as connections are modified Water Quick Disconnect Fittings The water quick disconnect fittings on the HPAG quick disconnect box are connected back to the main water supply for the system The fittings mate with the corresponding male fittings located on the ends of the water hoses supplied on the main system and auxiliary gradient coils Both the fittings on the disconnect box and the gradient coils have automatic spring loaded shut off values so that water supply can be disconnected with minimal spillage However it is bett
470. profile Set up pulse sequence for gradient calibration M setgcoil Update system gradient coil configuration Syntax setgcoil lt file gt Description Updates the system gradient coil configuration to correspond to changes in gradient hardware Imaging and localized spectroscopy experiments require proper gradient calibration information to properly function Gradient calibrations such as the maximum gradient strength gmax and rise time t rise are stored in calibration files found in vnmr imaging gradtables for each gradient hardware option and specified through the gcoil and sysgcoil parameters When a new or different gradient set is installed the configuration parameter sysgcoil must be set to the name of the file in gradt ables that describes the new hardware Because this config operation can be executed only by the user vnmr1 the special function set gcoil has been provided to allow any user to update this particular aspect of the system configuration file setgcoil updates the system gradient configuration permanently i e until setgcoil is run again or until the system gradient configuration is changed through the config program sysgcoil is asystem global configuration parameter and specifies to all users and all experiments the type of gradient hardware installed on the spectrometer A second parameter gcoil is found in all experiment parameter sets and is saved with the experimental data along with gmax and
471. quick disconnect fittings provide automatic water shut off through spring loaded valves located in the fittings Shut off allows the water supply to the gradient coil to be disconnected with minimal spillage of cooling water from the coil Locking Mechanism The rear housing of the 183 mm gradient coil is fitted with locking mechanism brackets to hold the coil in the correct orientation while the coil is being used in the magnet The holes in the brackets are located over the corresponding threaded holes located in the rear of the rf shield for the main system gradient coil The auxiliary coil can be locked in place using the locking screws During installation of the HPAG accessory the positioning of the locking mechanism brackets is adjusted to place the gradient coil in the correct orientation If the brackets become loose or misaligned in any way contact Varian Service to have them realigned HPAG Quick Disconnect Box The HPAG quick disconnect box allows the power and water connections to the main system and auxiliary gradient coils to be quickly and easily interchanged Figure 84 is a VNMR 6 1C User Guide Imaging 01 999163 00 A0800 7 1 HPAG 183 Hardware diagram of the quick disconnect box The following sections describe the various connections to the quick disconnect box Water Hoses to Auxiliary Gradient Coil Gradient Connector Port Quick Disconnect Fittings Power Lines from N Mater Hoses from Gradient Su
472. r have similar utilities VNMR 6 1C User Guide Imaging 01 999163 00 A0800 4 4 Data Processing Statistics from Multiple Images To retrieve statistics from a specific location within an image over multiple images perform the following steps 1 Define the area to be analyzed by reading in an image and drawing an ROI around the desired area Save the ROI to a file Create enough Gframes to hold all the images If all the images are in one directory read them all in using the Load All button Capture all of the Gframes by choosing Select All Frames ON Ye eo Load the saved ROI which is automatically drawn in all the selected Gframes that have images 7 Update the statistics if the Statistics window is open or select ROI Statistics if the window is closed This procedure generates statistics for the selected area in all the images and is the sort of operation that could best be put into a macro Note that ROIs are fixed to the image as opposed to the screen The Gframe can be made very large for positioning and drawing an ROI When reading in images Gframes can be made very small the ROI is automatically positioned in the previously selected area of the image Image Rotation Select the Image Rotation choice from the Process menu to open the small Rotation window shown in Figure 38 The arrows on the buttons show how the images are transformed when the button is selected The straight double headed arrows represe
473. r some input image is required in order to establish image parameters such as width and height as well as everything else that is in the file header for example 2 1 exp width 2 i width 2 i height 2 j height 2 j 2500 0 This expression creates a Gaussian spot in the middle of the image that is 100 data pixels wide The output image has the same shape and size as image 1 Note that the denominator 2500 is written in floating point 2500 0 so that the division does not give truncation errors and that the exp function gets a float type argument as it expects The C construct var expression1 expression2 is used in the previous example Expressions in parentheses are evaluated left to right and only the value of the last expression is kept So in this case var is set equal to the value of expression2 In this example the value expression is only a dummy to give the program information about the image format but it could affect the final value for example var x 2 x 3 sets var equal to 5 and x equal to 2 Finally there are variables available for temporary storage that are not preassigned any values The variables x y z and r 0 through r 99 are available for you to store floating point values The variables ii jj kk and n 0 through n 99 are integer variables These variables can be used for efficiency to avoid recalculating complicated expressions as in the following example 2
474. r Guide Imaging 357 Index string command 100 su command 191 197 substr command 100 subtracting images 67 77 95 SUN file format 107 susceptibility effects 39 48 svdat command 301 svf macro 63 svib macro 73 94 302 svp macro 63 302 sw parameter 331 sysgcoil parameter 19 20 310 syshelppath global parameter 256 342 sysmaclibpath global parameter 17 342 sysmaclibpath parameter 255 sysmenulibpath global parameter 17 256 342 system gradient coil 180 specific parameters 234 systole time period 209 T T1 weighting 237 aperiodic saturation 238 242 inversion recovery saturation recovery 241 tlimage macro 303 Tir parameter 229 Tirho weighting 238 242 T2 effects and loss 48 T2 weighting 229 240 pulse sequence 237 T2 effects 39 tabgen macro 271 table conversion commands 47 63 file 305 files 47 63 305 reformatting 63 304 table conversion file read sort and store 47 read sort store 305 table ordered data converting 46 tablib directory 46 303 target image 17 22 target imaging plane 23 target parameters 24 tbox 253 tcclose command 47 tcopen command 47 te parameter 21 39 63 237 240 243 245 246 templates directory 68 133 text annotation 69 90 TGA file format 107 theta loop number of projections 251 theta parameter 24 243 theta_ parameters 252 thk parameter 24 32 44 63 ti ir imaging sequence 40 ti parameter 40 TIFF file format 107
475. r Setting Up Experiments Calibration entries in the pulsecal file are stored for a square pulse of the specified length If a shaped pulse is used to determine the pulse calibration pulsecal uses the integral of the shape to determine the corresponding power for a square pulse of the same length which is why there is no pulse shape field in the pulsecal database file This does not mean that nonsquare shaped pulses cannot be used to create new calibration entries only that this information is converted and stored in the pul secal file as if it were acquired with a square pulse Thus an entry created with a square pulse has the power level that was used as the argument to pulsecal Anentry created with a sinc pulse however has a much lower power level in the pulsecal file because the integral of a sinc pulse is only 17 of that of a square pulse The pulse length is also adjusted to account for any round off to the nearest integer pulse power level name is the name of the rf coil or calibration pulse_shape specifies the rf pulse shape used to acquire the calibration data length is the length of the rf pulse in usec used for calibration flip is the flip angle calibrated in degrees power is the calibrated power level in attenuator units If entered without arguments pulsecal displays the current contents of the database file Using pulsecal with syntax 1 creates an entry in the file userdir pulsecal Using syntax 2 removes the en
476. r voxel selection P imprep Set up rf pulses imaging and pulse power levels M plan Interactive slice and voxel selection M resto NMR resonance offset frequency P vorient Voxel orientation P voxl vox3 Voxel dimensions P Voxel dimensions Voxel dimension for volume localized experiments Volume localized experiments such as STEAM and ISIS can be oriented so that voxel edges lie parallel to major magnet axes or edges may have oblique angle orientations relative to major axes For this reason parameters that define voxel dimensions do not refer to the X Y and Z axes in their names Voxel dimensions are most often determined through the interactive voxel planning procedure from a scout image but can be manually entered through the command line imprep updates other parameters that depend on vox1 vox2 or vOx3 voxl and gvox1 are related by the expression gvox1 10 BW y vox1 in which BW is the bandwidth of the rf pulse used for voxel selection similarly for vox2 and vox3 Number in mm gvoxl gvox3 Gradient strength for voxel selection P imprep Set up rf pulses imaging and voxel selection gradients M plan Interactive slice and voxel selection M posl pos3 Position of voxel center P Voxel orientation Orientation of a voxel in the magnet reference frame typically in localized single voxel spectroscopy experiments such as STEAM and ISIS vorient corresponds in its basic definitions to its sister parame
477. r with the Voxel Select tool After phase or baseline correction or both is done for the individual spectrum click the Store option to put the spectrum with the rest of the data Click the OK option in each section to save phase and baseline coefficients These saved coefficients can then be applied to all the voxels by using the Write all mode in the Global Phase Correction amp Global Baseline Correction section in the Baseline Correction window For the Global Correction a subset of voxels can be selected by using the Box ROI tool After this tool is selected the cursor can be positioned on the left hand corner of a selected group of voxels As the cursor is dragged across the screen arectangular field opens up and any voxels within it are selected when a global phase and baseline correction is requested Only a portion of the voxel need be in the region for it to be selected 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 159 Chapter 6 CSI Data Processing 160 Phase Correction Local Phase Correction corrects a voxel spectrum in a selected Gframe loaded by the Voxel Pos and the Load option The voxel can also be selected with the Voxel Select tool Click the Auto Go option to initiate the phasing The OK option is used to store a set of phase coefficients Using Phase Correction Phasing can be done on individual voxels or globally on all the voxels To see how the autophasing or certain phase values will work try it on a sele
478. r5 Pulse power levels P pipat Inversion pulse shape Description Holds the name of the rf shape used for inversion pulse pi Related ir Inversion recovery mode P pi Inversion pulse length P tr Inversion recovery time P tpwri Inversion pulse power level P satpat Presaturation pulse rf shape Description Holds the name of the rf shape used for a presaturation pulse 322 Related presat Presaturation pulse execution on off P psat Saturation pulse length P satpwr Saturation presaturation pulse power level P Dimensions Positions and Orientations The predefined field of view FOV parameters cover the majority of all imaging and localized spectroscopy applications in common use A number of these parameter names are expected by certain VNMR functions and it is advisable to retain these names to avoid any incompatibilities For example the dconi or imconi program gets the dimensions for axis display from the parameters 1 ro and lpe Units for the dimensional and positional parameters are in cm and mm depending on the particular parameter In general image FOV and slice and readout positions have units of cm Slice thickness and voxel dimensions for localized spectroscopy have units of mm Dimension and position parameters are created in VNMR as standard real type parameters with no special limits Orientation of an imaging plane is specified through a set of three Euler angle parameters The user normally does not di
479. races for element 3 Regardless of the requested FID element the resulting spectra are labeled as 1 to nf because multiple elements cannot be transformed using ft nf Subsequent numeric arguments are interpreted as previously described start is the index of a particular element to be transformed For an array start is the index of the first element to be transformed finish is the index of the last element to be transformed for an array step specifies the increment between successive elements that are to be transformed for an array The default is 1 inverse is a keyword specifying an inverse Fourier transform 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 287 Appendix A Commands Macros and Parameters Examples Alternate Related ft2d Syntax Description Arguments exp_number is the number of the experiment from 1 to 9 for storing the resulting FID from the inverse Fourier transform expansion_factor defines the expansion of the spectrum before the inverse Fourier transform is performed This argument is equivalent to a multiplier for the fn parameter The multiplier is restricted to between 1 and 32 and is rounded up internally to the nearest power of 2 ft ft 1 ft 3 7 fet 002 ft n 3 Transform button in the 1D Data Processing Menu dermv Remove dc offsets from FIDs in special cases P En Fourier number in directly detected dimension P lsfid Number of points to left shif
480. radients and spatial dimensions Refer to the manual VWMR Command and Parameter Reference for more complete descriptions of these parameters and to the definitions here for the small differences to these descriptions as they apply to imaging applications Description Values Spectral width in directly detected dimension Total width of the spectrum to be acquired from one end to the other as described in the manual VVMR Command and Parameter Reference In imaging experiments sw is generally used as the direct time axis associated with the acquisition of an echo or FID in the presence of a readout gradient The value of sw is thus determined by the relationship that includes the readout FOV dimension and readout gradient strength sw y lro gro Because of this dependence sw must be recomputed whenever 1 ro or gro are changed which can be accomplished with the imprep or set gro macros Though sw has units of Hz it is most common to display images with spatial axes of cm or mm The axis parameter is used to tell the display routines what units to place on axes and how to scale the aspect ratio in two dimensional images for proper representation of an image However some aspects of image display such as cursor positions output by the mark command may be represented in Hz by certain functions or macros Number in Hz 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 331 Appendix A Commands Macros and Parameters See also G
481. raphics Using the Mouse Buttons Because this is a point and click based tool you need to be familiar with mouse buttons and command panel functions before manipulating frames and loading images General use of mouse buttons is described in the OpenWindows User s Guide The following information describes how mouse buttons are used in Image Browser Left Button SELECT In the control panel use the eft button to select buttons In the graphics region use the left button to choose an object or to draw an ROI or text annotation Selecting an object deselects any previously selected objects Objects that can 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 69 Chapter 4 Image Browser be selected include graphics frames images ROIs and text annotations When an ROI type or annotation is selected in the graphics tools panel the eft button initiates the drawing of the ROI or placement of new text Middle Button ADJUST The middle button is not used in the control panel In the graphics region use the middle button to toggle the state of an object select it if it is not selected and deselect it if it is Right Button MENU In the control panel use the right button to display menus Using the Control Panel Menus The control panel shown in Figure 26 contains a set of basic command options Figure 26 Image Browser Control Panel Buttons with an arrow V have submenus that are activated by the right mouse butto
482. rate 310 rise time 189 set internal usable diameter 307 spoiling time 319 step size 309 strength 189 309 311 313 strength checking 236 switching EPI 56 waveform generators 191 waveshaping 23 gradient pulses setting limits for 204 gradient strength EPI 56 gradients setting gain on 205 gradtables directory 19 graphic frames See Gframes graphical display 93 graphics functions 132 G Tools window 136 147 region of CSI window 130 tools 74 80 gray scale image displaying a noninteractive 292 gro parameter 21 243 311 grof parameter 243 groupcopy command 100 gss parameter 21 243 312 gss2 gss3 parameters 313 gssf parameter 243 G Tools window 147 gvoxl gvox2 gvox3 parameters 313 VNMR 6 1C User Guide Imaging 351 Index H half FOV ghosts EPI 53 Hamming filter 251 hardware GEMS requirements 48 PGM description 209 header variables creating and setting 345 helium contact with body 12 helium gas flowmeters caution 14 high performance auxiliary gradients 175 high power amplifiers cautions 14 histogram display limits setting 91 enhancing 97 function 77 homo parameter 22 63 343 disabling 43 homodecoupling control 343 for first decoupler 63 homonuclear decoupling 22 horizontal projection of trace 278 horizontally stacked spectra 280 HPAG 183 accessory 175 178 180 185 187 189 I i_size parameter keyword 251 ib_ui process 69 ileft macro 297 image
483. ratic for each function you determine how the function is defined The signature of the function is shown in Figure 51 static int exp_guess int npoints int nparams float params int nvars Nbr of data points Nbr of parameters NOT USED Parameter values OUT Number of independent vars NOT USED float x npoints nvars values of indep var float y npoints values of dependent variable float resid Quality of fit OUT OPTIONAL float covar Covariance matrix OUT OPTIONAL Figure 51 GUESS Signature For an example of a trivial guess function see fixed_guess in the file fit c Note that the returned values resid and covar are optional which means that you must test these pointers to verify that they are nonzero before trying to store values TRI_ELEM Macro The TRI_LELEM macro is provided to easily reference any element of a matrix stored in this format The syntax TRI_ELEM mat row col references the element of the matrix at the row and column This macro requires that row be greater than or equal to col 126 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 5 5 Problems with Image Browser Math The covariance matrix contains only nparams nparams 1 2 values rather than nparams nparams Only the lower triangle of this symmetric matrix is stored The storage order is C 0 0 C L 0 C I L CZ 0 7 Cle lLiy Ct2 2 4 C 3 0 P
484. re a vs graysl numgray 64 0 b numgray 0 5 graysl grayctr 64 0 where the parameter numgray has a default of 4096 for m and i formats and a default of 256 for the b format grays1 has a default of 1 and grayctr has a default of 32 0 To scale 16 bit integer data other than 12 bits the global parameter numgray can be created using create numgray real global and set to the value 2 where n is the number of bits desired For example to scale to 15 bits set numgray 32768 The display parameters grays1 and grayctr are used by the macros svib and svsis to save data files for Image Browser file is the name of the data file The file is created in the current VNMR directory unless a full directory path is given If a file of the same name already exists the user is queried to overwrite the file If a fully qualified file name is not given the file is created in VNMR s current directory f is a keyword to write data in 32 bit floating point This is the default m or i is a keyword to write data as 16 bit integers scaled to 12 bits b is a keyword to write data as 8 bit byte integers svdat data45 svdat rodent b browser Start Image Browser U fdfgluer Make FDF file from header and data parts C grayctr Gray level window adjustment P graysl Gray level slope contrast adjustment P svib Generate and save images as Image Browser compatible FDF files M svsis Generate and save images as FDF
485. re in the auxiliary configuration shown in Figure 89 before powering on the system shim and gradient power supplies Shim Current Gradient Shim Supply Supply Auxiliary Gradient Coil Shim Current Thermocouple Gradient Current Magnet Water Hoses Ze from Main Supply Figure 89 Connections for Auxiliary Configuration 15 The ZO shim manual operation only can be reset to a value that places the transmitter offset for proton observation close to zero frequency Otherwise remember to compensate for the frequency shift that will be observed when using the auxiliary coil Removing the HPAG Auxiliary Gradient Coil This section describes how to remove the HPAG auxiliary coil from the system and switch over to using the main system gradient coil WARNING Certain steps in this procedure are essential for safety reasons These steps are marked with the keyword SAFETY The order of the operations is crucial therefore carefully follow the order to prevent accidents and damage to the system 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 185 Chapter 7 High Performance Auxiliary and Microimaging Gradients 186 The system configuration is assumed to be as shown in Figure 89 This is the auxiliary configuration Verify that the system is functional in the auxiliary configuration before proceeding to remove the HPAG auxiliary gradient coil If the connections are not made as shown in Figure 89 then the system ha
486. re root of power It is linear in the output current Values above 80 effectively turn off the duty cycle limit function When the programmed limit is exceeded error lights will flash on the front of the gradient compensation unit and safety interlock board will disable the gradient power supply The LED on the gradient compensation board will be lit when the duty cycle is exceeded The safety interlock board latches to error and will show errors with unblinking LEDs on the status panel if the problem persists and it will show errors with blinking LEDs if the problem was transient The values need not be defined precisely but are important safeguards that prevent equipment damage if the settings exceed the current the gradient coils can handle The slew rate controls the maximum speed at which the gradient input signal may change Its effect does not depend upon the gain setting The slew rate can be expressed as a maximum rate at which the input value may change in voltage as a percent of full scale demand or as the time to achieve full scale 5 V Table 15 gives some settings and the Table 15 Slew Rate Control corresponding slew rates Slower slew rates decrease mechanical vibration in the probe assembly Faster slew rates give a more accurate gradient pulse Input Slew Rate Achieved Full Scale Value mV as us shape The desired setting is a 0 8 8 568 0 compromise between these two 25 84 5 59 1 requirements A typical value i
487. re written out and one of two possible wildcards must be used in the file name Wildcards permit the basic name to be specified while allowing the program to fill in a specified field for each file The wildcard specifies the base name of the image everything up to the final x extension For example if the image is read from the file bee knee0013 fdf specifying jpg puts the output in the file bee knee0013 jpg The wildcard specifies the first numeric field in the image s file name In the previous example specifying my_knee_ writes the data to the file my_knee_0013 It is also possible to use the wildcard if there is no numeric field in the image s file name i e no digits In such a case the save_ command automatically assigns index numbers to the output images This feature is especially useful for saving slices that have been extracted from a 3D data set because then all the slices have the same name the name of the original data set For example if slices are extracted from the 3D data set heart fdf specifying either heart f df or fdf assigns the slices the names heart0001 fdf heart0002 fdf etc By default all data are stored in floating point FDF format Other formats can be selected from the File menu selection list Position the cursor on the File menu option press the right mouse button and then select Output Format The Output File Format window opens The basic format is se
488. records every user action currently supported by a corresponding macro command in the scrolling text window of the Macro panel The recording is in a form that when replayed duplicates user actions Macro commands can also be directly typed into the script Press the right mouse button in the scrolling window to display TextEdit options New user actions are always inserted at the current cursor position Remember to move the cursor to the end of the text below the last line after doing any manual editing Before running the macro script created in the scrolling window store it in your macro directory To store the script display the menu in the scrolling text window and select File VNMR 6 1C User Guide Imaging 01 999163 00 A0800 4 5 Macros Save As The default save directory is the directory from which Image Browser was started so manually create the directory BROWSERDIR macro before entering the file name Once the script has been saved run the macro by typing its name in the Name field then press Return Of course the macro can also be run from other macros just by using its name List The List button loads macro text specified in the Name field into the scrolling text window obliterating any existing text If the named macro does not exist List does nothing there is no error or warning message If macro recording is on make sure that the cursor is in the desired location after running List Execute Th
489. rectly set these Euler angle parameters but instead controls VNMR 6 1C User Guide Imaging 01 999163 00 A0800 A 5 Parameters the orientation of the imaging plane through the parameter orient or through interactive graphical planning of new imaging orientations Image Field of View and Orientation Parameters lpe Description Values Related lpe2 Description Values Related lpe3 Description Values Related Field of view size for phase encode axis The size of the image field of view along the phase encode dimension lpe is used by dconi and imconi to specify the phase encode axis dimensions when the axis parameter is set to positional units of cm or mm To change 1pe enter the desired value through the VNMR command line and then run imprep to update other dependent parameters lpe gpe and tpe are related by the expression y lpe tpe gpe 1 Number in cm axis Axis label for displays and plots P dconi Interactive 2D contour display C gpe Phase encoding gradient increment P imconi Display 2D data in interactive gray scale mode M imprep Set up rf pulses imaging and voxel selection gradients M izo Field of view size for readout axis P setgpe Set phase encode gradient levels M swl Spectral width in 1st indirectly detected dimension P tpe Duration of the phase encoding gradient pulse P Field of view size for 2nd phase encode axis The size of the field of view along a
490. rectory homo Enables homodecoupling control for first decoupler lpe Specifies length field of view in cm along phase dimension lro Specifies length field of view in cm along readout dimension np Sets number of points real and imaginary in readout dimension nt Sets number of averages nv Sets number of phase encoding steps If nv is set to zero a profile along the read dimension is obtained orient Defines orientation of imaging plane by setting the three commonly used orientations 1 sagittal sag perpendicular to X axis 2 coronal cor perpendicular to Y axis and 3 transverse trans perpendicular to Z axis It is also possible to set the orientation to an arbitrary oblique plane by using the plan macro For a more detailed description of orient see Chapter 9 Parameters pl Calculates length of excitation pulse in usec plpat Specifies shape of excitation pulse pcmapapply Apply Phase Correction Map to Data C used in echo planar imaging pcemapclose Close Phase Correction Map C used in echo planar imaging pcemapgen Generate Phase Correction Map C used in echo planar imaging pcmapopen Open Phase Correction Map C used in echo planar imaging presig Selects preamplifier signal level pad Specifies a preacquisition delay pss Specifies slice position in cm Can be entered manually or via the plan macro pw Specifies rf pulse width in psec resto Specifies resonance transmitter offs
491. red by this procedure The same phasefile cannot be used for both operands in a binary operation To do this make a copy of the desired phasefile and give it a different name Entering imcalc with no arguments displays a menu system that allows the following selection of a number of different 2D image mathematical or spatial manipulations Selection of the desired image operation menu button results in prompts to the user for required input information such as the name of a phasefile or a numerical constant Unary operations such as square root or log do not require user input and are immediately executed when selected by using the phasefile resident in the current experiment opt ype can be any of the following keywords place single quotes around the keyword when entering imcalc from VNMR add Add two images sub Subtract second image from first from UNIX use add with a negative multiplier mult Multiply two images div Divide first image the second with noise thresholding 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 293 Appendix A Commands Macros and Parameters Examples Related imcalci Syntax Description add Add two images vadd Add two orthogonal images to form vector sum result sqrt image1 2 image2 2 phase Compute phase angle determined by arctan of two images mean Arithmetic mean of two images result imagel image2 2 gmean Geometric mean of two images resu
492. red peak number PEAK_NUM 7 Peak ID p p m amplitude multiplicity J complex major shift fwhm p ME PEAK1 6 85 30 0 0 0 0 3 1 0 0 60 0 COMMENT1 PME Pi PEAK2 4 77 10 0 1 0 0 1 1 0 6 30 0 COMMENT 2 Pi PDE PEAK3 2 10 100 0 0 0 0 3 1 0 0 70 0 COMMENT3 PDE PCr PEAK4 0 00 40 0 1 0 0 0 1 0 0 40 0 COMMENT 4 PCr gamma ATP PEAKS 2 30 30 0 2 20 0 1 1 Oss D00 COMMENT5 r ATP alpha ATP PEAK6 7 46 300 2 20 0 1 1 0 2 50 0 COMMENT 6 a ATP beta ATP PEAK7 15 7 30 0 3 20 0 0 1 0 3 50 0 COMMENT 7b ATP Remark The order is very important Please make sure to register peaks from lower field to higher field from higher frequency to lower frequency Items p p m is a chemical shift value p p m amplitude is a reference not necessary a exact value multiplicity 1 for singlet 2 for doublet 3 for triplet J is the coupling constant Hz unit complex indicates a multiple peak or simple peak major indicates a main peak or not shift indicates how much the peak could move under some physiological condition p p m fwhm indicates Full Width Half Maximum value of the peak Hz m COMMENTn maximum 32 character Figure 81 Sample Prior Knowledge PEAK File 174 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Chapter 7 High Performance Auxiliary and Microima
493. reen intensity will vary exponentially with y 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 149 Chapter 6 CSI Data Processing 150 For any type of mapping function the Negative button can be selected to invert the intensity scale that is the minimum grey value will be white and the maximum black Curve Mode The type of mapping function is selected by the buttons at the upper left of the Vertical Scaling window The default is curve which provides a flexible functional form that includes power functions and a close approximation to exponential functions The two parameter family of curves are controlled by moving the curve s control point around with the left mouse button The left and right ends of the line can also be moved up and down The form of the function depends on which regions of the graph the control point is in If the control point is in region 1 as shown in the Figure 69 the following equation shows the defining function for these curves x y Eq 29 y xX axt a where a and b are the two adjustable parameters The ranges of a and b are a gt 0 1 lt b lt 10 Eq 30 Figure 69 Curve Control Point Note that if a 1 this reduces to a power function which is the case if the control point has x 0 5 If the control point is in region 2 the curve is reflected through the x y line This family of curves includes power functions of the form y x1 b Eq 31 which applies when the
494. region with the mouse 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 147 Chapter 6 CSI Data Processing The Frame tool properties menu consists of Split Selected Frames Divides graphics frames into specific number of graphics frames Delete Deletes all graphics frames all selected graphics frames or all unselected graphics frames Clear Clears all graphics frames all selected graphics frames or all unselected graphics frames Select All Frames Selects all graphics frames Load Frame Layout Loads graphics frames from a file in the CSIDIR gframe directory Save Frame Layout Saves graphics frames into a file in the SCSIDIR gframe directory Frame Color Changes the frame color of graphics Zooming Tool Currently not implemented for CSI localized FID or MVS data displays The Zooming tool selects a portion of an image or a spectrum to be expanded Cursors are displayed on all currently selected Gframes The cursors are XORed to the display The Zooming tool properties menu consists of Zoom Expands selected images Unzoom Contracts selected images Bind Adjusts the zoom lines to all selected images Zoom lines are the lines that control the portion of images to be zoomed Cursor Tolerance Controls cursor sensitivity for the zoom lines This specifies how close the mouse cursor must be to a zoom line to select it Pixel Interpolation Expands image size to display on screen Used not only when zooming but any time an
495. removes a table conversion file and frees the memory used to store the sorted table indices read in with the t copen command Setup Macro The macro gems loads the default parameters from the file gems par into the current experiment gems first searches for a parameter file in your parlib directory HOME vnmrsys parlib and loads the file if it is present otherwise the file from the vnmr parlib directory is chosen Because the parameters in the system directory might not always be suitable for your particular application you should use svp to save a parameter file in parlib to suit your application needs If there are multiple parameter files saved in your par1ib directory use the rtp macro to retrieve the relevant parameters into the current workspace The macro rt retrieves FIDs from a file file fid into the current experiment If file fid does not exist and file par does rt retrieves the parameters from file par Advantages GEMS has a number of advantages some of which are listed in the following sections Fast Imaging GEMS can be used whenever a quick image is required It is possible to obtain GEMS images in less than a second For example GEMS is commonly used to get a quick image during setup for positioning the sample or for planning oblique slices Time Course Studies Because GEMS images can be obtained in about 500 msec to 1000 msec it is ideal for time course studies such as flow studies However
496. rent compensation DECC module and decctool the associated software interface DECC is used in microimaging horizontal imaging and whole body imaging For setup see the DECC installation manual 8 1 The DECC Module The DECC module consists of the DECC board the Smart DAC SDAC board and associated cables a power supply is sometimes also supplied with the module in certain standalone situations A functional block diagram is shown in Figure 95 DECC relies on digital signal processing technology to create appropriate compensating signals the calculation being based on parameterized compensation requirements applied to the digital signal from the gradient wavefrm boards WFGs The parameters are sent to the board over the APbus The compensating signal is scaled as appropriate and added into the main gradient signal on the SDAC and sent out to the gradient power supplies The SDAC board is an improvement over previous versions of gradient DAC boards the following signal strength and or conditioning controls can now be set via the APbus e Shim input scaling e DECC input scaling e Rise time slew rate e Output gain e Output polarity Also on the SDAC board is a low power current driver that can be directly used for compensating BO shifts When BO shifts are too large for this on board current driver a jumper setting turns the signal into voltage mode so that an appropriate external current amplifier can be used 8 2 Theory
497. reshold is established and the inhibit out signal begins to respond in a periodic fashion as each QRS complex is detected The pattern visible in the inhibit out signal consists of a level change of 5 V decrease from 5 V to 0 V as the QRS complex is detected This state is maintained for 50 ms then the signal returns to its original level 5 volts until another QRS complex is detected Such fluctuation indicates that a cardiac trigger has been obtained The automatic threshold can be used to obtain cardiac gated images However it takes a few heart beats to recover from the disturbances induced in the ECG by rf and gradient pulses This recovery time makes it less suitable for applications that require a short TR or high duty cycle multislice imaging The manual threshold requires no such recovery time and supplies cardiac triggering as soon as the rf and gradient disturbance has left the ECG e Manual Threshold To set up the manual threshold first reduce the inhibit delay and ECG threshold voltage controls to their minimum value Observe the inhibit output on channel 2 of the oscilloscope The inhibit output signal appears to behave in an erratic fashion when the threshold voltage is close to zero Slowly raise the value of the ECG threshold voltage while observing the inhibit out signal Allow a few heart beats to pass between each adjustment of the control and carefully note the point at which the inhibit output begins to respond in a
498. resolving the spatial dimension along a particular direction In reality a sample is a three dimensional 3D object Therefore it is necessary to be able to resolve the spatial information in 3D space It is convenient to define a frame of reference for dealing with a 3D sample The orientation of the magnetic fields produced by the gradient coils inside the magnet defines a coordinate system for imaging experiments An understanding of the workings of this coordinate system will help you to operate the imaging instrument The origin of the whole system lies at the center of the magnet which is also the center of the gradient coil system Gradients produce a zero field in the center of the magnet Therefore the frequency associated with the origin or magnet center is the resonance frequency for the particular nuclear substance intended for imaging For example water is the chemical substance most often imaged for the proton and the frequency at the origin of the gradient reference frame puts the NMR signal from water on resonance There are two types of imaging magnets e Narrow bore vertical magnets which are used for MRI microscopy MRM e Wide bore horizontal magnets which are used for larger samples In the case of horizontal magnets shown in Figure 13 the z axis is defined as being in the direction along the bore of the magnet going from the cable end back of the magnet to the sample end front of the magnet The x and y
499. resonance imaging NMRI magnetic resonance spectroscopy chemical shift imaging the 2D spin warp imaging sequence and lists several additional references for more information about NMRI NMR Imaging NMR imaging or MRI is used to obtain a map of the distribution of spins in a sample for example protons in water The inherent properties of the spins such as spin density T T T gt diffusion coefficient etc affect the signal intensity in imaging experiments which makes the contrast in the resulting images easy to distinguish This feature of distinguishing different sample regions based on NMR related properties makes imaging an important tool in clinical biological and material sciences For example clinical MRI scanning techniques are the preferred method for distinguishing various soft tissues in the body The spin density T and T gt of water in different tissue 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 25 Chapter 2 Imaging Experiments regions makes the contrast between tissues easy to distinguish Experimental techniques can be designed to further enhance the contrast between tissues Special imaging techniques can also be used to study flow perfusion diffusion and susceptibility effects Methods for Obtaining Spectral and Spatial Information Magnetic resonance spectroscopy MRS is the study of spectroscopic information in different spatial regions in a sample Volume localized spectroscopic method
500. rf excitation pulse to the center of the resulting echo In multiecho sequences te also defines the time duration between successive echoes which is normally a constant interval Multiecho sequences with variable echo times are also possible in which case the te period between successive echoes may take on a range of values represented by a te array Some more unusual pulse sequences such as stimulated echo RARE and Fast Spin Echo use te in ways somewhat different from the previously described normal standards Consult the descriptions in Chapter 2 Imaging Experiments for specific definitions of te in these applications ne Number of echoes to be acquired P Post acquisition delay in EPI experiments P Systems with echo planar imaging EPI capabilities Delay used in the EPI sequence to adjust the beginning of data acquisition This correction is necessary to allow for the finite propagation delay of gradient pulses This allows the user to center the EPI echoes in the acquisition window Number in us Typically 0 to 50 us depending on the gradient hardware episet Set up parameters for EPI experiment M Pulse length control Timing parameter to control the length of a flow sensitizing gradient pulse gflow Flow encoding gradient level P Inversion recovery time Recovery time following an inversion prepulse in inversion recovery experiments t i generally has a strong impact on image contrast which 01 999163
501. rgument the field of view parameters are automatically copied from the current experiment from_exp is the number of the current experiment from which FOV parameters are copied The default is current experiment to_exp is the number of the destination experiment in which the copied FOV parameters are placed mvfov 2 5 mvfov 4 mf Move FIDs between experiments C mp Move parameters between experiments C transfer Move parameters to target experiment M Calculate and display absolute frequency offset at cursor offset lt silent gt lt parameter gt Determines the absolute frequency offset at the spectral position defined by the cursor parameter cr and accounts for any spectral referencing that might have been set of fset finds the frequency at a particular spectral position relative to the base spectrometer frequency sfrq It displays the result of its calculation and returns the value which can optionally be assigned to a parameter or internal macro variable Use offset in a 1D proton spectrum to determine the proper spectral reference frequency to be assigned to resto in imaging experiments It can also be used 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 261 Appendix A Commands Macros and Parameters to determine spectral frequencies for presaturation fat suppression chemical shift selective imaging etc The displayed value of sfrq is the sum of the base spectrometer frequency specified by the param
502. riment transfer type lt scout_exp gt target_exp Transfers planned slice or voxel position information from a scout experiment to a target experiment transfer takes the values found in the appropriate t_ parameters and places them in the corresponding parameters in the target experiment These values are normally selected through interactive graphical planning transfer is called by the Transfer buttons in the Slice planning and Voxel planning menus and is not normally executed from the command line transfer uses predefined sets of parameter names to extract the required slice or voxel values from the scout experiment For example the transfer of slice planning information takes the values of t_phi t_psi t_theta t_pss and t_thk from the scout experiment and places them in phi psi theta pss and thk in the new target experiment The parameters resto and rfcoil are also transferred type is a keyword that specifies the transfer type s for slice or v for voxel 2 6 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Examples See also Related voxmark Syntax Description Arguments See also Related voxplan Syntax Description See also Related A 3 Macros for Planning Experiments scout_exp is the experiment number 1 to 9 of the scout experiment The default is that the current experiment is the scout experiment target_exp is the experiment number 1 to 9 of the target experim
503. riments such as STEAM and ISIS are also written using t r with the similar definition that t r is the repetition time per transient tr describes the total duration of all events in a pulse sequence and is never directly found as an argument to delay Instead t r is generally used in precalculations to determine the time required to pad the sum of programmed events up to the desired repetition time This padding delay is often found in the pulse sequence as predelay Related seqcon Acquisition loop control P trelax Relaxation delay Description Timing parameter to specify a relaxation delay A common use for t relax tspoil would be as the inter image delay in a series of fast images Gradient spoiling time Description Delay parameter for use in controlling a spoiling gradient Many imaging sequences use t spoil to set the additional time that the slice select gradient is on symmetrically bracketing the 180 refocusing pulse to spoil any magnetization excited by the 180 itself Related gcrush Crusher gradient level P gspoil Spoiler gradient level P terush Crusher gradient control P RF Pulse Lengths Pulse Power Levels Shaped Pulse Patterns The predefined rf pulse parameters have been chosen to cover the majority of imaging and localized spectroscopy applications In most cases a trio of related parameters are available specifying the pulse length the associated power level and an rf waveform shap
504. rk function which is more appropriate for imaging data The dconi menu tailored for imaging is found in menulib imaging which is searched by VNMR before searching the vnmr menulib directory when appmode is setto imaging The search order is userdir followed by vnmrsys maclib maclibpath sysmaclibpath and then vnmr maclib The value of appmode can be set either by entering its value directly from the command line or by selecting the Setup button from the Main Menu and then clicking on the App Mode button New applications modes can be added by creating the appropriate subdirectories in vnmr maclib vnmr menulib and vnmr help and adding the desired applications mode name to the _appmode macro Subdirectories should be named by adding the file extension appmodename to the corresponding parent directory name for example maclib solids menulib automation Values standard sets standard application mode imaging sets imaging application mode Related config Display current configuration and possibly change it M 342 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 fn Description Values Related fn1 Description Values Related homo Applicability Description Values 01 999163 00 A0800 A 5 Parameters Fourier number in directly detected dimension Selects the Fourier number for the Fourier transformation along the directly detected dimension This dimension is often referred to as the f dimensi
505. roup will be found in any given sequence Many of the parameter names have been chosen in an attempt to provide an intuitive correspondence to the imaging literature There is no special significance however to names such as gf low or gspoil These names that have been chosen for their obvious descriptive nature but may be used arbitrarily in a pulse sequence as desired by the user Varian s standard imaging sequences use these names in an attempt to convey the most obvious connection to events and processes that an experienced imaging spectroscopist would recognize In all cases VNMR 6 1C User Guide Imaging 01 999163 00 A0800 A 5 Parameters please consult individual pulse sequence programs and manual pages for a detailed description of parameter use in that sequence Displaying Additional Parameter Groups Using dgm The primary parameters of any imaging experiment can be displayed in the text window with the dg command the same as for any VNMR parameter set Most secondary parameter groups such as dg1 and dgs will be found in each imaging experiment along with several other specialized parameter groups These additional parameter groups allow the display for example of all predefined gradient parameters or all predefined rf pulse parameters etc although some of the displayed parameters will be unused in any given experiment and have values set to zero or to a null string The dgm command allows menu selection of the various dg scree
506. rray of dimension nbr_infiles containing pointers to all the input image structures and which can be treated either as a single array containing every input image in every image vector or as several arrays placed end to end one for each image vector The starting index of each vector in the whole array is given in vecindx float in_data Array of dimension nbr_infiles containing pointers to all the input data arrays and which can be treated either as a single array containing every input image in every image vector or as several arrays placed end to end one for each image vector The starting index of each vector in the whole array is given in vecindx 116 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 int int pixel_indx nbr_strings char in_strings aint nbr_params float in_params int int out_ out nbr_outfiles out_width height depth out_size FDFptr out_object floa t out_data Macros IN_D ATA vec img pixel TRI_ ELEM matrix row col Functions FDFp FDFp tr clone_ddl tr create_ddl 01 999163 00 A0800 5 3 Image Browser Math Functions Used in the fit program to indicate which pixel is currently being fit It can be referenced by the user s FUNCTION JACOBIAN or GUESS routines Number of strings passed to the user s function Array of dimension nbr_st rings containing pointers to all the string
507. rt spatial coordinates M Convert spatial coordinates From UNIX log_mag phi psi theta x y z Converts spatial coordinates in the logical reference frame to spatial coordinates in the magnet reference frame 1og_mag is an executable macro command in vnmr bin It must be executed from a UNIX shell or called from a VNMR macro by the she11 command phi psi theta are the coordinates of a point in the logical imaging reference frame the coordinate system defined by the readout phase encode and slice select axes and the Euler angles that define the orientation of the logical frame e phi is the angular rotation of the image plane about a line normal to the image plane e psi is formed by the projection of a line normal to the imaging plane onto the magnet XY plane and the magnet Y axis e theta is formed by the line normal to the imaging plane and the magnet Z axis x y z are the magnet reference frame coordinates that are returned to standard output which is printed to the calling window unless picked up as return arguments to the VNMR shell command location Display spatial coordinates at a point in an image M orient Slice plane orientation P phi Euler angle for defining imaging plane orientation P psi Euler angle for defining imaging plane orientation P theta Euler angle for defining imaging plane orientation P 01 999163 00 A0800 plane_decode Syntax Description Arguments Related plan Syntax
508. run for all selected ROIs To open a Statistics window choose the Process button with the left mouse button Press the right button to see a selection of processing options VNMR 6 1C User Guide Imaging 01 999163 00 A0800 4 4 Data Processing Updating Statistics To update ROI statistics choose the Update option and use either the left or right mouse button to update statistics e Press the left button on the Update option to just update the statistics and the graph e Press the right button to choose one of the following options for when to automatically update statistics Now Same as pressing SELECT The statistics are updated but the mode is not changed This is the default selection Manual Statistics are only updated when the Update button is pressed or when ROI Statistics are selected from the Process menu Auto On ROI Change Statistics to be updated whenever an ROI is selected or deselected or when an ROI is moved or modified Updates only take place after a change is completed not as an ROI is being moved around This is the default mode Auto On ROI drag Same as Auto On ROI Change except updates are done in real time as an ROI is being moved or resized This mode can significantly slow down response time especially when a large ROI is modified or many ROIs are selected Setting Histogram Display Limits When statistics are requested for one ROI Name usr24 chrisp sw ib DATADIRS CATDATA image0
509. s e Line ROI drawing VNMR 6 1C User Guide Imaging 01 999163 00 A0800 6 2 Getting Started e Peak or baseline markers e Box ROI drawing e Vertical line markers e Text annotation e Interactive phasing and spectrum scaling e Voxel selection e Curve fittings e Interactive weighting filtering A tool is activated by pointing to it with the cursor and clicking the left mouse button After a graphics tool is activated items can be selected or dragged by using the left mouse button Commands can be performed by clicking on the properties option above the graphics buttons with the right mouse button Typical commands are Load Save or Delete in the case of Gframes or ROIs and Zoom or Unzoom in the case of zooming See Tools page 147 for a description of graphics tools that support CSI data set processing Processing a CSI Data Set To acquaint you with processing CSI data this section describes the CSI data set processing In the example used in this section the data is simulated data To view the processing steps that need to be performed compare Figure 57 with the data flow diagram in Figure 53 Both figures show the processing steps that must be taken after the data has been read in Phase amp we Baseline Cuve f g Correction Spatial Spectral Reconstruction Reconstruction Figure 57 CSI Data Basic Processing Steps Generating Simulated Data The first step is to generate data which can be read in
510. s 104 inhibit delay feature 213 214 218 219 220 221 222 inhomogeneity effects 48 initial scout image 17 initialization directory 133 input output jacks PGM receiver 214 data formats 67 PGM 223 integer formats 106 intensity trace 97 interactive fitting tool 163 planning 275 interactive image planning 253 interleaved sequences EPI 58 inverse Fourier transform 287 inversion prepulse recovery time 317 pulse power 321 time parameter 40 inversion recovery 229 241 experiments 317 mode 337 sequence 40 iplan macro 253 ir excitation 229 235 240 241 ir pulse 243 isis macro 259 01 999163 00 A0800 J JPEG file format 107 L labels storing 76 Idof macro 42 49 62 parameter 260 length command 100 line data processing 87 97 functions 97 intensity traces 97 ROI tool 153 ROIs 77 97 linear monotonic order data 46 303 scaling of image intensity 292 liquid relaxation times 39 list button 99 load frames button 78 layout 81 loading eddy current compensation files 43 203 files 104 graphic frames 81 image parameter file 41 43 images 73 74 105 macro text 99 parameter 22 parameters for imaging 41 ROI into Gframe 100 ROIs 88 location macro 274 lock parameter 42 disabling 43 lockpower parameter 43 looping processes control 339 lost phase coherence 52 Ipe parameter 63 Iphase dimension length specifying 63 Iright macro 297 lro parameter 63 M
511. s click NEAR the ROI Clicking near a vertex activates the ROI adjusting mode To avoid selecting a vertex and accidentally modifying an ROI hold down the Shift key while clicking the mouse 76 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 4 2 Getting Started 3 Use the mouse to drag the ROI then release the button at the new desired position Obtaining Statistics from ROIs The processing functions described in this section are used in conjunction with the graphics functions Some of the processing functions use the ROI tools to obtain statistics or information from regions of interest within images The Statistics Line and Cursor functions are used on selected ROIs Statistics Obtain statistics and histograms from regions of interest It uses any type of ROI Line Obtain distances traces and projections using a line ROI It uses line or polyline ROIs Cursor Obtain point intensities and distances between points It uses point ROIs The Arithmetic Math Filtering Histogram and Rotation functions manipulate or process data These functions are used on the whole image and selected Gframes Arithmetic Add subtract multiply divide images by other images or by a constant Math Apply general math operations to images Filtering Filter the data with a 3 x 3 or 5 x 5 pixel filtering functions Histogram Use histogram methods to enhance the data Selecting Source and Destination Gframes A source Gframe must be select
512. s not exist and file fid does rtp retrieves the parameters only from file fid rtp rtp vnmr stdpar P31 fixpar Correct parameter characteristics in experiment M PE Retrieve FIDs M rtv Retrieve individual parameters C svp Save parameters from current experiment M Set up parameters for standard two pulse sequence s2pul Converts the current experiment to an experiment suitable for the standard two pulse sequence S2PUL S2PUL button in the 1D Pulse Sequence Setup Menu spuls Load default single pulse sequence imaging parameters M Retrieve parlib parameters for SEDIFF imaging experiment sediff Retrieves the standard parameters for the SEDIFF imaging experiment from vnmr parlib Retrieve parlib parameters for SEMS imaging experiment sems 01 999163 00 A0800 Description setarray Description Arguments Ex Syntax amples Related setflip Description Arguments Examples Syntax Related setgcal Syntax A 2 Macros for Setting Up Experiments Retrieves the standard parameters for the SEMS imaging experiment from vnmr parlib Array any numeric parameter in constant increment steps setarray lt parameter start increment number gt Arrays a numeric parameter when a constant increment between arrayed values is desired set array works with any arrayable parameter and generates arrayed values in ascending or descending order When other parameters are alrea
513. s 20 50 160 3 31 2 100 311 8 16 0 eddysend Program The macro eddysend lt file gt identifies the stored data values needed by the gradient compensation boards translates them into machine form and executes a setup operation that programs the boards eddysend without arguments uses the file name specified by the user s global parameter curecc This is particularly useful when the gradient compensation boards have not been initialized on spectrometer power up or when ensuring the previous set of compensations are used eddysend with a file name as an argument causes the specified set to be sent to the gradient compensation unit and changes curecc to the last sent value eddysendis also used by the eccTool program when the setup function su is requested eccTool Program The eccTool program allows interactive review and alteration of all of the gradient compensation unit values in each channel Opening eccTool To open the window shown in Figure 93 type ecctool The eccTool Window The values of a default set of parameters or those last read are displayed as a page or form VNMR 6 1C User Guide Imaging 01 999163 00 A0800 7 4 Microimaging Hardware Figure 93 eccTool Window The following information describes the control buttons that appear in the window setup Takes the contents of the file named in the file field translates the values into control codes and sends the instructions to VNMR VNMR then executes a s
514. s are used to obtain spectral information from specific locations in a sample Chemical shift imaging CSI methods are another related class of experiments that are designed to provide both spectral and spatial information from a single experiment 2D Spin Warp Imaging Sequence 2D spin warp imaging is one of the simplest imaging sequences commonly used in NMRI Most of the other imaging sequences are variations of this fundamental sequence In Basic Imaging Principles page 25 the basic principles of imaging are discussed based on the spin warp sequence The information in that section is primarily meant to help a novice grasp the basic principles and terminology of NMRI The chapter contains a description of the experimental aspects of NMRI so that you can understand the correlation between the parameters and the resulting image For a more theoretical understanding of the imaging experiments refer to any basic text or reviews on MRI References The VNMR manual Getting Started contains more general information on operating Varian spectrometers Consult the manual VVMR Command and Parameter Reference for additional information on VNMR commands or parameters 2 2 Time Domain to Spatial Domain Conversion 26 As an example of Time domain to spatial domain conversion consider a tube of water inserted within an NMR probe and placed in the center of the magnet The magnet produces a homogeneous field in the region surrounding the water
515. s been left in an incorrect configuration and might possibly be damaged by the procedure In this situation perform the following three SAFETY steps and correct the cabling error so that the connections correspond to those shown in Figure 89 The system can then be powered up SAFETY Turn off the system shim power supply using the power on off button located on its front panel SAFETY Turn off the system gradient supply using the STOP button and the main power switch SAFETY Turn off the water flow to the gradient coil at the main water shut off valves WARNING Do not proceed with the following steps until the three previous steps 10 11 12 13 14 15 marked SAFETY have been performed Disconnect the thermocouple sensor cable P59X3 from the auxiliary gradient coil and connect it to the main gradient coil J5903 Disconnect the shim power cable P59X2 from the auxiliary gradient coil J5912 and connect it to the main gradient coil J5902 Disconnect the auxiliary coil gradient power cable P5911 from the HPAG quick disconnect box J59X1 and connect the gradient power cable from the main coil P5901 in its place Disconnect the auxiliary coil water hoses from the HPAG quick disconnect box Reconnect the water hoses from the main gradient coil Remove any samples and bore equipment from the auxiliary gradient coil Set aside for future use Remove the locking screws from the locking mechanism bra
516. s not load the image Load All Load All loads all the images in a directory Images can either be FDF files or VNMR phasefile directories If images have been loaded into all the Gframes and more images must be loaded the next image is loaded into the first Gframe and the process continues until all the image files have been loaded Storing Images Images can be easily stored by using the right mouse button and selecting the Save item from the file menu selection list The File Browser window is opened in Data Save mode or the current File Browser window is changed to that mode The initial File Browser directory is the directory in which Image Browser was started To store an image choose a directory a file name and select the Save button The image in the currently selected Gframe is saved As a default all data are saved as FDF files but there are a number of alternate data formats that can be chosen to save files Details are given in Saving Files page 105 Using Graphics Tools The Tools window is opened by selecting the Graphics Tools option from the Tools menu button on the control panel The window opens with the ROI Tools button designated by an arrow as the default The graphics tools in the Tools window can be used to support processing functions or used on their own for viewing images The tools support e ROI manipulation e Gframe manipulation e Zooming e Vertical scaling scales the pixel display valu
517. s of the selected images in the order that the images were selected The output should be a list of numbers which are the values to assign to parname in the headers For example if a file called data in the current directory contained a list of three numbers separated by spaces tabs or new lines the following commands select frames 1 2 and 3 and set the header parameter myparm in the three images to the respective values of the three numbers in the data file frame_select none 1 2 3 data_header_set myparm cat data data_load Shows the File Browser window in Load Data mode data_load file Loads an image in file into the next available frame If file does not begin with it is taken to be relative to the current directory shown in the File Browser Data window see Figure 45 Loading an image with this command from a different directory does not change the current directory data_load_all lt dir gt Loads all images in a directory If you specify a directory from which data is to be loaded it must be a full path If you do not specify a directory this command loads an image from the current directory as shown in the File Browser Data window data_save file Saves data in selected frame s in the named file If more than one frame is selected the name must include a wildcard character see Storing Images page 106 If file does not begin with it is taken to be relative to the directory sho
518. s passed to the user s function Number of numerical constants passed to the user s function In the fit program this is modified in fit c so that it does not reflect any threshold value that might have been passed Array of dimension nbr_st rings containing all the numerical values passed to the user s function In the fit program this variable is modified in fit c so that it does not reflect any threshold value that might have been passed Number of output files that caller has requested from user function In the fit program this variable can be adjusted downward if more output files are requested than fit knows how to supply Arrays of dimension nbr_out files that have the size of each output image These arrays are initialized to match the size of the last input image but you can adjust them before calling create_output_files Array of dimension nbr_out files containing pointers to all of the output image structures It is initialized by create_output_files Array of dimension nbr_out files containing pointers to all of the output image data arrays It is initialized by create_output_files References pixel number pixel in image number img in input image vector number vec In fit routines only If mat rix stores the lower triangle of a symmetric matrix references the matrix element in row row and column col Requires row gt col Makes an identical copy of the image structure old_ddl If dataflag is
519. sage window Retrieving the Parameter Set Next you must retrieve the parameter set to run the SEMS sequence 1 Join an available experiment For example to join experiment 6 enter jexp6 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 1 1 Making an Initial Scout Image 2 Retrieve the SEMS parameter set by entering the command sems You can also use the Files menu system to change to the system par1ib directory and load in the SEMS PAR parameter set Most of the parameters that you need to know about and work with should now be displayed A few may require being set or selected but the rest are computed for you Setting the rfcoil Parameter The pulse calibration information determined in Calibrating the Pulse Length page 18 is communicated to the system through the rfcoil parameter The automated setup routines use rfcoil to obtain information about probe performance from pulsecal and to set pulse powers for the two rf pulses in SEMS e Set rfcoil lic or use whatever name you chose for the pulsecal entry Setting the gcoil Parameter An imaging spectrometer is often equipped with multiple gradient sets which can be interchanged for different sample sizes and experimental requirements When a new gradient set is introduced into the lab a corresponding new calibration entry is required in the directory vnmr imaging gradtables Such a calibration file should have been created for any gradient set provided at
520. sample A single pulse experiment yields an NMR signal that on Fourier transformation FT produces the frequency spectrum of the sample as shown in Figure 1 Sample in a homogenous field Bo a CF FT WWW t FID ho mi Spectrum Figure 1 Frequency Spectrum Produced by an NMR Signal VNMR 6 1C User Guide Imaging 01 999163 00 A0800 2 2 Time Domain to Spatial Domain Conversion A single line at the resonance frequency fp is obtained The frequency is defined by the following Larmor equations fo y By Eq 1 y 2n y Eq 2 In Equation 1 and Equation 2 yis the gyromagnetic ratio rad gauss sec and Bo is the magnetic field strength gauss For protons yis 2 6752x104 rad gauss sec and y is 4257 Hz gauss In MRI the magnet strength Bo is usually expressed in tesla 1 T 10 000 gauss whereas in conventional NMR magnet strength is commonly referred to in terms of the proton resonance frequency in MHz The frequency spectrum that is displayed in NMR is referenced with respect to the rf transmitter frequency The center of the spectrum refers to the carrier frequency Therefore spectral components that are above positive and below negative can be measured by NMR In MRI the spatial frequency components are measured with respect to the resonance frequency of the major component in the sample usually water Therefore the carrier is placed on the water resonance frequency fo as
521. sation Y Compensation and Z Compensation Remove the compensation board for the X gradient from slot 3 and replace it with the new X gradient compensation card Remove the compensation board for the Y gradient from slot 6 and replace it with the new Y gradient compensation card Remove the compensation board for the Z gradient from slot 9 and replace it with the new Z gradient compensation card Flip up the gradient supply control panel and replace the panel retaining screws CAUTION Power up the gradient supply only after modifying the connections to the gradient coil If the gradient supply does not power up check all connections again including connections to the compensation board shim supply and thermocouple sensor line If all the connections are made correctly and the gradient supply still does not power up call Varian Service for assistance and do not proceed further 7 2 Experimental Setup The purpose of this section is to describe the use of the HPAG accessory for experiments It is important to be familiar with the individual hardware components and their interconnections Installing the HPAG Auxiliary Gradient Coil This section describes how to install the HPAG gradient coil for experimental use WARNING Be aware that certain steps in the procedure are essential for safety reasons these steps are start with the keyword SAFETY The order of the operations is crucial therefore to prevent accid
522. se saturation recovery sr or by a 180 pulse inversion recovery ir The pulse is controlled by pi and tpwri 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 237 Chapter 10 2D and 3D Backprojection 238 sec ms 19 ije us dy Ipi ype noslice 30000 ACQUISITION 00600 402 175 30000 i 64 i 00200 0 p o GRADIENTS PROCESSING orient xyz sb 0 002 gcal undefined sbs 0 000 date Mar 8 94 Iro 0 80 phfid 0 1 file home1 pe gro 4000 fn not used ter BPYAR_2 Schlau 1 450 proc ft chi O0 math f solvent none 0 500 CONTRAST DERIVED prep n sw 50000 0 value assigned to zero Figure 118 T Weighted 2D and 3D Pulse Sequence In acquisition phase B set te to a small value in order to reduce T weighting influence Figure 119 shows an example of a T weighting preparation phase T Weighting Using Aperiodic Saturation Aperiodic saturation is achieved by a sequence of 90 pulses in the preparation phase The time period between the pulses is continuously divided by two to achieve full dephasing corresponding to full saturation The particular advantage of the aps sequence is the short measurement time because there is no requirement on the initial state of magnetization prior to the aps sequence d1 may be chosen quite small Therefore measurements of the points of the T relaxation curve don t need a fully relaxed state requiring 3 to 5 times T as a recovery time The parameter nsat controls the number of pulses used
523. sec dssl dssl top left dssl value format 3 1f sec dss Display stacked spectra C write Write formatted text to a device C wysiwyg Set plot display or full display P Open eccTool window M Systems with computer controlled analog eddy current compensation 282 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Syntax Description eff echo Applicability Description Values Related epift Applicability Syntax Description Arguments Related epiph Applicability Syntax Description Related epirs Applicability Syntax Description Related epirun Applicability Syntax 01 999163 00 A0800 A 4 Commands and Macros for Processing and Display ecctool Opens the eccTool window to adjust eddy current compensation parameters Effective echo position in EPI experiments P Systems with echo planar imaging EPI capabilities Refers to the echo showing the highest signal in an EPI echo train The readout gradient dephaser is adjusted so that the maximum signal occurs at ef _echo Usually set to nv 2 iy Number of phase encode steps for 1st indirectly detected dim P Process and display image in EPI experiments M Systems with echo planar imaging EPI capabilities epift index Processes and displays an image in array number index The first data array must contain the reference scan The phase correction information saved in the fil
524. second R of the interferogram IR2 would thus represent the contribution from the imaginary part of spectra set 2 to the real part of the interferogram and so forth The scheme is depicted below ft20 RR1 IRL RR2 IR2 lt gt RIL 211 RI2 112 lt lt lt where RR1 REAL w2 element 1 gt REAL t1 IR1 IMAG w2 element 1 gt REAL t1 RR2 REAL w2 element 2 gt REAL t1 IR2 IMAG w2 element 2 gt REAL t1 RI1 REAL w2 lement 1 gt IMAG t1 ITI1 IMAG w2 lement 1 gt IMAG t1 RI2 REAL w2 element 2 gt IMAG t1 II2 IMAG w2 element 2 gt IMAG t1 ni is a keyword to selectively transform a particular np ni 2D plane within a non arrayed 3D data set To identify the plane ni is followed by the plane_number argument an integer from 1 through ni2 ni2 is akeyword to selectively transform a particular np ni2 2D plane within a non arrayed 3D data set To identify the plane ni2 is followed by the plane_number argument an integer from 1 through ni element_number is the number of an element within the explicit array when selectively processing an arrayed 3D data set it ranges from 1 to ni2 increment is the increment within the explicit array when selectively processing an arrayed 3D data set it ranges 1 to arraydim ni ni2 f t2d 1 0 0 0 0 0 1 0 ft2d 1 ft2d ptype dconi Interact
525. second indirectly detected dimension P sw3 Spectral width in third indirectly detected dimension P tpe Duration of the phase encoding gradient pulse P tpe2 tpe3 Length of 2nd and 3rd phase encoding gradient periods P thk 2D imaging plane slice thickness P Retrieve parlib parameters for ISIS imaging experiment isis 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 259 Appendix A Commands Macros and Parameters Description ldof Syntax Description Examples Related mems Syntax Description movetof Syntax Description Arguments Related movepro Syntax Description Retrieves the standard parameters for the ISIS imaging experiment from vnmr parlib Load resonance offset frequency ldof Initializes the resonance transmitter offset frequency resto to the value saved in SHOME vnmrysy Hloffset ldof resto NMR resonance offset frequency P setof Measure and save resonance transmitter offset frequency Retrieve parlib parameters for MEMS imaging experiment mems Retrieves the standard parameters for the MEMS imaging experiment from vnmr parlib Move transmitter offset movetof lt frequency gt Moves the transmitter offset parameter tof so that the current cursor position defined by cr becomes the center of the spectrum If referencing was used movetof maintains the referencing frequency specifies the transmitter frequency rather than using the cursor pos
526. sed internally within the pulse sequence to determine the phase encode gradient increment based on the computed refocusing time for readout and slice selection gpe depends on the field of view and the phase encode gradient duration according to the expression yegpe tpe lpe 1 and is set by either the imprep or set gpe macros imprep Set up rf pulses imaging and voxel selection gradients M gmax Maximum gradient strength P gpe2 2nd phase encoding gradient increment P gpe3 3rd phase encoding gradient increment P lpe Field of view parameter for phase encode in cm P nv Number of phase encode steps for 1st indirectly detected dim P setgpe Set phase encode gradient levels M tpe Duration of the phase encoding gradient pulse P 2nd phase encode gradient increment Phase encode gradient increment for 3D or 4D phase encoded applications gpe2 should be used when a second phase encode gradient is required For example 3D volume imaging application would use both gpe and gpe2 as VNMR 6 1C User Guide Imaging 01 999163 00 A0800 A 5 Parameters would a 3D chemical shift imaging experiment that is two spatial dimensions plus chemical shift dimension Related imprep Set up rf pulses imaging and voxel selection gradients M gmax Maximum gradient strength P gpe Phase encoding gradient increment P gpe3 3rd phase encoding gradient increment P lpe2 Field of view size for 2nd phase encode axis P setgpe Set phase encod
527. seen together in transverse Orient trans andincoronal orient cor or xzy images The atria are smaller chambers than either ventricle and are easier to assign in coronal images The atria can be seen in transverse images and for certain slice positions can be seen in conjunction with the ventricles The reason for this confusing appearance is that the major long axis of the heart lies at an angle to the symmetry axis of the body Electrocardiography The mechanical pumping action of the heart is associated with a series of electrical events that drive the contraction of the muscles in the walls of the heart These electrical events can be detected by measuring the voltage that exists between electrodes placed at various points on the surface of the body The appearance of the electrocardiogram depends upon the placement of the electrodes and certain conventions have evolved to standardize the measured response The PGM 1000 is designed to use three standard limb leads connected to both forelegs and the right hind leg of the animal subject With electrodes connected in these positions the unit records an electrocardiogram corresponding to that shown in Figure 100 The result is similar to that recorded for human subjects with conventional bipolar limb leads The electrical waves recorded in the electrocardiogram are known as the P Q R S and T waves as shown in Figure 100 The sharp spike formed by the Q R and S waves is called t
528. ser Guide Imaging 251 Chapter 10 2D and 3D Backprojection theta_start Specify the start and end values of the angles used for 3D BP theta_end acquisition The angles are set using degrees instead of radians The phi_start angle increment between subsequent steps of theta are derived by phi_end theta_increment theta_end theta_start n_theta and can be positive or negative The same applies to phi Typically the difference between the start and end values is 180 This is the default case If the difference between the start and end is 360 both start and end have to be specified in the command file 10 7 References 252 The following bibliography lists the references that were important contributions to the research and writing of this chapter Marr R B Chen C N Lauterbur P C On Two Approaches to 3D Reconstruction in NMR Zeugmatography In Mathematical Aspects of Computed Tomography 8 225 240 edited by G T Herman and F Natterer Springer Verlag New York 1981 Peters T M Algorithms for Fast Back and Re Projection in Computed Tomography IEEE Trans Nucl Sci 1981 28 4 Rowland S W Computer Implementation of Image Reconstruction Formulas In Image reconstruction from Projections Implementation and Applications edited by G T Herman Springer Verlag Berlin Heidelberg New York pp 9ff 1980 Project Report 3D Backprojection reconstruction Fraunhofer Institute Biomedical Engineering IBMT
529. ser menus 70 noninteractive gray scale image 292 stacked spectra horizontally 280 dividing images 67 77 95 dmi macro 51 62 280 double Fourier transform datasets 51 dpss macro 280 drawslice macro 273 drawvox macro 273 dslice command 24 dssh command 42 62 280 dss macro 282 duty cycle 194 and heat dissipation 189 setting 62 dynamic range limitations backprojection 244 E ECC boards 181 decctool 62 files loading 43 203 files saving 203 01 999163 00 A0800 Index gain setting on SDAC board 204 hardware 57 performance specification 189 preemphasis theory 199 procedures GEMS requirements 44 eccsend macro 197 eccTool program 43 49 62 191 194 197 282 ECG detection voltage threshold 219 echo command 99 position determining 311 echo planar imaging See EPI experiments echo time 39 245 317 specifying 63 echoes acquisition number 333 eddy current compensation See ECC eddy currents 191 effects 48 57 setting 62 eddy out file 197 eddylib directory 196 197 eddysend macro 191 194 electrocardiography 207 208 electrode connections cardiac electrode leads 215 electromechanical coupling 209 enhancing data 77 images 67 97 environment variables 133 EPI 51 advantages 58 artifacts 53 chemical shift effects 55 data processing 52 data collecting storing and processing 61 experimental procedure 59 field inhomogeneity effects 56 half FOV ghosts 53 imag
530. ser to read in the raw data file and the parameter file CSI does not currently process arrayed data sets except CSI data sets that use the standard ni arraying scheme VNMR Parameters The CSI program uses certain VNMR parameters in order to process the data The information it obtains defines the data set s size location orientation field of view and other descriptive information If some parameters do not exist default parameters are used in order to process the data sets Standard Parameters The following standard parameters can be used by the CSI program np ni nf These parameters determine the data sizes of the data set The flashc program is expected to be run on any image data set These parameters help determine the Rank and Matrix fields No default values but if the parameter is not found the values in the data headers are used sfrq dfrq Transmitter and decoupler frequencies used in the nucfreq field Default value is 170 MHz 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 171 Chapter 6 CSI Data Processing 172 tn dn Transmitter and decoupler nuclei used in nucleus field Default value is H1 sw swl sw2 Define the spectral widths Default value is 2000 Hz lro lpe Spatial dimensions of the reference image data in centimeters Default value is H1 lpe lpe2 Length of data in the phase encode directions 1pe is used for the medium y direction when processing CSI and reference imag
531. should have a 5 mm diameter and be about 20 mm 3 4 inches long 5 Insert this setup in the solenoid coil of the microimaging probe 6 Insert the probe into the bore of the magnet 10 6 BP Macros and Programs Details This section describes in more detail the reconstruction macro and programs Macro bp_reco The BP package contains the macro bp_reco to control the reconstruction process This macro initializes and executes the reconstruction of a 2D 2D arrayed or 3D data set The parameter ni 2 is used to decide between the 2D ni2 or nv2 lt 1 or the 3D ni2 or nv2 gt 1 case The following intermediate files are generated during reconstruction to pass information from one program to the other mchelp Executable command file to apply the magnitude calculation bp_cmd Parameter file to control the bp_2d and bp_3d programs bphelp Executable command file to run the bp_2d and bp_3d programs bp_reco first removes these intermediate files and already reconstructed slices Because the VNMR software does not allow a magnitude calculation on the profiles obtained after a Fourier transform a stand alone program bp_mc serves this purpose and is executed using mchelp The next step puts parameters to the file bp_cmd that controls the operation of the programs bp_2d and bp_ 3d The individual parameters are explained in conjunction with these programs Again a file bphe 1p serves to execute the bp_2d and bp_3d programs After reconstruction
532. similarly to single slice images except that the value of d1 is set so as to control the sequence to sequence repetition time in the multislice cascade VNMR 6 1C User Guide Imaging 01 999163 00 A0800 9 4 Performance Specifications The value of the rcvry delay is set greater than one heart period to allow the ECG signal to recover Use of the manual threshold for cardiac triggering is recommended 9 4 Performance Specifications The PGM 1000 is used to detect the cardiac signal of an animal The output of the PGM 1000 can be used to trigger a spectrometer or any medical instrument The preamplifier is nonmagnetic and is installed in the magnet bore An optical link transmits the information to the PGM 1000 Receiver where the gating signal is created The fiber optic link isolates the receiver from the preamp for safety and to prevent ground loops 50 to 500 beats per minute with signal levels between 0 1 mV and 5 mV can be detected The signal is FM modulated on a 33 kHz main carrier Table 19 lists the performance specifications Table 19 PGM 1000 Performance Specifications Function Specification Signal detection Signal modulation Cardiac signal conditioning Signal transfer Gating Indicators Outputs Input Power Nonmagnetic patient leads and clips Signal level 0 1 mV to 5 mV ECG rate 50 beats minute to 500 beats minute ECG main carrier FM 33 kHz 10 for 6 V battery Battery indicator subcarrier
533. sions before doing a 2D Fourier transform 14 Display the image by using the dconi routine for interactive manipulation It might be necessary to rescale the image to the full screen by typing full or fullt To adjust the vertical scale of images move the cursor to a particular part of the image and click the middle mouse button You can adjust image brightness and contrast by moving the cursor to the gray scale bar on the right side of the image and by pressing the left mouse button and dragging the mouse Collecting Time Course GEMS Images 1 For a time course experiment set up a list of preacquisition delay values pad Use the setarray macro to set up an array consisting of linear values for pad If an exponentially varying delay time is required use the exparray macro 2 Acquire the data by using the go command 3 Process the data by first using the 1ashc command and then the command ft2d index in which index refers to the image number 4 Use the command dconi to display and interact with for example zoom adjust brightness individual images 5 Use the dmi macro to display multiple images 3 5 Echo Planar Imaging and Phase Correction Map Files Echo Planar Imaging EPI is an elegant technique for very rapidly collecting imaging data in about 25 ms to 100 ms Using MRI EPI enables you to monitor changes that occur within fractions of a second For example studies that involve motion and flow can benefit fro
534. sired transformation you can salvage the original raw data by moving fid orig back to fid To gain more disk space explicitly delete fid orig after you are satisfied that conversion is successful You can use t abc on either saved data that has been loaded into a VNMR experiment or on data in an experiment that has just been acquired but not yet saved In the first case you have to save the converted data again if you want the saved data set to reflect the conversion tabc supports all 2D data types recognized by VNMR arrayed compressed multislice and arrayed compressed multislice VNMR 6 1C User Guide Imaging 01 999163 00 A0800 3 3 GEMS Multislice Imaging tabc requires that data must have the same number of traces as the table elements It is primitive in what it expects to find in a table file does not support any of the advanced features of table expansion e g the entire table must be explicitly listed in the table file and expects to find only one table in a file whether the table is t1 or t60 is unimportant Table Conversion Commands The following commands apply to table conversion files e tcapply rearranges the spectra in a 2D data set that resides in the current data file You must apply ft 1d to the data before you can use this command e tcopen explicitly reads sorts and stores in memory a table conversion file in Svnmruser tablib lt file gt tcopen uses the file when tcapp1y is called e tcclose
535. sition parameters unlike macro svf file is the name of the file with the suffix par added to be created to save the parameters The default is the system prompts for a file name You are warned if you attempt to overwrite a parameter set that already exists svp vnmr stdpar P31 svp usr george testdata Be Retrieve FID M ep Retrieve parameters M svf Save FIDs in current experiment M VNMR 6 1C User Guide Imaging 01 999163 00 A0800 svphf Syntax Description Arguments Examples Related tlimage Syntax Description Related tabc Syntax Description A 4 Commands and Macros for Processing and Display Save currently displayed phasefile to planes directory M svphf file Saves the currently displayed phasefile to a directory named planes in the current VNMR experiment directory If planes does not already exist svphf automatically creates it svphf can be used to save phasefiles in absolute value or phase sensitive modes The current phasefile found in the dat dir directory of the current experiment might be the result of Fourier transformation of experimental data or might be a phasefile previously loaded with the rt ph f command A phasefile is normally the result of apodization Fourier transformation and phasing or magnitude calculation but before contrast windowing and leveling controlled by the grayctr and grays1 parameters The phasefile is a binary data file and no
536. sitive vol_mip Extract one slice C Extract one slice C not in VNMR vol_mip xy yz xz first_slice last_slice y iner 345 VNMR 6 1C User Guide Imaging Appendix A Commands Macros and Parameters Description Extracts only one slice which is the pixel by pixel maximum of all the slices that vol_extract would have extracted used to process 3D data Arguments first__slice extracts only that plane number last__slice extracts planes gt first_slice and lt last_slice incr is the increment between successive slices it should be positive Related vol_extract Extract one plane orientation C 346 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Symbols par directory parameters getting 62 par directory saving parameters in 63 par parameters getting 62 xpan file suffix 197 _gcoil macro 20 Numerics 180 pulse length measuring 62 measuring 285 1D data Fourier transforming 62 Ist indirectly detected dimension 334 335 Fourier number 343 2D and 3D backprojection 225 2D data acquiring 290 compressed converting to standard 285 displaying 278 displays interactively adjusting 62 Fourier transforming 62 288 2D experiments acquisition submitting to 291 gray scale image 292 2D images 29 acquiring 237 reconstructing 232 2D spin warp imaging sequence 26 2nd indirectly dimension 336 3D data file displaying 279 3D data set changing a 2D plane within a 289
537. spatial dimensions of the data set 1D or 2D Matrix Defines the size of the spatial dimensions Filter Type Selects a weighting function if desired to be applied to the data Time Const Used with Filter Type to fit the weighting function to the data Shift Const Used with Filter Type to fit the weighting function to the data Voxel Shift Spatially shifts the voxels in both directions 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 157 Chapter 6 CSI Data Processing DC Correct Rotation number Apply Applies dc correction to the data Rotates the fields in 90 increments The default is a rotation of 3 which aligns fields for VNMR reference image data Transforms all the voxels by using the selected modifications Interactive Filtering or Weighting Interactive filtering can be performed with this operation in order to determine the best function and filter parameters As the filtering function is adjusted the Time Constant and Shift Constant sliders move to the adjusted values Spectral Reconstruction Performs a 1D Fast Fourier Transform FFT on the FID in each voxel of the localized FID data set to form the multivoxel spectra MVS data set Figure 72 shows the window Figure 72 Spectral Reconstruction Window The following list describes the functions of the spectral reconstruction processing attributes Voxel Pos Dimension Point f1 Phase Type Filter Type Uses values in this field and the Load S
538. specify a phase encode gradient shape Readout gradient shape Predefined string parameter to specify a readout gradient shape Spoiler gradient level Predefined parameter to set a spoiler gradient level It is often paired with the timing parameter t spoil torush Crusher gradient control P tspoil Spoiling gradient control P Slice select gradient shape Predefined string parameter to specify a slice select gradient shape 01 999163 00 A0800 A 5 Parameters gtrim Trim gradient level Description Predefined parameter to set a trim gradient level Timing and Delay Parameters A predefined group of timing and delay parameters is present in all imaging parameter sets covering the range of most imaging and localized spectroscopy applications All of these parameters have units of seconds and are created in VNMR as delay type parameters The parameter names generally start with either the letter such as te and tr or d such as d1 and d2 the first letter has no particular significance The names have been selected to correspond as much as possible with common literature usage but some variation in usage occurs from sequence to sequence particularly for names with no standard literature definition such as tcrushandtspoil It is common within a pulse sequence to use a timing or delay parameter to compute one or more internal delays that are then used directly to control sequence timing As an example te is never d
539. spectrometers without gradient waveform capabilities 2047 to 2047 units in integer steps Systems with 16 bit DACs all UNIT Yplus and beyond and SISCO spectrometers with gradient waveform capabilities 32767 to 32767 units in integer steps VNMR and Solaris Software Installation gxmax gymax gzmax Maximum gradient strength for each axis Applicability Description Values See also Related Systems with three axis gradients Defines the maximum gradient strength for each gradient axis Values are read in from the selected system gradient table whenever the parameter set is retrieved or the gradient coil defined by gcoil has changed When the values are read in gmax is set to the lowest value of the three gxmax gymax and gzmax are used instead of gmax when the gradients strengths are not equal for each axis Unequal gradient strengths per axis are generally true for systems with three axis PFG coils which have a strong z gradient and may be true for microimaging systems Horizontal bore imaging systems usually have gradients set to the same maximum value and gmax can be used Number in gauss cm for each parameter Getting Started VNMR User Programming creategtable Generate system gradient table M gcoil Current gradient coil P gmax Maximum gradient strength P 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 309 Appendix A Commands Macros and Parameters sysgcoil Description See also
540. splay pcmapgen creates opens and closes a phase map file unless the file has been explicitly opened with the pcmapopen command file specifies the phase correction map file name residing in your Svnmruser expN datdir directory The default file is Svnmruser expN datdir pcmap If you do not provide file pcmapgen defaults to the file name pcmap You must always provide index which ranges from to n this value is usually 1 and specifies the desired correction map block within the file pcmapgen 1 pcmapapply Apply phase correction map to data C pemapclose Close phase correction map file C pcmapopen Open phase correction map file C Open Phase Correction Map C Systems with echo planar imaging capabilities pemapopen lt file gt lt max_index gt Explicitly opens a phase correction map file which can significantly speed up data processing file must reside in your vnmruser expN datdir directory where N is the current experiment number After the map file is open use pcmapgen and pcmapapp1y to generate maps and correct data Use pcmapclose to close the file when you are finished with it file specifies the phase correction map file name residing in your Svnmruser expN datdir directory Without this argument ocmapopen defaults to pcmap max_index specifies the maximum number of phase correction maps in the file and ensures memory mapping extends to or past the end of the file You must always provide max_index
541. steps for 1st indirectly detected dimension P 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 263 Appendix A Commands Macros and Parameters rt Syntax Description Arguments Examples Related rtp Syntax Description Arguments Examples Related s2pul Syntax Description Alternate Related sediff Syntax Description sems Syntax 264 VNMR 6 1C User Guide Imaging Retrieve FIDs rt lt file lt nolog gt gt Retrieves FIDs from a file into the current experiment file is the name of the file that with the suffix f id added contains the FIDs to be retrieved The default is that the system prompts for the name in that case the name can be given without single quotes If file fid does not exist and file par does rt retrieves the parameters from file par nolog is a keyword specifying that the log file is not to be retrieved rt rt vnmr fidlib fidld fixpar Correct parameter characteristics in experiment M rtp Retrieve parameters M rtv Retrieve individual parameters C svf Save FIDs in current experiment M Retrieve parameters rtp lt file gt Retrieves parameters from a file into the current experiment file is the name of the file that with the suffix par added contains the parameters to be retrieved The default is that the system prompts for the name in that case the name can be given without single quotes If file par doe
542. stinction between VNMR commands and macros e Commands are compiled executable files incorporated into the VNMR software e Macros are interpreted text files written in Varian s MAGICAL language Macros therefore have one distinct advantage to the user they can be modified and customized See the manual VVMR User Programming for a complete description of macro language syntax and tools Most parameters found in VNMR such as np d1 or sw are common to all experimental applications For general information on parameters parameter entry and definitions refer to the manuals VWMR Command and Parameter Reference VNMR User Programming and VNMR Pulse Sequences A 1 Setting the Path to Imaging Macros Most of the macros described in this appendix are in a special directory for imaging macros vnmr maclib maclib imaging VNMR is directed to look in this directory through the sysmaclibpath parameter To set the parameter sysmaclibpath e Set it directly for example by entering it through the VNMR command line sysmaclibpath vnmr maclib maclib imaging e Set it by using the VNMR menus system 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 255 Appendix A Commands Macros and Parameters a Click on the Main menu button then Setup and finally App Mode b Click on the Imaging button to set sysmaclibpath to the maclib imaging directory This approach is recommended because it also creates sysmaclibpath if it does n
543. strings match Case differences are ignored in the comparison The bracketed lines show what needs to be done in case of a match Set to the number of parameters in the fit In this case the number of parameters is fixed but it could depend on arguments on the Image Browser Math line Set to one of the following values LINEAR is a function in the following form y C x PO fO x P1 f1 x where PO and P1 are the parameters to be estimated and the constant C which might depend on x and the functions 0 and f1 of the independent variable x are the same for every pixel LINEAR problems are solved by calculating your design matrix containing the fn x at each x and inverting it to get a matrix that transforms a vector of observed y C values into a vector of parameter values Thus matrix inversion needs to be done only once and the calculation for each pixel simply involves subtracting the constant C from the observed y values and doing a matrix multiply LINEAR_RECALC_OFFSET is the same as LINEAR except that C can be a function of pixel number In y C x PO fO x P1 f1 x your FUNCTION is called with a zero parameter vector for each pixel in order to reevaluate C x LINEAR_RECALLC is also the same as LINEAR but now both C and the fn functions can be a function of pixel number This means that you must construct a new design matrix and invert it for each pixel NONLINEAR the default is used for
544. support the OpenLook interface some Image Browser features may be unavailable In particular some window managers do not support pinup menus If a large number of images must be processed at once the host system should have as much memory and swap space as possible In particular smooth image animation displays require that the X display server have enough memory to simultaneously keep all the images in the movie in memory For systems with imaging software the vnmr user_templates cshrc file should contain the following statement setenv BROWSERDIR SHOME ib_initdir If a new user is created with the makeuser script this variable is automatically set BROWSERDIR points at a user initialization directory Initialization Directory The initialization directory ib_initdir contains the files bitmaps frame directories ROI directories and filter directories used for starting up tuning and running Image Browser This directory is in vnmr user_templates and is copied into the user s home directory when makeuser is used This directory can be copied into any location within the user s area as long as the environment variable BROWSERDIR is set to point to the new location All files ending with a bm are bitmap files and should not be changed The initialization directory contains the following relevant files and directories that have useful and important information colormap init File containing the colormap definition Col
545. t 10 usec to 50 usec so that the Tap water 3s images can be acquired very rapidly Table Degassed distilled water 26s 2 lists the approximate relaxation times at 4 7 T of some commonly used liquids te Echo Time Unlike in conventional NMR spectroscopy imaging experiments usually generate either gradient or spin echo signals The resulting signal intensity therefore depends on the echo time te Echo time is the time between the center of the rf excitation pulse and the position of the echo maximum as shown in Figure 15 Signal decay caused by T gt 180 Won Echo maxima decay caused by T gt Figure 15 Signal Intensity Echo time delay results in some loss in signal because of spin dephasing which is caused by T effects T is defined as a combination of spin spin relaxation T gt magnetic field inhomogeneity and susceptibility effects Susceptibility effects are caused by interactions of the magnetic field with the heterogeneous sample which produces localized field gradients within the sample T gt effects tend to get worse at higher fields Signal loss caused by T gt effects is exponential Therefore at long te values a dramatic loss of signal intensity can result leading to degradation of image quality It is therefore advantageous and sometimes even necessary to shorten the te value to improve image quality However there is a limit to the minimum t
546. t BO ECC and the BO amplitudes track Overall scaling button is off increasing the Overall scaling on an axis decreases the BO ECC that is generated for a given linear gradient amplitude as measured in gauss When the button is on the BO amplitudes are proportionately changed to keep the correction the same Therefore it is important to turn on the tracking button if the Overall scales are touched up after the ECC values are set Graphing Values The eccGraph window lets you graph enabled values To open this window do the following steps 1 Inthe decctool window select the line number 1 through 3 in the box to the right of the Graph button you can display up to three functions on the graph 2 Click on the Graph button The window shown in Figure 98 opens The equation for each line appears in the text input fields you can graph arbitrary functions by typing an expression into one of the boxes and pressing the Return key A legend indicates the line colors used for each expression Left clicking the mouse on a legend entry highlights the corresponding line in the graph In Figure 98 line number 2 is highlighted By default a logarithmic scale is used for the time axis but you can select a linear scale with the scale buttons Zooming in the eccGraph Window To zoom in on an area in the window do the following procedure 1 Click the left mouse button on one corner of the desired region 2 Drag the mouse notice that t
547. t about it or if the ECC scale does need to be changed the values of the ECC parameters do not need to change The purpose of having this scale factor available is related to resolution of the DAC creating the compensation waveform and only in rare circumstances is the scale factor of concern The Shims scale factor controls the gain of the incoming shims The x1 y1 and z1 shims are summed into the gradient signal on imaging systems Overall scale sets the gain on the entire set of signals gradients compensation and shims This is used mostly to correctly set the size of the image for the applied demand gradient It accepts negative values so it can also be used to reverse the polarity of the gradient signal In the Scale panel there is a check button labeled BO amplitudes track Overall scaling When this button is on highlighted changing the Overall scale for an axis also changes the axis gt B0O cross term amplitudes Changing those amplitudes is usually desirable because the BO drive amplitude is not affected by the Overall scale and in fact bears no fixed relation to the amount of drive on the X Y and Z channels BO drive amplitude is unaffected because the BO field corrections are driven by a separate coil through a separate amplifier whereas the X Y and Z corrections can be set as a known percentage of the gradient strength because they modify the demand to the gradient amplifiers If the BO amplitudes are set for correc
548. t the desired expression from the Expression menu 2 Click on the Gframe where you want the result to appear The number is inserted and the cursor advances to the next 3 Click on source images until all the image numbers are filled in 4 Click on Execute 112 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 5 3 Image Browser Math Functions Variables Used in Image Browser Math Expressions Certain variables can be used in an expression Variables i j and k respectively contain the column row and plane of the current data pixel as shown in this example 3 abs i j lt 30 1 2 This expression copies a 60 pixel wide diagonal band of image 1 into Gframe 3 and sets the rest to image 2 An expression should not modify i j or k Note that the C construct expressionO expression expression2 is a compound expression that returns the value of expression if expression0 is true or nonzero and the value of expression2 otherwise The variables width height and depth contain the number of columns and rows in the image For example the following expression copies image 1 to Gframe 2 leaving a 6 pixel wide border of zeros around the edge 2 i gt 5 amp amp i lt width 6 amp amp j gt 5 amp amp j lt height 6 1 0 An expression should not modify width height or depth These i j k width height and depth variables appear to make it possible to construct a synthetic image without any input image Howeve
549. t the np FID P lsfrq Frequency shift of the fn spectrum in Hz P ne Number of FIDs P phfid Zero order phasing constant for np FID P proc Type of processing on the np FID P ssfilter Full bandwidth of digital filter to yield a filtered FID P ssorder Order of polynomial to fit digitally filtered FID P wft Weight and Fourier transform 1D data C Fourier transform 2D data C 1 t2d array_element 2 t2d lt lt options gt lt plane_number gt lt coefficients gt gt 3 t2d ni ni2 element_number increment 4 t2d ni ni2 increment lt coefficients gt Performs the complete 2D Fourier transformation without weighting in both dimensions If the first Fourier transformation has already been done using ftld wft1ld ft1lda or wft1da the ft 2d command performs only the second t transform array_element is a single array element to be transformed options can be any of the following all string arguments must precede the numeric arguments e ptype is a keyword to transform P type data to yield a P type contour display e ntype is a keyword to transform N type data to yield a P type contour display This is the default e t2dc is a keyword to apply a de correction to each tz FID prior to the first Fourier transform The last 1 16 th of the time domain data is used to calculate the dc level e t1dc isa keyword to apply a dc correction to each t interferogram prior to
550. t x in_memory_prof int x 0 filter _name string x band_pass filter_bw double x 1 0 meta_image string x prof_file meta prof_filtl string x prof_file filtl prof_filt2 string x prof_file filt2 image_file string x prof_file r_size int x m_size m_center_x double X m_size 2 0 m_center_y double x m_size 2 0 m_center_z double x m_size 2 0 r_center_x double x m_size 2 0 r_center_y double x m_size 2 0 r_center_z double X m_size 2 0 theta_start double x 0 0 theta_end double x theta_start 180 0 phi_start double x 0 0 phi_end double x phi_start 180 0 Parameters Set by bp_setup The following parameters are set by the macro bp_setup Refer to page 234 for a detailed description of this interface prof_file Name of the profile file e g bp 3d_prof Do not omit m_size Specifies the measurement size and is equivalent to the number of complex data points during acquisition or to the number of real valued data points in the profile file If m_size is not set bp_3d tries to obtain its value from the profile file and sets m_size np 2 250 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 i_size n_phi n_theta in_memory_prof filter_name filter_bw meta_image prof_filtl prof_filt2 image_file r_size m_center_x m_center_y m_center_z r_center_x r_center_y r_center_z 01 999163 00 A0800 10 6 BP Macros and Programs Details Size of the reconstructed volume The resulting i_size images are
551. ta Generating Simulated Data The CSI tool can be used without collecting data CSI can generate simulated data with truncation effects Gen Data Truc or with basically clean data Gen Data Cont These data types can be selected from the command panel File option 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 137 Chapter 6 CSI Data Processing 138 A reference image is generated along with the CSI data The CSI data that is simulated is P31 data VNMR Raw Data Files CSI is made to process raw CSI data which is generally assumed to be in the VNMR raw data file format This data can be retrieved by descending into the directory that contains the FID file selecting fid and then selecting Load Double clicking on the directory or pressing Return after its name does not load the data it opens that directory For example to analyze VNMR CSI data in exp3 start CSI open the FileBrowser double click on directory names until the vnmrsystem exp3 acqfil file appears select fid then select Load Remember that file loading in CSI is different from file loading in ImageBrowser To load files in ImageBrowser specify the directory in which VNMR phasefiles are to be stored and then select Load FDF Files CSI can store data as FDF files at intermediate steps for later processing This data along with other data that can be more easily imported by using the FDF format can be loaded with the FileBrowser An FDF file can be
552. ta Definition Language DDL The ASCII header makes it easy to decipher the image content and makes it easy to add new fields and remains in keeping with the ASCH format of the procpar file The data portion is binary data described by the fields in the header It is separated from the header by a null character For a definition of all the fields see the section File Format in the manual VWMR User Programming VNMR 6 1C User Guide Imaging 01 999163 00 A0800 6 5 Files and Other Items Creating FDF files Use the svsis macro to create FDF files from VNMR and FID files saved from standard SISCO imaging sequences svsis can be modified for special user defined sequences If standard SISCO parameters have been used the modification can be as simple as adding a line to define the sequence The sv sis macro is described in the manual VNMR Command and Parameter Reference Another way to create FDF files is to edit or create a header defining a set of data with no headers and attach the two by using the dfgluer command with the syntax fdfgluer header_file lt data_file lt output_file gt gt This executable takes aheader_fileandadata_fileand puts them together to form an FDF file fAfgluer also calculates a checksum and inserts it into the header If the data_file argument is not present fdfgluer assumes the data is from the standard input If the output_file name is not present dfgluer puts the FDF file to the stand
553. tained by doing multiple scans and then interleaving the imaging data as described on page 58 Phase Correction One of the source of artifacts in EPI images is caused by a shift of the echo position in the t2 dimension The phase shift caused by the echo shift can be corrected by EPI phase correction routines The phase shift or phase error is determined by collecting a reference scan with the phase encode gradient turned off using the episet macro 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 57 Chapter 3 Imaging Pulse Sequences 58 The phase correction procedure is strongly dependent on the quality of the reference scan For example poor signal to noise ratio of the reference scan data can cause errors in the phase correction calculations These errors can result in artifacts in the final images Advantages EPI has recently gained in popularity because of the growing interest in functional MRI Due to advances in gradient technology namely actively shielded gradients and special post processing methods EPI experiments have become routine in some applications Collecting images using EPI offers the following advantages e Fast images can be obtained in 25 ms to 100 ms e Images are T weighted e EPI is ideal for studies such as functional MRI flow studies and bolus tracking e FPlis less affected by motion and flow induced artifacts e The efficiency of other imaging techniques such as inversion recovery T1 a
554. takes significantly longer than replication and unlike most selections in the Zoom Properties menu this selection is used throughout Image Browser Thus any time an image needs to be updated for any reason such as a change of size or vertical scale it is done by pixel interpolation if this option is chosen Vertical Scaling The vertical scaling function multiplies the data values by a number that maps them into the pixel values in the grayscale portion of the colormap 0 to 63 in the default colormap init file This value can either be entered by hand or by using the point and click method with the mouse To enter a value by hand select the V Scale entry from the V Scale Properties menu A window opens with the current default mapping from data value to displayed intensity A new scaling value or functional form can then be entered and new settings are applied to all selected frames To enter a value using the point and click method position the cursor within any image the Gframe that holds the image does not need to be selected and press the eft mouse button The intensity at that part of the image is used to select a vertical scale value The brightest pixel within a few pixels of the cursor position is set to the top of the intensity range Vertical scaling also has a bind property When Bind is in effect all the images in selected frames are scaled to the same value as the image that you click on with the eft mouse button
555. tch can be used to adjust the ECG to the correct polarity for triggering FILTERS Hz HIGH PASS sets the high pass portion of the user selectable bandpass filter The control has multiple positions selecting filters at 0 5 1 5 5 and 10 Hz Frequencies below the selected value are attenuated in the filtered ECG signal FILTERS Hz LOW PASS sets the low pass portion of the user selectable bandpass filter The control has multiple positions selecting filters at 20 40 80 and 160 Hz Frequencies above the selected value are attenuated in the filtered ECG signal e ECG THRESHOLD V AUTO MAN selects the type of threshold applied to detect the QRS complex in the filtered electrocardiogram The upward setting of the switch selects the automatic threshold feature which disables the ECG voltage level control used to select the manual threshold level The downward setting of the threshold selection switch selects manual control of the ECG threshold level The ECG Voltage Level Control is active when the manual threshold mode is selected The threshold voltage level is continuously variable between 0 V and 12 V Selecting the setting of the PGM 1000 receiver gain switch adjusts the amplitude of the QRS complex in the filtered ECG in this range INHIBIT TIME SEC sets the value of the time delay used by the PGM receiver inhibit feature The inhibit feature allows the frequency of the trigger pulses used to gate the spectrometer to be controlled
556. tely 128 or 256 2 5 Phase Encoding 34 During slice selection the preparation phase of an experiment it was possible to restrict the signals to a plane Spatial frequency distribution in a plane is achieved by using the evolution phase encoding and detection readout phases of a2D NMR experiment In a spin warp imaging experiment a 2D dataset is collected and each orthogonal dimension contains information about the phase encode and readout dimensions respectively Slice selection and frequency encoding detection phase are easily visualized by viewing the slice profiles and readout profiles shown in Figure 5 and Figure 11 The concept of phase encoding is less obvious gro because information is preserved in the second dimension as a phase gpe modulation Fourier transformation along the second dimension provides ADC spatial frequency information Spatial information corresponding to the phase dimension is encoded by the use of a gradient pulse during phase encoding as shown in Figure 11 rf AN gss Figure 11 Gradient Echo Imaging Sequence For example consider a spin at a specific location y in cm along the phase encode dimension The phase of the spin is affected by the phase encoding gradient amplitude gpe and its duration t pe For an arbitrary pulse the phase is proportional to the integral area of the eu pulse defined by the following equation t gt Y y gpe dt eq 14
557. tems or YN YINOVA and UNITYplus spectrometers with selectable large signal mode preamplifiers Description Controls preamplifier signal level selection Values h signifies high signal mode at the preamplifier If the signal level is unusually high this value provides increased signal handling capacity at some reduction in signal to noise This mechanism is separate from the receiver gain control which should be optimized before changing presig 1 signifies low signal mode at the preamplifier This value provides the best signal to noise performance and should be used in normal operation for low to moderate signal levels n signifies not used presig defaults to low signal mode at the preamplifier if the hardware is present Related gain Receiver gain P 344 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 rfcoil Description Related rfphase Description Description Related A 6 Image Browser Commands Not in VNMR RF pulse calibration identity Specifies an entry in the pulsecal pulse calibration database Information from pulsecal is used for automated computation of rf power levels imprep Set up rf pulses imaging and voxel selection gradients M pulsecal Create modify or delete entry in pulsecal rf calibration file M Phase angle Phase angle used for rf spoiling in sequences that include this capability Number in degrees rfspoil RF spoiling on off P A 6 Image Browser Commands Not i
558. ter orient with the substitution of the axis designators 1 2 and 3 for the descriptors readout phase encode and slice select vorient in turn determines three Euler angle parameters vphi vpsi and vt heta which are analogs to the phi psi and theta parameters For example if vorient sag posi lies along Z pos2 along Y and pos3 along X with voxel Euler angles vtheta 90 vpsi 90 and vphi 0 trans sag cor oblique orient Slice plane orientation P plan Interactive slice and voxel selection M posl pos3 Position of voxel center P vphi vpsi vtheta Euler angles for voxel orientation P 328 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 A 5 Parameters vphi vpsi vtheta Euler angles for voxel orientation Description Euler angles used to define voxel orientation Definitions are similar to the imaging plane orientation definition parameters phi psi and theta Generally voxel Euler angles are not directly set by the user but instead are set either by entering a string value into vorient or through interactive graphical planning of a voxel plane from an existing scout image Related phi Euler angle for defining imaging plane orientation P pei Euler angle for defining imaging plane orientation P theta Euler angle for defining imaging plane orientation P plan Interactive slice and voxel selection M vorient Voxel orientation P Special Purpose Orientation Parameters
559. the Voxel Pos field and the Load option in the Spectral Reconstruction window 2 Select the Filtering tool from the G Tools window to open a Filter display in the selected Gframe After the filtering application is done the processing features in the Spectral Reconstruction window can be used along with the left and middle mouse buttons to manipulate the filter Clicking the left and middle mouse buttons within the weighting function display manipulates the values of the Time Const and Shift Const fields and displays the resulting spectrum Changing fields within the window also updates the resulting spectrum Other spectra can be selected and processed by using the Voxel Pos field and the Load option However selecting spectra by using the Voxel Select tool disables the Filtering tool until it is reselected Phase and Baseline Correction Phase Correction and Baseline Correction corrects MVS data This process is selected after spectral reconstruction if phase or baseline correction are needed for the data Figure 59 page 141 and Figure 60 show the Phase Correction and Baseline Correction windows respectively that open when those options are selected from the Process menu The processes allow for correction of a single voxel at a time or global correction of all the voxels Individual spectrum can be phased or baseline corrected Correction is done for both processes by selecting the spectrum with the Voxel Pos and the Load option o
560. the experiment started with ga next at the head of the queue of experiments to be submitted to acquisition wait isa keyword to stop submission of experiments to acquisition until wexp processing of the experiment started with ga wait is finished VNMR 6 1C User Guide Imaging 01 999163 00 A0800 go Alternate Related Syntax Description Arguments A 4 Commands and Macros for Processing and Display Go Wft button in the Acquire Menu au Submit experiment to acquisition and process data M change Submit a change sample experiment to acquisition M gain Receiver gain P go Submit experiment to acquisition M go_ Pulse sequence setup macro called by go ga and au M load Load status of displayed shims P loc Location of sample in tray P lock Submit an Autolock experiment to acquisition C method Autoshim method P sample Submit change sample Autoshim experiment to acquisition M seqfil Pulse sequence name P shim Submit an Autoshim experiment to acquisition C spin Submit a spin setup experiment to acquisition C spin Sample spin rate P su Submit a setup experiment to acquisition M usergo Experiment setup macro called by go ga and au M wft Weight and Fourier transform 1D data C wshim Conditions when shimming is performed P Submit experiment to acquisition M go lt lt acqi gt lt nocheck gt lt nosafe gt lt next gt lt wait gt gt Performs the e
561. the second Fourier transform The last 1 16 th of the time domain data is used to calculate the dc level e f2sel is a keyword to allow only preselected f regions to be transformed along t The t interferograms in the non selected f2 288 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Examples Related A 4 Commands and Macros for Processing and Display regions are zeroed but not transformed The same mechanism used to select baseline regions for baseline correction bc is used to select the f2 regions to be transformed along ty Set intmod partial and partition the integral of the spectrum into several regions The even numbered f2 regions e g 2 4 6 are transformed along t1 the odd numbered regions are not transformed along ty e nf is a keyword to transform a non arrayed 2D experiment that has been collected as a single 2D FID with multiple nf traces e ni2 isa keyword to transform non arrayed 2D data that have been collected with ni2 and sw2 instead of ni and sw1 addpar 3d creates the necessary processing parameters for the ni2 operation e noop is a keyword to not perform any operation on the FID data This option is used mainly to allow macros such as wft 2da to have the same flexibility as commands coefficients area series of coefficients according to the following scheme RR1 is the coefficient used to multiply the real part first R of spectra set 1 before it is added to the real part
562. thus selecting a slice Any NMR weighting in the preparation phase is done with hard pulses thereby not allowing multi slice experiments However you may array any parameter to measure several slices according to the arrayed parameter The bp_2d reconstruction is able to reconstruct these arrayed slices The reconstructed intensity in each pixel of the slice refers to the signal obtained from the particular pixel position x y The pulse program consists of a preparation phase A and acquisition phases B and C The preparation phase A takes the recovery time t r and any NMR weighting applied with sr ir and aps The acquisition phase starts in B with a 90 slice selective pulse p1 tpwrl and plpat In Figure 122 the pulse selects an xy plane using the z gradient After the pulse the magnetization along the slice thickness is refocused z gradient and dephased in the plane x y gradient The 180 slice selective pulse pw tpwr or pwpat inverts the magnetization in the selected slice and results in a spin echo in phase C The slice profile is controlled by the pulse pattern owpat or plpat and the duration of the pulse p1 and pw The position of the slice is set by the frequency offset to sfrq tof of the selective pulses T Weighted 2D Slice Selective BP Pulse Sequence The T weighted pulse sequence is shown in Figure 123 The preparation phase A contains only the recovery time t r T weighting is achieved during the phas
563. tical Magnet ices cee echoes bis nnn R E EEN E E E ei 38 Figure 15 Signal Intensity seisen nonn E E EE A EEE EE E 39 Figure 16 Equilibrium Magnetization 0 0 0 cece eecesseseceseeseceeceseceeeeeeseaeeeecaeesaecaeesaecnessaeseeeaees 40 Figure 17 Gradient Echo Imaging Sequence 000 0 eee eeeessessceeceseceeeeeeeeseeeeecoeesaecacesaecnessaeeneenaees 45 Figure 18 Gradient Echo Version of EPI Pulse Sequence 0 0 csi eeeeccsseseeeeeeecneeseeseesecaeeeeeaeeesenes 53 Figure 19 Spin Echo Variant of the EPI Pulse Sequence o eee ceeecsseseeeeeeeceeeseeeeeecaeeeeeaesaeenes 54 Figure 21 Ghost ATACE sreo ne eE E a A EEE A A EEE R 54 Figure 20 Time Domain Data Processing Steps eesseesessereersseerssresrerssreresrrreseerrsrenterreerreeeneesenens 55 Figure 22 EPLECHO ITAIM piirre aeara e KEE EAE A ENE E EGE 60 Figure 23 Echo Train After groa Adjustment seesseseesesssesisseesresrststsrsesstsrersesrereersrereenrsesreeeeee 60 Fig r 24 Alipned ECHOCS asec sievietses diviseies sctelaebscavsbasebeysenvesSedunasiivdsevubatvbsnesdesseaetcsawsuaues SEAE 60 Biss 25 Centered ECHOES as seve tee tren sont E oe as pE autos viarie EE ETEEN ENESA EE EEEN EEEE 60 Figure 25 Default Layout of Main Image Browser Screen oo cei eeeecesesceeeeeeceeeeceseeaeceteeeeaeeasenes 66 Figure 26 Image Browser Control Panel oi cs ccsssices esses secvecustesteessebuesctvesssesseedeseesacbssneseavevnvanedss 70 Figure 27 Frame Properties Menu sscsscssscsosessocsc
564. time constants 197 time domain data processing steps 55 358 VNMR 6 1C User Guide Imaging to spatial domain conversion 26 time constants changing 204 time course collecting GEMS images 51 EPI experiments 58 GEMS sequence 49 studies 47 time shared decoupling 343 homonuclear decoupling 22 title macro 305 tof parameter 42 tofc parameter 243 Tools panel showing 100 Tools window 80 total repetition time 21 tpe parameter 243 tph parameter 243 tpwr parameter 63 234 tpwrl parameter 21 50 64 234 240 243 tpwr2 parameter 21 tpwrcal macro 272 tpwri parameter 237 238 241 242 tpwrj parameter 243 tr parameter 21 38 43 64 240 243 245 transfer macro 276 Transform button 288 transients to be acquired 335 transmitter frequency offset for observe 268 nucleus of observe 268 offset frequency measuring and saving 268 offset frequency setting 62 offset moving 260 setting frequency 42 transverse image orientation 20 orientation 63 transverse slice specification tool 253 triggering frequency 220 221 trise parameter 243 U uleft macro 306 underflow and overflow menus 85 151 unweighted Fourier transform 232 unzoom function 81 update gradient characteristics 63 updating pulsecal database 62 ROI statistics 91 statistics 103 updtgcoil macro 272 upper barrel warning 12 uright macro 306 V values range of data 83 ventricular diastole and systole peri
565. ting up 44 183 216 single pulse sequence using a 41 submit to acquisition 291 submitting to acquisition 62 experiments starting ecc 203 explib2 command 24 macro 284 exponential array list setting up 62 pre emphasis 191 expr executing 103 297 extracting one slice 345 F fast Fourier transform 131 faulty projections 245 FAX file format 107 FDF 65 67 74 108 133 137 commands 109 173 files 279 utility functions 117 fdfgluer command 109 173 fdfsplit command 173 FIDs button 291 current data block 333 data saving 63 fid and fid orig files 46 304 Fourier transform 1D FIDs 287 getting 47 62 number acquired 334 retrieve from a file 264 save in current experiment 301 showing 50 350 VNMR 6 1C User Guide Imaging field inhomogeneity effects EPI 56 field of view phase encode 323 readout 324 File Data Format FDF commands 173 file formats 106 FDF 67 108 FITS 106 ImageBrowser 107 portable gray map 107 PostScript 107 VNMR phasefile 67 FileBrowser 73 104 168 files FIDs retrieving from 264 FIDs saving in experiment 301 input output 104 parameters retrieving from 264 parameters saving from experiment to 302 saving 105 filter macro 285 Filter window 96 filter_ parameter keywords 251 filtering functions 77 images 67 tool 156 filters data 77 directories 68 69 saving to a file 105 types of 251 findpw macro 42 62 285 first delay in pulse seq
566. tional frames Clicking on a frame captures it if it was not already selected or releases the frame if it was already selected There is also a menu selection in the Frame Properties menu that selects all Gframes You do not need to click on the Frame option a to select and deselect Gframes Use the Zooming G tool to choose a frame wi e left mouse button You can use the ROI G tool to select frames with the left mouse button and toggle between selections with the middle mouse button make sure the cursor is not in an ROI You can also use Voxel Select Peak Select and Annotation to select frames To select a number of Gframes click on the Frame option in the graphics tools menu shown in Figure 55 Select each frame with the middle mouse button to append each frame to a selection list VNMR 6 1C User Guide Imaging 01 999163 00 A0800 6 2 Getting Started Moving Gframes 1 Select a frame then position the cursor within the selected Gframe 2 Hold down the left mouse button and drag the frame to a new location Resizing Gframes 1 Select a frame then position the cursor on the desired highlighted corner 2 Hold down the left mouse button and drag the corner to the desired position Splitting Gframes Graphics frames can be split into a number of smaller frames which allow viewing formats to be easily and quickly set up To split a Gframe do the following steps 1 Activate the Frame tool Select the Gframe or frames to be sp
567. tire line associated with the calibration name pulsecal pulsecal quad6 sinc 2000 180 40 pulsecal quad8 remove imprep Set up rf pulses imaging and pulse power levels M plist Pulse length parameter list P feoid RF pulse calibration identity P Calculate spatial resolution of an image rescal lt silent gt Computes and displays the 2D imaging pixel dimensions in mm for both the original data as acquired and the processed data as displayed on the screen Pixel size for the acquired data is computed as the field of view in the readout and phase encode directions divided by the number of points np 2 and the number of phase encode increments nv respectively Pixel resolution for an image as displayed on the screen might be different than for the raw image data because of zero filling The displayed resolution is computed as the field of view in the readout and phase encode directions divided by the Fourier transform sizes n 2 and fn1 2 respectively rescal returns these four values for optional use in a calling macro and also displays the results in the VNMR text window silent is a keyword to prevent display in the text window En Fourier number in directly detected dimension P iml Fourier number in 1st indirectly detected dimension P lpe Field of view size for phase encode axis P lro Field of view size for readout axis P np Number of data points P nv Number of phase encode
568. title string Writes a title to the plotter in the upper left corner of the page string is a string containing the title title June 17 1H STEAM with 25 mm surface coil write Write formatted text to a device C 305 VNMR 6 1C User Guide Imaging Appendix A Commands Macros and Parameters uleft Set chart parameters to display 2D data in upper left corner M Syntax uleft Description Computes the chart position and size parameters sc sc2 wc and wc2 to place the 2D display area in the upper left quadrant of the VNMR graphics screen Related lleft Set chart parameters to display 2D data in lower left corner M ivight Set chart parameters to display 2D data in lower right corner M title Write a title to the plotter M uright Set chart parameters to display 2D data in upper right corner M uright Set chart parameters to display 2D data in upper right corner M Syntax uright Description Computes the chart position and size parameters sc sc2 wc and wc2 to place the 2D display area in the upper right quadrant of the VNMR graphics screen Related lleft Set chart parameters to display 2D data in lower left corner M iright Set chart parameters to display 2D data in lower right corner M title Write a title to the plotter M A 5 Parameters 306 This section provides a targeted overview of the specialized parameters used in imaging and localized spectroscopy applications The information here is a s
569. to 180 or 360 depending on whether a 180 or 360 rotation is desired when acquiring data This is the only BP specific parameter that needs to be set Taking a Measurement You are ready to make a measurement 1 Look ata profile of the image before acquiring the full image In this case set nv 0 2 Enter go to start the measurement When the acquisition is complete enter ft to Fourier transform the data Figure 111 shows a projection profile 3 If the profile is acceptable set nv to the desired number of projections and enter go a 137992 9 cr vs Figure 111 Profile of Fourier Transform of One Projection Running Reconstruction Reconstruction involves a Fourier transform followed by the macro bp_reco 1 Enter ft to execute a Fourier transform A counter in the upper right of the screen counts for all projections taken nv times 2 Enter bp_reco to start the reconstruction process Messages appear for monitoring the status of the reconstruction The following list shows only the most important messages e Magnitude calculation is running If an error occurs in this step transform the data again and start the reconstruction 2D BP is running e 2D BP is finished 228 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 10 4 Routine Usage 3 At the end of reconstruction process for a 2D dataset the first or only slice is copied into the data and phasefile files in expn datdir This slice is also displayed
570. to about 2 5 and I is the background intensity due to room illumination or poor adjustment of the monitor The Value field next to the Gamma switch controls the value of y used in the above equation The Contrast field next to the Log switch specifies the value of the ratio of maximum to minimum displayable intensities in effect Z in the previous equation Normal values for a properly adjusted monitor are 50 to 100 for 7 and about 2 5 for gamma If the monitor brightness is not properly adjusted it is still usually possible to get a good fit by adjusting y the function is relatively insensitive to the Contrast value When the Gamma switch is on a control point is displayed near the middle of the gamma correction curve This control point can be dragged with the left mouse button to adjust the Gamma value The Contrast value can only be changed by typing a new value in the text field If the Gamma switch is ON and the Log switch is OFF correction is made for equal steps in intensity according to the formula J V VNMR 6 1C User Guide Imaging 01 999163 00 A0800 6 3 Tools This correction is not ideal but it might be useful for emphasizing the contrast in some region of the colormap which could normally be done with the V scale function instead Vs Prop Menu Unbind or Bind The last choice in the Vertical Scaling Properties menu is Bind or Unbind e If Unbind is displayed the current mode is bound and the new VS val
571. to the manual VNMR Command and Parameter Reference Table 1 Experimental Macros and Parameters Macro Function plan Displays a menu that provides access to the target scan plan utilities plan allows users to define slice positions offsets gap and the number of slices by using a graphical tool The parameters can then be transferred to a target experiment using the transfer macro Parameter Function ns Sets the number of slices to be acquired for multislice sequences pss The position of slice offset in cm pss is an arrayed parameter therefore an arbitrary number of slices can be directly entered A more convenient way to enter slice offset parameters is to use the plan macro resto NMR resonance offset frequency in Hz thk The slice thickness in mm 2 4 Frequency Encoding 32 In the presence of a readout gradient the spatial frequency components can be directly visualized by observing the profiles along that direction Even though the presence of a readout gradient during the FID signal gives the necessary information in practice it is desirable to collect an echo signal The echo signal when Fourier transformed generates only absorption components in the resulting spatial frequency spectrum or profile The broad dispersive components are cancelled because of the symmetry of the echo signal The cancellation of dispersive components is a big advantage when dealing with imaging data because the image or prof
572. tore and Transform Loaded FID options to allow changing one voxel at a time Defines the spatial dimensions of the data set 1D 2D and 3D 3D is currently not supported Defines the size of the spectral dimension The number of points comes up as the default value but the value can be changed for zero filling Defines whether the data will be processed as phase sensitive data REAL or amplitude data ABS Selects a weighting function if desired to be applied to the data Exponential Gaussian Sinebell not supported at this time 158 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 6 4 Processing Functions Time Const Used with Filter Type to fit the weighting function to the data Shift Const Used with Filter Type to fit the weighting function to the data Shift points Shifts data left or right by points A positive number shifts data to the right a negative number shifts data to the left Delay us Reflects the time in us of the left or right data shift performed by the Shift function Positive and negative delays corresponds to positive and negative shifts Apply To All Transforms all the voxels by using the selected modifications Interactive Filtering or Weighting Perform the following steps to apply a weighting function to a localized FID and interactively manipulate it to see the effect on the resultant spectrum in a selected Gframe 1 Copy a FID into a selected Gframe by using the Voxel Select tool or by using
573. tton of the mouse while moving the cursor inside the display panel The image can also be rotated about the Z axis perpendicular to the screen by moving the Rotate slider in the control panel The Snap button rotates the image to the nearest orientation that makes all the orientation angles multiples of 15 degrees e Adjust the displayed slice of the 3D image by using the face selector and the Slice plane slider The plane selector selects one face of the data cube and the slider moves the active slice through the volume If the 2D display selector is On each slice is displayed in the lower left corner as the slice position slider moves through the volume The disp3d display window also includes the following features e The 3D Display selector selects viewing the 3D volume in image mode image plus wire frame or wire frame only mode e You can adjust the background color of the display panel through the Bkgnd entry point by controlling the levels of the red green and blue channels of the color display Examples of color settings are 255 255 255 for white 0 0 0 for black and 128 128 128 for gray Acquisition and Reconstruction with Sequence bp_image This section describes how to use the bp_image pulse sequence which uses an older style of imaging pulse sequence development bp_image provides a number of NMR weighting and excitation schemes Loading Parameters Parameters for the bp_image c pulse sequence are located in the bp_i
574. turation Tirho Weighting The Tiho Weighting is achieved by a 90 pulse that flips the magnetization in the xy plane and a subsequent spin lock pulse pj which phase is perpendicular to the 90 pulse After the spin lock duration pj the magnetization is flipped back in the z direction and the standard imaging sequence follows Between the 90 pulses and the spin lock pulse a small delay typically 4 us is necessary to allow for transmitter phase switching Note that the spin lock pulse is in the range of milliseconds 242 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 10 4 Routine Usage seg ms lS E E T 20 3 7 20 pi tpe pi dx trise trise dy tris 2 0 1 0 3 0 2 0 i PAN 3 7 a hrm90 hrm90 BACKPROJECTION TRANSIENTS TIMING SPECIAL bptype slice nt 1 di 0 10000 gain 16 ACQUISITION ct 1 te 0 02000 temp not used sfrq 402 175 np 256 tr 1 50000 FLAGS tn H1 ni 64 tpe 0 00300 il y tof 23800 0 ni2 Oo trise 0 00200 in n tofc o GRADIENTS PROCESSING cp y RF_PULSES orient xyz sb 0 002 SAMPLE pi 2 00 gcal 0 002000 sbs 0 000 date Mar 30 94 tpwri 50 Iro 0 80 phfid 0 1 file fhomei pe pipat hrm90 gro 4000 fn not used ter BPYAR_2 Schlau pi 2000 0 grof 1 450 proc ft chi tpwr1 47 gss 5000 math f solvent none pwpat hrm90 gssf 0 500 CONTRAST DERIYED pw 2000 0 prep sr sw 30000 0 tpwr 53 tpwrf 4095 Figure 125 7 Weighting Inversion or Saturation Recovery Parameters in BP Package The following
575. ture and each digital element is referred to as a pixel or picture element In the case of a 3D image each digital element is referred to as a voxel or volume element Resolution of an image depends on two factors e Frequency spread over the field of view which is determined by gradient strengths gpe and gro e Pixel size which is determined by the number of complex data points in the readout dimension np 2 and the number of phase encode steps nv 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 35 Chapter 2 Imaging Experiments 36 Minimum resolution is determined by linewidth which determines whether the signal from one region can be confined to a single pixel Linewidth is mainly determined by spin spin relaxation time and also susceptibility and inhomogeneity at a specific location in the sample Resolution along the phase encode dimension is defined in the following equation Rpe Ipe nv Eq 19 Similarly resolution along the readout dimension is defined by the following equation Rro lro np 2 Eq 20 To illustrate image resolution assume the image is from a sample consisting of three spheres filled with water as shown in Figure 12 Pixel size ni np 2 8 Pixel size oO ni np 2 16 Pixel size o ni np 2 32 Figure 12 Image Resolution of Three Water Filled Spheres When the number of data points is small one pixel can contain both a large region that does give an NMR signal and a large re
576. two points and the frequency at a specific point Move Axis Origin Moves the origin of the axis Color Changes the tool color Aperture Adjusts the sensitivity of the cursor Cursor sensitivity determines how close the mouse cursor must be to a marker to select that marker Vertical Line Marker Tool The Vertical Line Marker tool allows specific locations to be marked in the data and is used only on spectra data in the CSI tool Use this tool to display the frequency difference between two points and the frequency at a specific point The Vertical Line Marker tool is also used to remove unwanted peaks in a spectrum Use the Baseline Correction process to remove peaks After a Spline or Polynomial baseline correction has been specified mark a region with two points Select the rm Peak option to perform the correction and fill in the data between the two points with the baseline correction data The properties menu of the Vertical Line Marker tool is the same as for the Picking tool Curve Fitting Tool The Curve Fitting tool displays a cross hair cursor This tool is used for interactive curve fitting When clicked the height and width of the desired curve can be adjusted by selecting the endpoints of the cross hairs with the cursor and dragging the ends to their desired length 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 155 Chapter 6 CSI Data Processing Filtering Tool This section describes the weighting and f
577. ty and susceptibility effects resulting in the loss of phase coherence 7 gt Susceptibility gradients are caused by heterogeneous interfaces within the imaging sample T effects can be minimized by shimming and by reducing the te delay At higher fields T effects are further enhanced so shimming becomes even more important Slice Thickness and Resolution T loss and image distortions are caused mainly by phase variations across the slice T loss can be minimized by reducing the slice thickness Similarly phase variations within a pixel can also cause signal loss Therefore increasing the resolution in the image plane by increasing the matrix size or by decreasing the field of view can also reduce T gt loss and distortions However reducing the effective voxel size 1s associated with a loss in SNR Furthermore increasing the number of phase encode steps results in a significant increase in the overall scan time Eddy Current Effects Residual eddy currents act like additional field gradients in the magnet and cause further degradation of the gradient echo signal Eddy currents can be significantly reduced by using actively shielded gradients or applying gradient pre emphasis adjustments and slew gradient pulses Nonsteady State Artifacts The brief recycle time used in the GEMS sequence tends to cause a nonsteady state condition resulting in some residual transverse magnetization Subsequent rf and gradient pulses can
578. u displays the Vertical Scaling window in which vertical scaling can be set as shown in Figure 31 The range of data values to be mapped to grayscale values and the form of the mapping function can both be changed Any changes in vertical scaling are applied to all the selected Gframes Changes to the mapping function are also applied to any new images when they are loaded but the data range is scaled to match the data in the particular image The graph at the bottom of the Vertical Scaling window is a plot of gray level as a function of data value The gray level corre sponds to the index into Image Browser s colormap The intensity of the screen pixel as a function of colormap index is set by the Gamma Correction window discussed in VsProp Menu Gamma Correction page 85 Data Range Figure 31 Vertical Scaling Window The range of data values to map to the full range of gray values is set by the two type in fields labeled Data Range The data values are plotted linearly along the horizontal axis between the values in the Data Range fields You must press the Return key in at least one of the fields for the changes to take effect Mapping Function The shape of the mapping function is selected by the buttons at the upper left of the Vertical Scaling window The mapping function translates the data value in a pixel to a corresponding grey level In the following discussions normalized variables are use
579. uction window and interactively manipulate the shape of the filtering function middle window Zero filling can be accomplished by increasing the Point f1 field Left shifting or right shifting of the FID can be accomplished by using the Delay field All parameter changes appear in the Spectral Reconstruction window Parameters in the window can also be manipulated the changes appear in the filter Gframe Phase Correction After spectral reconstruction phase correction is the next step in CSI data processing Most of the time automatic phase correction can be used A phase can be adjusted globally on a subset of the voxels or voxel by voxel Automatic 1 Open the Phase Correction window shown in Figure 59 and select Both in the Phase Order field for Const and Linear phase correction 2 Select the Automatic mode for Global Phase Correction and click Apply to All Write All If a large linear phase correction is needed or if autophasing is not giving the desired results the following procedure can be used Figure 59 Phase Correction Window 1 Select a spectrum from the just processed MVS data 2 Select the desired phase order option then select Auto Go directly set the phases or use the spectrum tool To apply the phase values to the entire data set perform the following procedure 1 Select the OK option in the Global Phase Correction field 2 Select Write All 3 Select Apply To All 01 999163 00 A
580. ue e For items with a range of 0 0 to 100 0 typing Z sets the field to zero typing H sets it to 50 0 and typing P sets it to 100 0 e For time constants typing d or D sets the value to the minimum valid value while typing L will set to the longest maximum value Files Window EccTool Files The eccTool Files window see a nocomp Figure 94 allows you to view a list oe 5 mp of files ina directory and to perform testgrd some limited operation upon them bob 7 techron You can scroll the window to see all narb628 of the files in the eddylib norb624z directory Point to a file in the list and click the left mouse button to loads its contents in all three pages of forms Figure 94 eccTool Files Window The file name is highlighted and becomes the contents of the current file field Preceding values in the forms are erased if unsaved Locking and Unlocking Files Small key symbols to the left of the file names in the window indicate that a file has been write protected or locked To lock or unlock a file if you have permission to do so click the center mouse button on the file to toggle the write protection If a locking or unlocking operation fails for some reason the key always represents the current state of the file The locking mechanism is designed to prevent inadvertent changes to files that might represent settings for various probes or applications To see a quick help reminder about write protection
581. ue is applied to all selected images as well as the one clicked on e If Bind is displayed it means that the current mode is unbound When an image is clicked on only that image is rescaled The Bind mode has no effect on the operation of the Vertical Scaling window because values entered there always are applied to all selected frames ROI Tools This section describes the functions of graphics tools for selecting drawing marking annotating text phasing and scaling spectra and selecting voxels on graphic regions of interest ROD ROI Selector Tool The ROI Selector tool selects and adjusts any of the regions of interest This tool is the default mode of the graphics tools After any ROI has been drawn the ROI Selector tool becomes active The tool has the following ROI Properties menu as do all the ROI tools Delete Deletes ROI Load Loads ROI tools from a file in the SCSIDIR roi directory Save Saves ROI tools to a file in the CSIDIR roi directory Color Changes the ROI tool color The colors of all the ROIs and labels are changed Font Size Sets the size to use for the next annotation entered The size cannot be changed after the label has been created Choices are 10 pt 12 pt 14 pt and 19 pt Cursor Tolerance Adjusts the sensitivity of the cursor This is how close the mouse cursor must be to an ROI vertex to select that vertex Bind Unbind Bind and unbinds current mode Line ROI Tool The Line ROI t
582. uence 315 first pulse width 340 FITS file format 107 108 flag parameters 337 flags 333 flammable gases warning 12 flash macro 47 49 flash3d macro 258 flashc command 45 50 51 62 285 Flexible Data Format See FDF Flexible Image Transport System See FITS file format flip angle list 340 set rf power levels 265 fliplist parameter 50 63 64 float type header creating 102 flow studies 47 fn parameter 63 343 fnl parameter 63 343 format command 100 conversion 45 Fourier number 343 selecting phase and read dimensions 63 Fourier transform 231 1D data 62 287 2D data 288 data collecting and displaying 42 signal showing 50 01 999163 00 A0800 frame directories 68 properties button 71 properties menu 80 Frame Props window 136 Frame tool 70 80 147 frame_ commands 100 frequency difference maps 131 encoding 32 of NMR resonance offset 330 offset to cursor location set 62 offset determine 42 offset setting to cursor location 62 ranges 28 settings 22 ft command 46 50 62 228 234 ft2d command 22 24 51 62 ftnf macro 50 62 290 full and fullt commands 51 functional imaging 48 G ga macro 21 62 290 gain parameter 50 234 gain controlling incoming shims 205 gains setting on SDAC board 204 gamma correction property 151 property 82 Gamma button 75 Gamma Correction tool showing 101 window 85 151 gated spin echo imaging 222 gating PGM 223 gcal para
583. uld be n_parameters constants after the constant for the threshold value USE_PREVIOUS_P Used only for NONLINEAR functions Setting to TRUE should speed up ARAMETERS the fit if the routine uses a fixed guess or if the GUESS function is likely to be very far off for example USE_PREVIOUS_PARAMETERS TRUE This command means that the first pixel is fit with the values from the GUESS function or fixed guess values but that subsequent pixels use the parameters from the last successful fit for the guess If the fitting routine fails with these previous parameters the GUESS function or fixed guess values are used to try the fitting routine again This option can speed up the overall fit time by an order of magnitude if the initial guess is not very accurate For most data if it is possible to find an initial guess that will make the fit converge even if it takes many iterations an initial guess is almost as good as using an accurate guessing function PARFIX Set only if the parameters in the functional form specified in the FUNCTION are different from what you want to be reported This method is used in t1f it c where the functional form of the fit is y PO Pl exp x P2 but the parameters reported are for the fit ofy P2 P1 P2 exp x PO0 Therefore tl_parfix calculates the estimated Pn from the estimated Pn and also calculates new covariances Writing a parfix rout
584. ulse powers and lengths correspond for example tpwr2 usually describes the power level for pulse p2 pw pl p5 Pulse length P pwpat plpat p5pat Pulse shape P Inversion pulse power level Pulse power level for an inversion pulse It specifies the peak power of transmitter pulses corresponding to pi iF Inversion recovery mode P pi Inversion pulse length P pipat Inversion pulse shape P Bi Inversion recovery time P Pulse Shape Parameters 01 999163 00 A0800 321 VNMR 6 1C User Guide Imaging Appendix A Commands Macros and Parameters decpat decpat5 Pulse shape Description General purpose rf decoupler parameters used to specify pulse shapes for pulses mtpat on a second rf channel Related dpwr dpwr5 Power levels for second channel events P Magnetization transfer pulse rf shape Description Holds the name of the rf shape used for a magnetization transfer pulse Pwpat Related mt Magnetization transfer on off P mtpwr Magnetization transfer pulse power level P pmt Magnetization pulse length P plpat p5pat Pulse shape Description General purpose string parameters used to specify rf pulse shape names when a descriptive name is not required Definitions and usages vary from sequence to sequence but there is a general correspondence between names for pulse shapes for example p2pat is commonly used to describe the shape name for pulse p2 Related pw p1l p5 Pulse length P tpwr tpw
585. ulse sequence setup macros to determine the validity of the field of view and slice offset input It is defined in the system gradient table files found in Svnmrsystem imaging gradtables and is automatically set from one of those files when a value is entered for gcoil Values 18 31 33 40 nominal in cm Related creategtable Generate new gradient calibration file M gegi Current gradient coil P gmax Maximum gradient strength P 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 307 Appendix A Commands Macros and Parameters gcoil Description Related sysgcoil System gradient coil P trise Gradient rise time P Current gradient coil Reserved parameter that specifies which physical gradient set is currently installed This allows convenient updating of important gradient characteristics when one gradient set is interchanged for another When set gcoil reads the gradient table file of the same name in vnmr imaging gradtables and sets the gradient calibration parameters gcoil is local to each individual experiment It is normally set the same as sysgcoil for acquiring new data but can be set to other gradient names when working with saved data or data from another instrument Each possible gradient name should have an associated file of that name located in the directory vnmr imaging gradtables Look at any file in this directory for an example of the proper gradt able format or use the macro creategtable to
586. upplement to the more comprehensive manual VWMR Command and Parameter Reference Additional descriptions for some parameters that are commonly used in liquids and solids NMR application such as pw and t pwr can be found in that manual Predefined Parameter Names A large number of parameters useful for imaging and localized spectroscopy have been included in each imaging parameter set and predefined for use in pulse sequence programming Any imaging parameter set will contain all of the parameters described in this section so there is no need to create them Similarly all of these parameters are declared as variables in the file standard h for use in pulse sequence programming and are automatically retrieved from the parameter set Some parameter names are used throughout VNMR to provide automated setup of imaging experiments such as gro and gss New sequence applications using other parameter names can be written However in certain cases automated setup features do not function as desired if alternate names are used The list of specialized imaging parameters that VNMR expects to find includes gcoil gmax gro gss pro pss rfcoil andthk Further descriptions of these and all other predefined parameters are found in this section While a large number of parameters have been predefined for ease of use in pulse sequence programming it is unlikely that any imaging sequence will use every parameter name Instead some subset of the entire g
587. uration effects For example the result of sliceorder a pss 3 2 1 0 1 2 3is pss 3 1 1 3 2 0 2 The adjacent slices 1 and 2 are separated by three time intervals instead of just one a isa keyword to list physical slice positions in alternating order This is the default d is a keyword to list physical slice positions in descending order i is a keyword to list physical slice positions in ascending order sliceorder sliceorder d pss Slice position P Compute slice position and orientation for target imaging plane sliceplan Computes the slice position and orientation for a new target imaging plane from a pair of marked positions found in the t_mark parameter sliceplan is called by the Compute Target button in the Slice planning menu and is not normally executed from the command line sliceplan first determines the coordinates of the two marked points in the scout imaging plane reference frame then calls a separate program to compute the orientation and position of the new target slice The computed results are stored in the target planning parameters t_pss t_thk t_phi t_psi and t_theta for later transfer to a new target experiment Target Parameters page 341 plan Interactive slice and voxel selection M slicemark Store marked positions for planning target imaging planes M voxplan Compute position and orientation for new target voxel M Move field of view information to a target expe
588. uring power up indicates a failure of the preamplifier circuits If the new battery provides power to the unit reassemble the preamplifier by seating the battery holder correctly in to the base of the unit Replace the lower cover by sliding the cover until it mates with the black flange that surrounds the front panel Replace the black flange and retaining screws that were removed from the rear panel Final test the preamplifier by powering on and observing the LED in the optical fiber jack Receiver Panels Controls and Connections CAUTION The PGM receiver contains several ferromagnetic subassemblies The unit is subject to a significant force when placed close to the magnet bore and represents a hazard if brought into regions of magnetic field exceeding 30 gauss The PGM 1000 receiver receives optically encoded signals from the cardiac preamplifier module and reconvert these to electrical signals The reconverted ECG is then filtered using a selectable bandpass filter The QRS complex in the filtered ECG is detected using either an automatic or manual voltage threshold Trigger pulses are generated for gating the spectrometer as each QRS complex is detected A controlled number of trigger pulses can be suppressed through the use of an inhibit delay feature if desired The decoded ECG filtered and unfiltered inhibit output threshold voltage and gate output signals can be observed with an oscilloscope The controls for this module are l
589. urned on and enabled d The air cooling or water cooling accessories are connected and functioning e The gradient amplifiers are turned on and enabled f On systems with computer controlled analog eddy current hardware the appropriate eddy current file has been loaded by ecctool g The shim power supply has been turned on 2 Run the gems macro to load the default parameters from the vnmr parlib directory or from your parlib directory SHOME vnmrsys parlib 3 Set the parameters for observing the profile nv refers to the number of phase encoding values If nv 0 phase encoding is disabled which allows the profile to be observed The profile can be very useful for setting up various parameters and for positioning the sample along the read dimension 4 Set the reference transmitter frequency The resonance frequency of spins corresponds to the position 0 origin in the magnet gradient frame of reference Therefore you must set the resto parameter equal to the resonance offset frequency Setting the parameter can also be conveniently done by using the 1dof macro You must have run the set of macro to use ldof To run setof see the section Initial Setup 5 Set the rf and gradient calibration parameters The rfcoil parameter defines the rf calibration entry in the pul secal database rfcoil allows proper calibration of the rf pulse power in imaging experiments 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 49
590. used One image in the movie can be scaled or all the images in the movie can be scaled if Bind is selected A movie frame can contain ROIs but drawing an ROI on one movie frame does not affect the other frames in the movie To put the same ROI on all frames in a movie step through the movie frame by frame and load the desired ROI file into each frame VNMR 6 1C User Guide Imaging 01 999163 00 A0800 4 2 Getting Started Using Keyboard Accelerators Since it can be inconvenient to switch back and forth between different graphics tools a few commonly used functions can be performed by using various key combinations The following keys work ONLY when an ROI graphics tool is selected If any text annotation is currently selected pressing a key causes text to be added to the label To prevent this action hold down the Control key while using the keyboard accelerators or deselect any text annotation z lowercase z zooms OUT on the image under the cursor by the same factor that Z zoomed in C capitalized or lowercase moves the image under the cursor to the center of the point under the cursor in the Gframe Shift Z capitalized Z zooms IN on the image pointed to by the mouse cursor The point indicated by the cursor is moved to the center of the Gframe unless such a move would result in blank space between the image and the frame By default each time that you press Z the image scale is enlarged by a factor of 2 Changing Zo
591. used as a convenient means of evaluating the progress in shimming A more elegant approach to shimming is the use of image based shimming where an arbitrary region of interest is selected and the shim currents optimized using an analytical method Other EPI Limitations Signal Loss The data acquisition time per echo train for EPI experiments usually lasts for about 25 ms to 100 ms which is significantly longer than for conventional imaging sequences Because of the longer acquisition time the images are heavily T weighted T gt refers to the loss of phase coherence of the spins caused by spin spin relaxation T gt and inhomogeneous fields T gt weighting can result in a significant loss of signal However T weighting can be used to enhance the 7 contrast in images High Gradient Strength Large gradients are needed for EPI experiments Therefore the gradient hardware gradient coil and gradient amplifiers must be able to deliver the high gradient strengths required for EPI Gradient Switching The typical acquisition time per echo is approximately 500 us Therefore the rise and fall time of the readout gradients must be sufficiently short so that rapidly switched gradient fields can be generated VNMR 6 1C User Guide Imaging 01 999163 00 A0800 3 5 Echo Planar Imaging and Phase Correction Map Files Temperature Increase In EPI large gradients are used for relatively long periods of time particularly during time
592. using keyboard accelerators See Using Keyboard Accelerators page 79 for more information 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 81 Chapter 4 Image Browser Vertical Scale Tool ns The Vertical Scale tool is used to adjust the vertical scale of an image When this tool is active frames must not be selected or deselected with the mouse because clicking on an image changes the displayed intensity However a frame does not have to be selected in order to adjust its vertical scale with the mouse any image that you click on is rescaled j There are three methods to adjust vertical scale e Click the left mouse button on the image The program finds the maximum data value within a 10 pixel square box centered on the cursor and the vertical scale is adjusted to put this pixel at the top of the grayscale Hold down the Shift key while clicking the mouse to put the zero data value at the bottom of the grayscale Hold down the Control key to force the image clicked on to be autoscaled In this case it does not matter where you click on the image e Click and drag with the middle button in the Graphics Region This method operates on all selected Gframes and adjusts both the brightness and contrast Dragging the mouse left or right makes the displays darker or lighter respectively dragging down or up decreases or increases the contrast While you drag the mouse a preview of the new settings is displayed by
593. utine because ft 2d expects data to have been acquired in monotonic phase encode order ft2d Fourier transform 2D data C petable Table name for tablib P tabc Convert data from table specified order to monotonic order C Set up imaging power calibration tpwrcal start end Sets up a simultaneous array of the parameters tpwr1 and tpwr2 typically used in imaging sequences as the excitation and refocusing pulse powers for imaging power calibration This array provides a convenient method of calibrating pulse powers using the readout profile tpwr2 is arrayed in steps of one over this range and a tpwr1 array is also constructed with a difference of six units between each tpwr1 element and the corresponding tpwr2 element 12 units for older SISCO VXR and Unity systems The difference of 6 dB in power gives a factor of two in pulse amplitude which is appropriate for any spin echo sequence using 90 and 180 pulses The resulting arrayed data can be used to create a new pulse calibration entry by choosing the power value that gives the profile with the largest amplitude start is the first value for the tpwr2 part of the arrayed pairs The starting value for tpwr2 is 6 less than tpwr2_start end is the last value for the tpwr2 part of the arrayed pairs The ending value for tpwr2 is 6 less than end_tpwr tpwrcal 46 51 produces this data tpwrl 40 41 42 43 44 45 tpwr2 46 47 48 49 50 51 array tpwrl tpwr2 array Par
594. utput image addressed as out_data 0 i If you were defining mathfunc you have already checked the desired output number 0 at the beginning of the routine At this stage you must determine if output number is desired If it is desired write the index of the image with the maximum value in output image number one e IN_DATA i j k references the kth pixel of the jth image in the ith vector Creating a New Function Creating and compiling a new Image Browser Math Function is currently done manually To create a function perform the following procedure 1 Create a file that defines the function mathfunc e g myfunc c This file must reside in the SBROWSERDIR math functions src directory 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 115 Chapter 5 Image Browser Math Processing 4 Edit the makemathfunc file to add my func c to the list of source files The make macro variable USRSRC is a list of the source files for simple user programs those that only involve one source file Add the new file to the list by typing the following statement USRSRC maxof c myfunc c If the list increases to more than a single line continue on the next line by putting a backslash as the last character on the line After editing the makemathfunc file enter the following command make depend This command updates the list of files that the program depends on and changes the makemathfunc file awarning fit c includes userfit c more
595. uty Cycles siscisscssussosesesscecssssvescseasssesseosessvesorspasssniseescevesaveabeepasiiys 189 Table 14 Eddy Current Interface Commands and Parameters 0 eceeeseceeceeeseeseeeeeeceaeeeeeereees 191 Tapie 13 Slew Rate COmmol csisisdcsscesscseeavesseceacssaceitdeess tuscan sdsepscrgnadsdeiegs ssdeecaszswsseacegvosnteckddesoedeceve 194 Table 16 decctool Macros and Parameters cccccccssssssssssscsceccecesececscecececeseseesesesesssssesnenenseses 202 Table 17 PGM 1000 Parts Last vsssccssusetsvesssssict sevcagevscosesaccuisautenandevbucescntevesseesesabecacoudgscecgavsonenss 210 Table 18 Cardiac Preamplifier Electrode Connections 0 eceesssesecseeseeseceeceeeeeaeceeeeceaeeaeeeseres 211 Table 19 PGM 1000 Performance Specifications 20 0 0 eceeeeseesecsecseeeeesecaeceeeeceaeceseeceeenaeeeteees 223 Table 20 Implemented NMR Excitation Schemes 0 0 0 0 ee eceeeeeseseeeseceeeceeceesaecaeeaeeeseeseeeeeees 229 Table 21 Estimated Acquisition and Reconstruction Times 0 0 eee eee ceeceseceeeeseeeeeeseeeeeeeeees 230 Table 22 Parameters Passed to the bp_2d and bp_3d Programs 0 0 eeeeseeeeeceeneceeeeeeteceeeeeeee 250 Table 23 plan COmttols ereunna hel ki Revie ba anata dice dada aE E TEES EES 254 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 10 SAFETY PRECAUTIONS SAFETY PRECAUTIONS The following warning and caution notices illustrate the style used in Varian manuals for safety precaution notices and explain when each t
596. vailable for use with spectral reconstruction The effects on a selected spectrum can be seen by using different weighting functions pre zero filling and post zero filling before applying the processing parameters to the entire data set To use the tool select a Gframe load a spectrum into the Gframe and select the Filtering tool The filtering display in Figure 58 appears A localized FID can be loaded either by using the Voxel Pos field and Load option in the Spectral Reconstruction window or by using the Voxel Select tool described on page 154 in the G Tools window The following example describes how to use the Voxel Select tool 1 Select the Voxel Select tool in the G Tools window 2 Move the cursor to an empty Gframe and capture it with the left mouse button VNMR 6 1C User Guide Imaging 01 999163 00 A0800 6 2 Getting Started 3 Move the cursor over a voxel in the previously processed Localized FID grid and click the left mouse button The FID from that grid appears in the selected Gframe 4 Ifthe Localized FID display has already been overwritten by the MVS display use the walking menus of the View option in the main command panel to redisplay the Localized FID display 5 After the FID is in the selected Gframe select the Filtering tool in the G Tools window 6 Use the left mouse button then the middle mouse button within the filtering window to select filtering weighting functions in the Spectral Reconstr
597. ve currently displayed phasefile to planes directory M Interactive prompt for imcalc M imcalci optype Serves as an interactive interface to the imcalc macro by prompting for any required inputs which vary with operation type imcalci canbe run from the VNMR command line or accessed via the imcalc menu system by selecting 294 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 Arguments Examples Related imconi Syntax Description Related imconn Syntax Description Arguments Examples Related imfit Syntax Description A 4 Commands and Macros for Processing and Display the ImageCalc option in the Analyze menu or by entering the command imcalc with no arguments optype has the same values as described for the imcalc macro imcalc add imcalc Interactive prompt for imcalc M Display 2D data in interactive grayscale mode M imconi Calls the dconi program with the arguments required for grayscale image display dconi dcon gray linear dconi Interactive 2D contour display C Display 2D data without erasing the screen M imconn lt file gt Displays a noninteractive grayscale 2D image without erasing the screen before drawing imconn can be used to display two or more images on the screen simultaneously from the same or different experiments For example to display two image phasefiles in a single experiment first adjust the chart size and position a
598. when one ROI has been selected VNMR 6 1C User Guide Imaging 01 999163 00 A0800 4 1 Overview Filtering Images can be processed using a 3 x 3 or 5 x 5 pixel convolution filter Default filters can be selected or user filters can be generated and saved Enhancementof Images can be processed using equalization low intensity emphasis images high intensity emphasis and hyperbolization histogram methods Arithmetic Images can be arithmetically combined with other images or functions constants Image rotation Images can be rotated in increments of 90 and reflected Line functions Intensities can be viewed as traces on a line or projections across a line Distances can be viewed on the line Cursor The coordinates and image intensity can be viewed at a cursor functions location The distance between two cursors either in the same image or in different images can be also be viewed Graphics Functions Tools are provided to create and modify various types of objects in the graphics region Examples of objects are graphics frames that hold images ROIs that define regions of the images cursors that define locations on the images and text annotation on the images Image Browser uses an 8 bit frame buffer which can show only 256 colors or gray levels at a time The default colormap structure is 64 levels for grayscale and 12 levels for miscellaneous On 24 bit graphics machines about 200 levels of grayscale can be used Image An
599. which must be greater than or equal to the maximum number of phase maps stored in the file pcmapopen pcmap 2 pcmapapply Apply phase correction map to data C pcmapclose Close phase correction map file C pcmapgen Generate phase correction map C Return a stored phasefile into the current VNMR experiment C rtphf phasefile Copies a stored phasefile from the planes directory in the current experiment directory to the working phasefile file in the dat dir directory of the current experiment Copying a stored phasefile allows the display and manipulation of previously transformed images or results of image calculations from imcalc or imfit It also allows the display of multiple images in VNMR see imconn rtphf is commonly used to load stored phasefiles that have been processed and saved in a single experiment from a single data set for example a multislice imaging experiment However any phasefile from any experiment or image processing routine can be retrieved using rt phf if it has the right pixel dimensions and header information The phase file must first be copied into the local experiment planes directory rtphf matches the pixel matrix 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 299 Appendix A Commands Macros and Parameters Arguments Related setgn Syntax Description Related spuls Syntax Description Related ssprep Applicability Syntax Description Related
600. wn in the File Browser Data window 3D Data Commands vol_extract lt xy yz xz gt first_slice last_slice lt incr gt Extracts one orientation of planes as selected by xy the default yz or xz Operates on the 3D data set to which the slice extractor is pointing if you just loaded a 3D data set it is that one Specifying only first_slice extracts only that plane number Specifying last_slice extracts planes from first_sliceto last_slice incr the increment number between successive slices must be positive if used vol_mip lt xy yz xz gt first_slice last_slice lt incr gt VNMR 6 1C User Guide Imaging 01 999163 00 A0800 4 5 Macros Constructs an image which is the pixel by pixel maximum of all the slices that vol_extract would have extracted Arguments are the same as vol_extract Processing Commands info_save filepath saves the contents of the Info Messages window to the file filepath If filepath is not an absolute path the contents are saved in the current directory in the File Browser Info Messages window filepath also erases the current info window contents Sets the number of bins used for histogram in the Statistics panel to n math expr Executes the expression expr in the same way as if it had been typed into the Image Math panel stat_bins n Sets the number of bins used for histogram in the Statistics panel to n stat_print Prints current statist
601. xperiment described by the current acquisition parameters checking parameters loc spin gain wshim load and method to determine the necessity to perform various actions in addition to simple data acquisition This may involve a single FID or multiple FIDs as in the case of arrays or 2D experiments go acquires the FID and performs no processing If free disk space is insufficient for the complete 1D or 2D FID data set to be acquired go prompts the user with an appropriate message and aborts the acquisition initiation process Before starting the experiment go executes two user created macros if they exist The first is usergo a macro that allows the user to set up general conditions for the experiment The second is a macro whose name is formed by go_ followed by the name of the pulse sequence from seqfil to be used e g go_s2pul go_dept The second macro allows a user to set up experiment conditions suited to a particular sequence acqi is a keyword to submit an experiment for display by the acqi program All operations explained above are performed except acquisition of data is not initiated The instructions to control data acquisition are stored so that acqi can acquire the data when the FID button is clicked The gf macro is recommended instead of running go acqi directly Using gf prevents certain acquisition events from occurring such as spin control and temperature change See the description of gf for more information
602. yed at a time and assigned to red green or blue colors Interpolation can be performed between voxels to achieve a more continuous image Color maps overlaid on the current reference image can also be displayed The intensities for each map can be independently scaled or scaled in common The Display Mmap Info option writes out a list of currently registered maps to the Info Messages window Display Properties CSI allows certain display properties to be selected Figure 80 shows the Display Control window Figure 80 Display Control Window The following list describes the processing attributes in the Display Control window Spectrum Scaling Controls how the spectrum is scaled when it is displayed in its own Gframe Auto Normalized or Fixed Auto scales each spectrum individually to the Gframe This allows the full range of the spectrum to be seen but it does not give a perspective to the rest of the voxels Normalized scaling normalizes the scale across the CSI data set and displays each spectrum in proportion to the other spectra in the data set Fixed scaling allows the scaling to be fixed Spectrum Scale Displays a scale below the spectrum Fit Parameter Show If on displays the curve fitting results in the Info Messages Voxel ROD window when a voxel select is performed on MVS Curve Fit data 170 VNMR 6 1C User Guide Imaging 01 999163 00 A0800 6 5 Files and Other Items Misc Menu The Misc menu on the CSI
603. yntax createpfgtable file Description Generates a new gradient calibration file for gradient sets with nonisotropic strengths Files are created in the vnmr imaging gradtables directory in cases where the X Y and Z axes have different maximum gradient strengths Arguments file is the new gradient calibration file name Examples createpfgtable pfg5mm Related creategtable Create gradient calibration file isotropic strengths M gxmax gymax gzmax Maximum gradient strength for each axis P trise Gradient rise time P deccgo Perform an action for decctool M Syntax deccgo Applicability Systems with digital eddy current compensation DECC 256 VNMR6 1C User Guide Imaging 01 999163 00 A0800 Description Related deccgo Syntax Applicability Description Examples Related decctool Syntax Applicability Description exparray Syntax Description Arguments Examples Related A 2 Macros for Setting Up Experiments Executed by the decctool program when the Save amp Go button is pressed By default deccgo executes go but deccgo macros that perform other actions can be created If the deccgo parameter exists this macro executes the contents of the parameter deccgo Action to perform for decctool P Action to perform for decctool P deccgo Systems with digital eddy current compensation DECC Contains a command that is executed by the deccgo macro By default the deccgo para
604. ype is used WARNING Warningsare used when failure to observe instructions or precautions could result in injury or death to humans or animals or significant property damage CAUTION Cautions are used when failure to observe instructions could result in serious damage to equipment or loss of data Warning Notices Observe the following precautions during installation operation maintenance and repair of the instrument Failure to comply with these warnings or with specific warnings elsewhere in Varian manuals violates safety standards of design manufacturing and intended use of the instrument Varian assumes no liability for customer failure to comply with these precautions WARNING Persons with implanted or attached medical devices such as pacemakers and prosthetic parts must remain outside the 5 gauss perimeter from the centerline of the magnet The superconducting magnet system generates strong magnetic fields that can affect operation of some cardiac pacemakers or harm implanted or attached devices such as prosthetic parts and metal blood vessel clips and clamps Pacemaker wearers should consult the user manual provided by the pacemaker manufacturer or contact the pacemaker manufacturer to determine the effect on a specific pacemaker Pacemaker wearers should also always notify their physician and discuss the health risks of being in proximity to magnetic fields Wearers of metal prosthetics and implants should contact their ph
605. ysician to determine if a danger exists Refer to the manuals supplied with the magnet for the size of a typical 5 gauss stray field This gauss level should be checked after the magnet is installed WARNING Keep metal objects outside the 10 gauss perimeter from the centerline of the magnet The strong magnetic field surrounding the magnet attracts objects containing steel iron or other ferromagnetic materials which includes most ordinary tools electronic equipment compressed gas cylinders steel chairs and steel carts Unless restrained such objects can suddenly fly towards the magnet causing possible personal injury and extensive damage to the probe dewar and superconducting solenoid The greater the mass of the object the more the magnet attracts the object Only nonferromagnetic materials plastics aluminum wood nonmagnetic stainless steel etc should be used in the area around the magnet If an object is stuck to the magnet surface and cannot easily be removed by hand contact Varian service for assistance 01 999163 00 A0800 VNMR 6 1C User Guide Imaging 11 SAFETY PRECAUTIONS Warning Notices continued 12 Refer to the manuals supplied with the magnet for the size of a typical 10 gauss stray field This gauss level should be checked after the magnet is installed WARNING Only qualified maintenance personnel shall remove equipment covers or make internal adjustments Dangerous high voltages that can kil
606. ysiological Gating Module csssscccssseeeessseceeeeseeneneeeees 207 9 1 Cardiac Anatomy and Electrocardiography eeceeseceeceeesecenceceeeeenaeeeneesseeeeneens 207 92 Hardware Description ssistselsei dacsesies cas vaceisee uns Asati an asi s o aeit ei 209 9 3 Experimental Setup heroesi a e e E EEEE EEE ONER i 216 9 4 Performance Specifications csccsssseccossesssssesssssneesnscesosenensensscensesssseenssooneeessens 223 Chapter 10 2D and 3D Backprojection ccs ecccssseeecesseeeeeeeseseeeeeenees 225 HOE Installations sio ie elastin taclaea arlene eis 225 10 2 Backprojection Image Generation 20 0 eee eeeeesee cece cae ceseeaeceseaecseesecneseeeeeeeeeetees 226 10 3 Gethin eS tant cisco sc iaccodassascescassevnacdats ances posbeadsvsshsubevanestevous soavesavies vestadueasubesopeses 227 IOA ROUUMS WW SARS Persipnei a E enses svesacoseasbsrvonsepedver OER 229 10 5 Artifacts in BP Imaging onesie eneee neteis E i E bens Aaah 244 10 6 BP Macros and Programs Details 0 eee cee cee cneceseeeeceseeeceeeeeeeeeeeeeseneeeeeeas 249 TOT REPETENCES oats cosceeadvecaccbeherities ea tesbencaest O sevens bearteeesseateveseeeee Gat nena ee 252 Chapter 11 Interactive Image Planning csssseccssseeeeesseeeeeeeeeseeeeenees 253 11 1 Imtroduction 20 0 cccccessscecessececsscecessccecesaeceseacecesacesssaecesesaeeeseasesssaeeeseaeesseeeeeees 253 11 2 Starting the Planning Session eee eeeeeeesceesecneeceecsaesaecs
607. yzx gives a yz Slice in a 2D imaging sequence For 3D sequences the sequence of gradients must comply with a clockwise oriented coordinate system plpat Pulse pattern 90 pulse The pattern selected is modified by bpt ype pwpat Pulse pattern 180 pulse The pattern selected is modified by bpt ype bptype Sets slice selective excitation Two strings are valid bpbt ype noslice results in a non slice selective excitation and bpt ype slice results ina slice selective excitation prep Sets weighting and can take the following values prep none for no NMR weighting in the preparation phase prep sr for T weighting using saturation recovery prep ir for T weighting using inversion recovery prep aps for 7 weighting with aperiodic saturation and prep t1r for Tip weighting 10 5 Artifacts in BP Imaging 244 This section is intended to assist you in identifying problems while you carry out BP imaging sequences Particular problems and their effects imposed on the resulting images are described Object Size and Field of View BP imaging is based on profiles and can reconstruct planes with circular boundaries or volumes with spheres as boundaries Probes used for BP imaging must fit in these boundaries for obtaining proper images Therefore make sure to meet these conditions e Take the maximum diameter of your probe and increase the diameter by 20 to set the field of view in your imaging setup e Align the probe s ge

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