Vespa – RFPulse User Manual and Reference - VeSPA
Contents
1. Each pulse project tab will contain sub tabs at the bottom of the page that describe the transformations used to design the RF pulse There will typically be two or more of these transformation tabs The first tab is standard to all pulse projects and is called Basic Info The second tab is always a create transformation tab such as SLR or Hyperbolic Secant see Appendix B Additional tabs containing general transformations such as Interpolate Rescale see Appendix B can be appended after the create transformation tab The pulse project tab can be resized by adjusting the RFPulse application window and each transformation tab has a vertical splitter bar through the middle that can be used to resize the right and left sides Parameters for each transformation tab are displayed on the left side of the tab the right side of the tab contains a plotting canvas to visually display the current RF pulse waveform and profile results Typically when a transformation tab is added to the pulse project there are no results to be displayed until the Run button has been clicked A new pulse project is typically created set up and run After this other changes to parameters can be made and the Project re run until you are satisfied with the pulse performance Results from running a pulse project are only saved to the database when specifically requested by you Transformation tabs are updated to display results after each2. Pulse Project Add Transformations Management View Help j Welcome Info gt Welcome to Vespa RFPulse W Currently there are no pulse projects loaded You can use the Pulse Project menu to load an existing pulse project or create a new one Re ady Use the RFPulse menu to open an existing pulse project or to create a new project for designing an RF pulse Shown below is a screen shot of a Vespa RFPulse session with two pulse project tabs opened side by side for comparison The functionality of all tools algorithms and transformation will be described further in the following sections 10 11 2 Quick Guide The Nuts and Bolts of RFPulse The creation and modification of RF pulses for use in MR experiments is as much an art as a science We hope that the modularity and flexibility of design steps as presented in RFPulse will allow and encourage you to play with and better understand the effects of changing parameter values in each step of the design Also since each step is on a separate tab within the pulse project you can see the results of each step To facilitate your initial usage we offer here a quick description of how to get started using and learning from RFPulse We start with the assumption that you have already installed and launched the RFPulse application You should see the Welcome screen displayed with no pulse project tabs displayed The easiest interaction requires just a few
3. bar One or more pulse projects can be loaded at a time Each project is displayed in its own tab located at the top of the window Each project contains input data and results from one pulse project design As described above a pulse project is a Oe ee BER steps that create and Pulse Project Add Transformations Management View Help modify an RF pulse Each welcome info x pulse project tab contains a group of tabs at the bottom Welcome to Vespa RFPulse of the page that represent the transformations in the project Transformation tabs contain the input values and results for that step of the pulse design The pulse project window is initially populated with a welcome text window but no pulse projects are Currently there are no pulse projects loaded loaded From the RFPulse You can use the Pulse Project menu to load an existing pulse project or create a new one menu bar you can 1 load a previously run pulse project from the Vespa database Pea into a tab or 2 create a new pulse project and set it up and run it In either case a tab will appear at the top of the window for each pulse project that is loaded or created The Management menu allows you to access pop up dialogs to create edit view delete and import export pulse projects and Machine Settings which will be explained fully later The status bar provides information about where the cursor is located within the various plots and images in the interface thr
4. basic steps e From the PulseProject menu select New to create a new pulse project e In the Basic Info tab fill in the project name and investigator fields e Select Add Transformations Create SLR and a new SLR tab appears e Hit the Run button and a time domain RF pulse waveform is displayed in the right panel e optional select other plot control options at the bottom of the tab to see other results plots e optional vary parameters and hit Run again to observe desired pulse performance e Select PulseProject Save menu item to store your results to the Vespa database so you can re open them later From here you can change parameters on the SLR creation tab to refine the shape duration or other features of the pulse You can also select other transformations from the Add Transformations menu Each transformation appears on a new tab and allows you to further refine your pulse The motivations for manipulating RF pulses have been briefly discussed in the Case Studies section There are two types of transformations create transformations and general transformations As shown above pulse projects start with a create transformation Create transformations are the algorithms by which an initial RF pulse is designed e g Shinnar LeRoux hyperbolic secant etc Each pulse project has just one create transformation The create transformations are selected from the Add Transformations Create menu General transf
5. click on the Run button If there are transformation tabs downstream from the tab where the Run button was hit the program will automatically propagate changes through those tabs as well ie essentially automatically triggering their Run functions Pulse projects can be modified in any tab multiple times All saved pulse projects start life as private That means they re only in your database no one else has seen accessed them Once you export a pulse project to share with another user the pulse project is designated as public That means the pulse project result has been shared with the world Public objects are frozen and become mostly unchangeable Once a private pulse project has become public it can never become private again There are two ways that a public pulse project can be re used First cloning a public pulse project using the Manage Pulse Projects dialog which is described more fully in Section 6 will create a new private pulse project in the database with exactly the same properties as the original but with a different name This clone can then be openend into the pulse project window and modified Second any pulse project can be loaded into the pulse project window whether it is public or private From there the Pulse Project Copy to New Tab menu item will create a new pulse project tab with a copy of the current tab This copy will be private and ready to be modified Note that an important differenc
6. hyperbolic secant pulses and adiabatic pulses generally is that they typically involve high SAR though as described in the case studies section above there are techniques for lowering the SAR associated for a given hyperbolic secant pulse Hyperbolic secant pulses constitute one of the few analytic solutions of the Bloch equations Silver MS Joseph RI Hoult DI Selective spin inversion in nuclear magnetic resonance and coherent optics through an exact solution of the Bloch Riccati equation Phys Rev A 1985 Apr 31 4 2753 2755 and are actually solitons yes this is a real word or non dispersive solutions For power n 1 they have the form B Ape AUT Le A sechi DI a t H I Lan DI where A t is the modulated time dependent amplitude and q t is the modulated time dependent frequency and u and D are parameters For the form of higher order hyperbolic secant functions see Tannus A and Garwood M Improved Performance of Frequency Swept Pulses Using Offset Independent Adiabaticity 1996 J Mag Resonance A 120 133 137 RFPulse takes the specified user input parameters and generates a hyperbolic secant pulse of the above form 32 B 4 Interpolate Rescale Tab general transformation B 4 1 Tab Diagram Pulse Projecti gt X Interpolate Current Dwell Time 125 0 microseconds New Dwell Time 62 4 microseconds Rescaling IT Rescaling On Resonance hip 90 0 Run Plot Control
7. list 23 Currently that list is implemented as a linear group of transformation objects The first transformation object is always Basic Info This is a special transformation object in that it occurs prior to any RF pulse waveform results being created This object modifies meta data within the pulse project and sets up global parameters that can affect pulse creation modification algorithms in subsequent steps Specifically it allows you to select the Machine Settings and Master Parameters for the pulse design The second transformation is always a create transformation that implements an RF pulse design algorithm such as Shinnar Le Roux or hyperbolic secant that creates an initial RF pulse waveform result Subsequent steps always contain a general transformation which uses the waveform result of the previous step as an input to be modified by the current transformation step The transformation design was selected to allow more modularity in RF pulse design and increased flexibility in the display of intermediate results Each transformation tab in the pulse project has a manageable number of parameter widgets in its GUI These can be modified and applied to the local set of results without having to run all previous steps Results are plotted in the transformation tab to allow you to visually inspect the effects of their settings for each design step The figure below is a visual representation of two steps in the transformations that make u
8. of the pulse in degrees As of this writing this parameter is limited to shallow tip angles just above zero e g 0 001 to 30 degrees 90 degree or 180 degree angles Note that the pulse is shaped for the specified tip angle To see the effect of the pulse at the wrong power that is producing the wrong tip the pulse must be re scaled and the profile recalculated with the Bloch Equations Time Steps integer number of steps in the pulse The number of pulse steps is usually selected in powers of two to speed the calculations The profile shape is not improved by increasing the number of steps beyond around 128 However the smoothness of the pulse and minimization of out of band effects is improved with more steps For 90 degree pulses the minimum number of steps recommended is 64 while for 180 degree pulses the recommended minimum is 128 Note that the calculations are more rapid for a small number of steps e g 64 steps and a larger number of steps may be selected after the other pulse parameters have been decided upon Duration float in milliseconds total time of the pulse Values selected may not be achievable due to the minimum dwell time and dwell time increment set in the machine settings In this case an achievable value will be suggested 28 Bandwidth float in kHz width of the pass band in kHz as measured at full width half max amplitude value Separation float in kHz optional This control is only a
9. or Cosine Filter Application float percentage how much to apply the filter 0 0 to 100 0 31 B 3 4 Algorithm Applied at Run Time When you hit the Run button Hyperbolic secant pulses are adiabatic pulses that are typically used for inversion and are relatively insensitive to inhomogeneities in the B1 field and transmitter power setting and result in very uniform frequency profiles For adiabatic pulses both the amplitude and frequency of the pulse are typically varied The pulses are adiabatic in that the amplitude is large enough and the frequency variation is slow enough the adiabatic condition that the longitudinal magnetization follows the direction of the effective magnetic field generated by the combined BO and B1 fields More specifically the adiabatic condition is that the precession of the magnetization vector about the effective field vector is more rapid than the change in angle of the effective field vector For a hyperbolic secant inversion pulse the initial effective field is aligned with BO and the final effective field is aligned in the opposite direction Hyperbolic secant pulses have the remarkable property that once B1 is strong enough inversion is achieved over a frequency selective range slice such that further increases in B1 do not result in increases in flip angle Due to the frequency dependent phase that is generated by a hyperbolic secant pulse they can not be used as refocusing pulses A disadvantage of
10. suppression of other spectroscopy signals close to water The use of pulses with improved selectivity e g SLR pulses as designed with RFPulse can reduce this problem Case 4 Lowered Peak Voltage Pulses The peak voltage or power that can be applied by the MRI instrument to the coil is limited This can prevent a desired RF pulse from being implemented on the instrument For example spin echo pulses require 3 to 4 times the peak voltage required by a 90 degree pulse producing the same bandwidth In addition hyperbolic secant inversion pulses require high peak voltage There are several approaches to lowering the peak voltage of these pulses Spin echo pulses An RF pulse can be expressed in terms of a pair of polynomials designated A and B see e g the paper by Pauli et al cited above For an SLR pulse the B polynomial represents the magnitude of the selection profile that will result from the pulse while the A polynomial contains the phase information for the pulse For a so called minimum phase pulse the roots of the A polynomial lie within the unit circle in the complex plane Reflection of one of the roots of the A polynomial across the unit circle altering the value of the root from z to 1 z doesn t alter the profile produced by the pulse but may lower the peak voltage required Typically the peak voltage can be reduced to around 0 6 of the original voltage required While the peak voltage is decreased the price to
11. 329981263 ABSI NT 12 869012534 0 043329947 3 141592654 0 0 026630458 3 141592654 1 0 029410526 3 141592654 2 0 027636394 3 141592654 3 0 020032857 3 141592654 4 0 006048280 3 141592654 5 0 014027609 0 000000000 6 0 038877678 0 000000000 7 0 066164780 0 000000000 8 0 092508011 0 000000000 9 0 114093901 0 000000000 10 36 C 3 Siemens Vision Format This is a format that is compatible with older Siemens MR scanners The code for this format was derived from Jerry Matson s MatPulse program rather than directly from Siemens documentation Many of the fields are the same and have similar meaning as those for Siemens IDEA format Third Party Export x Output Format and Location Format JEE el Output Location Browse C bsoher Simple_64pt_SLR pta Siemens Vision Pulse Description Pulse_Name Simple _64pt_SLR Entry_Description Exported from Yespa RFPulse project name Siemens Vision Pulse Characteristics Family Name vespa Min Slice Thickness mm fi D Max Slice Thickness mm fa0 0 OK Cancel C 3 1 Format Specific GUI Fields Siemens Vision format ASCII files have some user set and automatically calculated parameter header lines at the top of the file These lines are followed by magnitude phase value pairs one pair per line for each time step in the RF waveform We refer you to the Siemens Vision documentation for more specific details for each au
12. Each pulse project object must start with a single create transformation but can contain zero or more general transformation tabs Each transformation object contains results for that step in the RF pulse design For more detail on how to get started on creating and manipulating RF pulses see Section 2 Quick Guide and the Case Study section on pulse design in this manual 5 3 Transformations each contain a plot on the right hand side This plot can display any and all of the five results plots in any combination by selecting from the check boxes in the Plot Control Visualizing Pulse Project Results 17 panel on the left side of the tabbed window Turning a check box on or off adds or removes the plot from the figure on the right You can modify other aspects of the data display from the View menu The plots displayed in each transformation tab are the cumulative results for all transformation tabs to the left of and including the current tab When a transformation tab is added to a pulse project RFPulse won t display results until you click the Run button Changing transformation parameters on the left panel does not typically change the results plotted until after the Run button is hit iE RFPulse Basic SLR 8ms lolx Pulse Project Add Transformations Management View Help as Pulse Project 1 X Pulse Project3 Pulse Params Frequency Profile Tip Angle foo degrees Time Steps ka o increment
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14. IT Freq Profile Abs Freq Profile IT Ext Profile Ext Absolute Profile M Waveform Usage Type Excite S Basic Info SLR LR x B 4 2 General Usage This is a general transformation tab B 4 3 Widgets and Parameters Interpolate checkbox turns Interpolation algorithm on off Current Dwell Time float the dwell time from the previous results i e the results from the previous transformation or tab If there are no previous results then this value will be zero New Dwell Time float the target dwell time for the interpolation If this new dwell time violates the minimum dwell time or the dwell time increment set in the Machine Settings an error is reported Rescaling checkbox turns Rescaling algorithm on off On Resonance Tip float equal to the new value for either the net rotation or total rotation B 4 4 Algorithm Applied at Run Time When you hit the Run button 33 Interpolate will perform a linear interpolation to recalculate the waveform The new dwell time will be used to create the time axis and the number of time points will be changed to span the duration up to the last point The interpolation routine is performed in one direction and assumes the points are at the beginning of each time slice For data points added after the last point in the waveform the last B1 value will be used extended Rescaling changes the on resonance tip angle either the net tip angle or
15. Pulse Vespa Online Help Help About 4 Appends an Hyperbolic Secant create transformation tab to current pulse project Appends an Interpolate and Rescale general transformation tab to current pulse project Launches the Manage pulse projects dialog Allows you to view clone delete import and export pulse projects Launches the Manage Machine Settings dialog Allows you to create edit view and delete templates for machine settings information Changes plot options in the selected transformation tab of the active pulse project tab including display zero line turn x axis on off or choose units selecting data type and various output options for all plot windows Launches the user manual from vespa docs into a PDF file reader Online wiki for the RFPulse application and Vespa project Giving credit where credit is due The Pulse Project Window The pulse project window offers considerable flexibility You can open multiple projects simultaneously and they can be moved around arranged and dockeda as desired by left click and dragging the desired tab to a new location inside the main window The tabs can be positioned side by side top to bottom or stacked They can also be arranged in any mixture of these positions The pulse project window can be populated with one or more pulse project tabs each of which contains the results of one pulse project Pulse project tabs can be closed using the X box o
16. TE Special concatenated RF pulses used in a variety of experiments For example concatenated RF pulses are used in arterial spin labeling experiments such as the TILT experiment and in so called pseudo continuous arterial spin labeling experiments B1 insensitive pulse design particularly at high magnetic field the B1 field becomes inhomogeneous and it may be desirable to use RF pulse designs that perform uniform tipping even in the presence of inhomogeneous RF fields RFPulse provides optimization methods to obtain such designs Using RFPulse A User Manual This section assumes Vespa RFPulse has been downloaded and installed See the Vespa Installation guide on the Vespa main project wiki for details on how to install the software and package dependencies http scion duhs duke edu vespa In the following screenshots are based on running Vespa RFPulse on the Windows OS but aside from starting the program the basic commands are the same on all platforms 1 Howto launch Vespa RFPulse The usual case If you installed RFPulse by downloading and unzipping the package and by running python setup py install then you should already have an icon on your desktop called RFPulse Double clicking on this icon will launch the application Shown below is the Vespa RFPulse main window as it appears on first opening No actual RF pulse project windows are open only the Welcome banner is displayed im RFPulse loj x
17. Vespa RFPulse User Manual and Reference Version 0 2 0 Release date May 4 2011 Developed by Brian J Soher Ph D Philip Semanchuk Duke University Medical Center Department of Radiology Durham NC Karl Young Ph D David Todd Ph D University of California San Francisco Department of Radiology San Francisco CA Developed with support from NIH grant EB008387 01A1 Table of Contents Overview of the Vespa Package nsnnssnnneessnerrereerernrrrrssrerrneeee 4 Introduction to VespaHtbulse 5 Case Studies in RF Pulse Design 7 Using RFPulse A User Manual 10 1 How to launch Vespa RFPulse EE 10 2 Quick Guide The Nuts and Bolts of RFPulse seseeeeeeeeeeeerre 12 3 The RFPulse Main Window eee 14 4 The Pulse Project WEE ee ee te oi ee ee E 15 5 The Pulse Project ebe deet eege geheegt 16 5 1 Loading an existing pulse Project cccccceeeeeeeeeseeeeeeeeeeeeeeeeeeeecenseeeneeeeeenenenes 17 5 2 Running a new pulse project ccccseceeecnceeeeeseeeeseeeceeeeeeeeeeeesneneeneneeeeeeneeeseeoes 17 5 3 Visualizing Pulse Project TEE 17 6 Management Dialogs EE 20 6 1 Manage Pulse Project dialog eeeseeeeneeeeeseeeiiirrtteeeerrirrrtesssrrirnnrrnssssrrrreeens 20 6 2 Manage Machine Settings Templates dalog 20 T Res lts Output rese riie peaa fa a dee 22 7 1 Plot results to image file formats ce ecancseie aebroheegalsacsuadunascaneataeners anne ee edegeeaeonte
18. be paid is that the SAR for the pulse is increased A second approach to lowering the peak voltage of a spin echo pulse is to use the VERSE technique see for example the paper by Matson cited above which can be thought of as lengthening the center portion of the pulse to enable the voltage of this section of the pulse to be reduced The FOCI technique is similar and can be considered as a particular implementation of the VERSE method A flexible implementation of the VERSE method is known as remapping This method enables the RF pulse and associated gradient to be altered to lower the peak voltage of the pulse While this method does not necessarily increase the overall length of the pulse depending on the parameters used it may increase the SAR Hyperbolic secant inversion pulses The hyperbolic secant pulse represents an adiabatic pulse where the performance of the pulse does not change once the total power of the pulse is above a certain threshold The advantage of this type of pulse is that it can perform well even in an inhomogeneous B1 field The voltage shape of the hyperbolic secant pulse can be expressed as sech ft where t is the normalized time extending from 1 to 1 This shape produces a high voltage at the center of the pulse Garwood et al have shown that by using a shape function of the form sech ft the peak voltage of the pulse can be reduced while the pulse retains its adiabatic character The original hyperbol
19. ctivated if Dual Band is selected This is the separation in kHz between the two passbands as measured at full width half max amplitude values Single or Dual Band radio button sets whether one or two passbands will be included in the design of the pulse Single Band produces conventional slice selective pulses The Dual Band selection can be used to produce a dual band pulse such as a dual band saturation pulse Non Coalesced Phase Type dropbox selections linear max or min Refocused i e linear phase pulse is generally preferred for an excitation or spin echo pulse while Max Phase or Min Phase are preferable for inversion or saturation pulses Filter radio button selects whether the SLR algorithm uses a Remez or least squares optimization algorithm Passband Ripple float in percent of the RF pulse profile See notes below in Reject Ripple Reject Ripple float as a percent of the RF pulse profile amplitude These ripple parameters are used to estimate a transition band which is the parameter actually used in the calculations Although the ripple estimates are quite accurate for 180 90 and very shallow tip pulses they would be in error for pulses calculated at intermediate angles B 2 4 Algorithm Applied at Run Time When you hit the Run button The following description is based on content from the Handbook of MRI Pulse Sequences Bernstein MA Kevin F King KF Xiaohong JZ Aca
20. demic Press 2004 The SLR algorithm was developed to solve the difficult inverse problem of finding what RF pulse to apply given a desired slice profile and the initial condition of the magnetization For small flip angles the shape of an excitation pulse can be approximated by an inverse Fourier transform of the slice profile but this approximation breaks down for pulses in the range of 30 90 or larger Iterative numerical optimization methods can be used for large tip angles but the SLR method allows for a direct non iterative solution in certain situations Characteristics such as RF bandwidth pulse duration tip angle percent ripple in the passband and percent ripple in the stopband can be specified as well as acceptable tradeoffs between these parameters The algorithm returns the exact RF pulse through a straightforward computational process The SLR algorithm uses two key concepts The SU 2 group theoretical representation of rotations and the hard pulse approximation Two typical ways of describing rotations in three dimensional space are 1 via 3 x 3 orthogonal rotation matrices and 3 x vectors i e via the special orthogonal 3D group GOU 2 via 2 x 2 unitary matrices and 2 x 1 complex vectors called spinors i e via the special unitary group SU 2 Pauly et al 1991 These two representations are completely equivalent ways of describing macroscopic rotations such as those experienced by the magnetization vector But
21. e hun 000000 microseconds Gradient Slew Rate bon 00 mTjmjms Gradient Maximum ban 00 mT meter OK Cancel Edit The highlighted metabolite is opened in the machine settings editor All fields are editable View Similar to Edit but no fields are editable Clone Select a template in the list hit clone and a copy of that template is made that is now fully editable Delete Deletes selected template s Set Default Used to designate the currently selected template as the default template that sets the machine settings in a new pulse project object 21 7 Results Output 7 1 Plot results to image file formats Results plots in each transformation tab can all be saved to file in PNG portable network graphic PDF portable document file or EPS encapsulated postscript formats to save the results as an image The Vespa RFPulse View menu lists commands that only apply to the active transformation tab in the active pulse project tab Select the View Output option and further select either the Plot to PNG Plot to PDF or Plot to EPS menu item You will be prompted to pick an output filename to which will be appended the appropriate suffix 7 2 Plot results to vector graphics formats Results in each transformation tab can be saved to file in SVG scalable vector graphics or EPS encapsulated postscript formats to save the results as a vector graphics file that can be decomposed into various parts This is particularly desi
22. e 22 7 2 Plot results to vector graphics formats ccccccceceececeeee eee eeeeeneeeneeeeeeeneeeeneces 22 Appendix A RFPulse Desom 23 Peck What EINEN 23 A 1 1 Vespa RFPulse Basic Concepts eseeneeeeeeeeeeeeeeeeeeeeeereeeenerrennrnnnnnnnnnnnn ennnen 23 ASV PUISG IPIO OCIS 2 facreo EE 0 EAE SEENEN 23 Appendix B RFPulse Transtorms 26 B t r Loi eral ks EE 26 B 14 Ee Ee Ti EE 26 Bi EE ENEE CEET 26 B 1 3 Widgets and Parameters eu e7euEREER ESEREEEAENEOE SEENEN EEEEEEEAENSSEEEEEEENNEER REECH 26 B 1 4 Algorithm Applied at Run Time 27 B 2 SLR Tab create le Ce Ce EE 28 B 2 1 Tab Diagram E 28 B 22 SONG ER CET 28 B 2 3 Widgets and Parameters saisutitie eege deegegecddeEet ENEE inter ee EE 28 B 2 4 Algorithm Applied at Run Time 29 B 3 Hyperbolic Secant Tab create transformation sssseennnnnnnnrenenennnnrneenne 31 EN ER DIETS TE WEE 31 B52 General SAG Gare tet arna esac EE 31 B 3 3 Widgets and Parameters keete ccedectedecpeecepthastavantehededaadeteabeehitenes 31 B 3 4 Algorithm Applied at Run Time 32 DA Interpolate Rescale Tab general Iransiormaton eects 33 B 4 1 Tab H RUE TE EE 33 IR Ee CT 33 B 4 3 Widgets and Parameters E 33 B 4 4 Algorithm Applied at Run Time 33 Appendix C Third Party Export 35 Ga General Eppes EE ance dberaneedeccdecedberanceabertseedbeteneeesetane 35 C2 Siemens IDEA ee ee 36 C 2 1 Format Specific GUI Fields ccccccccccccecccccceeeece
23. e between cloning and copying tabs is that the clone is automatically saved into the database on creation while the copied tab is only created in memory until you specifically save it The View menu on the main menu bar can be used to modify the display of the plots in the active pulse project tab The resulting modifications only affect the settings in the active pulse project tab More specifically only the plot options in the selected transformation tab in the active pulse project tab are affected These options are preserved as you switch from transformation tab to transformation tab The following lists the functions on the View menu item 16 On the Menu Bar View this menu affects the plots in the currently active PulseProject Transformation tab Show ZeroLine Xaxis Show Data Type Output lt format gt 5 1 Loading an existing pulse project toggle zero line off on in waveform and profile plots turns off on vertical grid lines and values along the x axis select Real or Real Imaginary in waveform and frequency profile plots writes the plot panel to file as either PNG SVG EPS or PDF format The pulse project Browser dialog is launched from Pulse Project Open menu which is shown below A list of pulse project names is shown on the left When a pulse project listed in the browser is clicked on once its comment and other information are displayed on the right When the Open button is clicked or a pulse p
24. e fourth F2 represents the frequency offsets for an offset slice used with B2 and G2 In addition the constant gradient for a conventional selective pulse is labeled G1 The following chapters run through the operation of the Vespa RFPulse program both in general and screen by screen In this manual command line instructions will appear in a fixed width font on individual lines for example Vespa RFPulse 1s Specific file and directory names will appear in a fixed width font within the main text Online Resources The Vespa project and each of its applications have wikis with extensive information about how to use and develop new functionality for each application These can be accessed through the main portal at http scion duhs duke edu vespa Case Studies in RF Pulse Design Note The following case studies discussion was generously contributed by Dr Jerry Matson based on the functionality of his MatPulse program Not all features discussed below are implemented in the Vespa RFPulse application Although your MRI instrument has a slew of RF pulses installed and available for use in new experiments there are many reasons why you may want to consider designing new RF pulses The figure below shows a generic pulse profile to define terms used to describe a pulse profile Amplitude A w Transition Band T W2 W1 0 D D M Frequency radians The following sections list some of the reasons why yo
25. e of consistency as results are shared However a frozen pulse project can still be deleted from the database if needed This file can be imported into another Vespa RFPulse installation using the Import function If additional changes are desired a new pulse project cloned from the original frozen object can be created then modified 6 2 Manage Machine Settings Templates dialog Access this dialog by clicking on the Management Manage Machine Settings Templates menu item Actions that can be taken on the dialog include New Edit View Clone Set Default and Delete An example of this dialog is shown below The Is Default column indicates which template is used as the default settings for the machine settings object in a newly created pulse project object The Set Default button is used to designate the currently selected template as the default template Only one template can be set as the default at one time 20 Manage Machine Settings Templates x Name 1s Defaut Generic 3T New A dialog will pop up that gives you a blank form to fill out Fill in the settings in the widget fields and hit the OK or Cancel button See the sample in the figure below Edit Machine Settings Templatews 4 Unique Name s Machine Type whole Body MR e Field Strength Bo 00000 Tesla Max B1 Field 22 0 microTesla Zero Padding tc Min Dwell Time fio 00 microseconds Dwell Time Increment 2 000 microseconds Gradient Raster Tim
26. eeeeeceeeeeeeenaeceaeceaeseaeeeaeenaeeaas 36 C 2 2 Example Siemens IDEA Output File 2 cccccccccccccececceeeeceeeeeeeeeeeeaeeeaeeeaeeees 36 C 3 Siemens Vision e ru EE 37 C 3 1 Format Specific GUI Fields 37 C 3 2 Example Siemens Vision Output File 37 GA ASCII Magn Phase Format ssssssesrerrrrrrrrrrrrrtrrrrtrrtrrtrnrnnnnrrnrtrnnnn nennen 39 C 4 1 Format Specific GUI Fields irsinin inea iiia etie iea E E AE A eE 39 C 4 2 Example ASCII Magn Phase Output Elei 39 Overview of the Vespa Package The Vespa package enhances and extends three previously developed magnetic resonance spectroscopy MRS software tools by migrating them into an integrated open source open development platform Vespa stands for Versatile Simulation Pulses and Analysis The original tools that have been migrated into this package include e GAVA Gamma software for spectral simulation e MatPulse software for RF pulse design e IDL_Vespa a package for spectral data processing and analysis The new Vespa project addresses current software limitations including non standard data access closed source multiple language software that complicates algorithm extension and comparison lack of integration between programs for sharing prior information and incomplete or missing documentation and educational content Introduction to Vespa RFPulse Vespa RFPulse is a graphical control and visualization program written in the Python programmin
27. functions Note 6 1 Manage Pulse Project dialog Access this dialog by clicking on the Management Manage Pulse Projects menu item The dialog opens and blocks other activity until it is closed An example of this dialog is shown in the figure Pulse project names are listed in the window on the right You can View Delete Clone Import or Export pulse projects These functions are summarized below View Displays a textual summary of the EIERE x pulse project Clone Copies the currently selected pulse project s to a new pulse project with a genn Der different unique id and name The new Clone SLR Example x pulse project is automatically saved in the database This is typically used on pulse projects that have been designated as mec public in order to have a modifiable copy with which to work Delete Removes the selected pulse bet export ges project s from the database Import Allows you to select an XML file that contains a pulse project If the UUID in the file is unique it is added to the pulse project database Export You select a pulse project from the list A second dialog allows you to browse for the output filename select if output should be compressed and allows an additional export comment to be typed in Note that the action of exporting a pulse project or other objects caused it to be marked as frozen in the database This means that no changes can be made This is for the sak
28. g language that provides a user friendly front end for calculation of Shinnar LeRoux SLR frequency selective RF pulses and many other calculations and manipulations Although RFPulse is meant to be intuitive and is entirely menu driven a cursory reading of the information below is recommended A description of the original MatPulse program beta version 1 0 is provided in reference 1 below The RF pulses and gradient waveforms created by RFPulse follow the general procedures and nomenclature provided in references 2 and 3 Along with SLR based pulses analytical pulse shapes such as hyperbolic secant are also available as are additional transformation steps such as pulse interpolation and re scaling 1 Matson G B An integrated program for amplitude modulated RF pulse generation and re mapping with shaped gradients Magn Reson Imaging 12 1205 1225 1994 2 J Pauly P Le Roux D Nishimura and A Macovski Parameter Relations for the Shinnar Le Roux Selective Excitation Pulse Design Algorithm IEEE Trans Med Imaging 10 53 65 1991 3 S Conolly D Nishimura A Macovski and G Glover Variable Rate Selective Excitation J Magn Reson 78 440 458 1988 What can RFPulse do 1 Create new RF pulse projects from a list of design algorithms 2 Store pulse projects and their design parameters into a database 3 Re load previous pulse projects 4 Display pulse results for each step of the design process in a flexible plo
29. he i lal aa results of the RF pulse at that step as well as the parameters used to create that result The pulse project can be saved at any time but changes made in the GUI will not be copied into internal objects and thus saved until after the Run button is hit for a given transformation e Pulse Project Object Transformation List e Each pulse project contains exactly one create transformation This transformation is the first one selected by you and is positioned as the second transformation tab in the GUI after the standard Basic Info tab e Each pulse project can add any number of general transformations after the create transformation e Each pulse project has only one set of machine settings e Each pulse project has only one set of master parameters We expect users to share data via RFPulse s export and import functions For this reason the RFPulse pulse project object has a universally unique id UUID Machine settings used in a given pulse project are stored in that project when it is exported and are thus available when imported A 1 2 Pulse Projects Pulse projects are the main focus of the RFPulse application A Pulse Project s raison d etre is to help you design an RF pulse through a series of transformation steps These transformations first create and subsequently modify an RF pulse to achieve the desired results This set of transformations is the pulse project s transformation
30. ic secant pulse is thus designated HS1 while the reduced voltage pulses are designated HSn where n indicates the power to which t is raised RFPulse enables HSn pulses to be designed over a range of values of n Although larger values of n lower the peak voltage the selectivity of the pulse is degraded at higher values of n Case 5 Reduced SAR Due to the high peak voltage required both spin echo and hyperbolic secant pulses generate high SAR and lower SAR versions of these pulses may be desired For spin echo pulses the remapping method discussed in the previous section can be employed with parameters chosen to lower the SAR and lengthen the pulse duration of a spin echo pulse For a hyperbolic inversion pulse the pulse can be implemented as an HSn pulse discussed in the previous section to lower the SAR Case 6 More Exotic Pulses While RFPulse can already be used to create Multiband pulse designs future additions to RFPulse will include the following Multiband pulses in which two separate selection bands are included within a single pulse design For example in a spectroscopy editing experiment editing may be desired simultaneously in two separate regions or suppression in two regions e g water and lipid Increased bandwidth pulse designs useful in spectroscopy to suppress the two compartment artifact which causes signal loss for J coupled metabolites unless the experiment is conducted with very short
31. l 1991 Vespa RFPulse uses these DSP tools to turn user input parameters into the appropriate complex polynomials and apply the inverse SLR transformation to generate a corresponding RF pulse 30 B 3 Hyperbolic Secant Tab create transformation B 3 1 Tab Diagram Pulse Project1 gt X Total Rotation 1440 0 degrees Time Steps E increments Specify Dwell Time or Bandwidth SE Dwell Time ER microseconds Bandwidth kilohertz Cycles ka Powerini fi Sharpness mu 4 0 Filter Type Filter Application None selected e ba Plot Control T Freq Profile I Abs Freq Profile IT Ext Profile Ext Absolute Profile M Waveform Usage Type Jexcite X Basic Info Hyperbolic y B 3 2 General Usage This is a create transformation tab B 3 3 Widgets and Parameters Total Rotation float in degrees Time Steps integer number of steps in the RF pulse Dwell Time or Bandwidth float microseconds or kHz respectively Either the bandwidth or the dwell time must be provided when one parameter is given the other is automatically calculated However the width or dwell time calculations are only approximate Cycles float number of cycles before truncating pulse Power n integer power of hyperbolic secant function Sharpness mu float parameter that defines the sharpness of the function Filter Type droplist apodization filter type Hamming
32. listing the name of the currently selected machine settings Edit button opens an editable dialog that displays the current machine settings for modification 26 Calculation Resolution integer the number of points used in the Bloch equation calculations to create pulse profiles More points result in a more finely sampled bandwidth but at the expense of longer calculation times Bandwidth Type droplist B 1 4 Algorithm Applied at Run Time There is no Run button on this tab To proceed to the next step you select a create transformation from the Transformation Create menu 27 B 2 SLR Tab create transformation B 2 1 Tab Diagram Pulse Project 1 gt X Pulse Params Tip Angle foo degrees Time Steps 250 increments Duration ku milliseconds Bandwidth honn Hz Separation fiooo 0 Az Single or Dual Band Single Band Dual Band Non Coalesced Phase Type Linear ind Filter SLR Remez Least Squares Passband Ripple fi o Percent Reject Ripple fi o Percent Plot Control TI FreqProfile I Abs Profile TI Ext Profile Ext Absolute Profile M Waveform Usage Type Excite X Basic Info SLR x B 2 2 General Usage This is a create transformation tab The SLR tab provides for creation of computer optimized SLR shaped amplitude modulated RF pulses typically denoted as B1 B 2 3 Widgets and Parameters Tip Angle float effective tip angle
33. long the z axis Spin Echo The Mx real part and My imaginary part if turned on magnetization is plotted in all profile plots with the assumption of initial magnetization along the y axis The mouse can be used to zoom in on the X and Y dimensions in all plots and to set vertical reference spans along the x axis The left mouse button draws a box which designates the region into which to zoom the plot Click and drag the left mouse button in the window and a yellow box will appear Drag the mouse to size the zoom box appropriately release the left button and the plot will zoom into that region XRange YRange plot value and AX and AY values will be shown in the status bar while dragging Click and release the left mouse button in place and the plot will zoom out to its max setting In a similar fashion two vertical cursors can be set inside each plot window Click and drag the right mouse button then release to set the two cursors anywhere in the window This Cursor Span will display as a light gray span Click and release the right mouse button in place and the cursor span will be turned off 19 6 Management Dialogs The Management dialogs allow you to create delete edit import export or view pulse projects and machine settings templates These dialogs thus allow you to manage the data in the RFPulse database It also provides the means for users to share information between themselves via XML files created using the Import Export
34. n the tab or with a middle click on the tab itself When a pulse project Tab is closed the pulse project is removed from memory but can be reloaded from the database at a future time assuming it was previously saved im RFPulse Basic SLR 8ms Pulse Project Add Transformations Management View Help 15 x Pulse Project 1 gt lt Pulse Project 3 Pulse Params Tip Angle 90 0 degrees Time Steps 64 increments Frequency Profile Bandwidth kilohertz Separation 41 0 dia Single or Dual Band 6 Single Band Dual Band Mx My normal 2 1 0 1 frequency kHz Absolute Preudehey Profile flinear L Filter SLR Remez Least Squares Passband Ripple 1 0 Percent Reject Ripple 1 0 Percent ER Phase Type Mx My normal H A i 2 1 D 1 RE BORE Weber Run Plot Control Freq Profile T Ext Profile IV Abs Freq Profile I Ext Absolute Profile M Waveform Usage Type jExcite 3 4 time ms Basic Info SIR x Y 0 00684 Value 0 00027 15 5 The Pulse Project Tab A pulse project tab is one page in the pulse project window Each tab contains one entire pulse project design A pulse project tab can be used to run a new pulse project and view the results of that design It can also be used to load an existing pulse project from the database to view results or to change parameters or other modifications to the pulse project
35. n the selection in the Format pull down list All formats save ONLY the waveform result from the last transformation tab in the project Specify the file to which you wish to export results by clicking the Browse button This selection is used slightly differently in each format The Output Location typically defaults to the last location where something was saved The differences in default file names will be discussed specifically for each format in the sections below Parameters specific to the format are listed in the next sections if any and are also described more fully below 35 C 2 Siemens IDEA Format The Siemens Pulsetool utility can import RF pulse or gradient waveforms that are saved in the ASCII file format described in the Siemens IDEA manual Typically only one RF pulse or gradient waveform is stored in each file At the moment only RF pulses are exportable from the RFPulse application The first figure in this section shows the Third Party Export dialog configured for the Siemens IDEA format output C 2 1 Format Specific GUI Fields Siemens IDEA format ASCII files have some user set and automatically calculated parameter header lines at the top of the file These lines are followed by magnitude phase value pairs one pair per line for each time step in the RF waveform We refer you to the Siemens IDEA manual for more specific details for each automatically calculated header parameter User set header parameters that are
36. nder as to what is in each file Third Party Export x M Output Format and Location Output Location Browse C bsoher Simple_64pt_SLR txt ASCII Real Imaginary Format Note This is a very simple format that outputs the final result of a project as ASCII pairs of magnitude phase value pairs one per line For each time point in the waveform There is no header information included You may want to include pulse parameter reminders in the File name OK Cancel C 4 1 Format Specific GUI Fields There are no format specific fields for this format C 4 2 Example ASCII Magn Phase Output File Here is a short example of the data output to an ASCII Magn phase format output file Values are separated by a space ee EE E E E E E E E E E E EH EH EE E bai bai ba beae e ee eh EE EH EH EH ent bs CO tabA FA tant tae FA FA F Ar amp Ae FAL tal zl zl Es FACE Es CDe LE EEN GA 4 E LA eu dE EH La Ee e e En Es EEN GA POYE CtatAueaen A FA Es Gitt Wr nde Es ll LI GA OO E zl OO FA Ennen e LE ELL EP LA vi Ee d ED ED FA E GA LE LE DEE EE HE Ae Es CO ll Lal F LaAl batae Ou e A Es HOA W w o oD oOo oOo oOo oOo oOo oOo oOo Oo Ww w w www kaktae e e e e eene EE bah bake toatoateh JE E ee ee e eene ee E E E E E E ka ktae e e e e eene EE bah bake toatoateh an aA o o o o oOo eeh ee LL LD LD GL LE LE E E E E E EE E E E E L I L I L I LE LE LE RWNVDODODDOOOCOMYNYNYNNNY en Ce e EE E DODD E E
37. nsformation the tab s name will contain an asterisk next to it Hitting Run will clear this 25 Appendix B RFPulse Transforms This section provides some basic information about the transformations both create and general types available in the RFPulse application A description of the user interface and the parameters that can be set for each transformation is given A brief overview of the algorithm applied when the Run button is hit is also presented B 1 Basic Info Tab B 1 1 Tab Diagram Pulse Project 1 gt X Name ER 3kh 256steps max phase pulse UUID 1de12263 7100 45a2 8a7f 1356eFF923d6 Creator ke Created 14 April 2011 Project Comments some comment and more general trivia gt Machine Settings Whole Body MRI 3 07 Edit Master Parameters Calculation Resolution 5000 steps Bandwidth Type FW at Half Height X Basic Info SLR B 1 2 General Usage This is a special transformation tab neither create nor general type which you must always fill in so that RFPulse can correctly identify the pulse project to from the database The name field MUST be filled in before the pulse project can be saved to the database B 1 3 Widgets and Parameters Name text must be a unique text string within the group of pulse project names in the database Investigator text optional UUID and Created not editable just given FYI Machine Settings label
38. ormations are listed below the Create submenu General transformations operate on the results of the previous transformation e the transformation in the tab to the left Notes 1 Another typical workflow might be to load a saved pulse project from the database add edit or delete general transformations and then save the changed results back to the database 2 A third typical workflow might be to load a saved pulse project from the database and copy that into a new pulse project by using the PulseProject Copy Tab to New Tab menu item Then modify the RF pulse in the copied tab and compare the results plots to the original pulse project results 3 Changes can be made to parameter settings in any transformation tab in a pulse project When you click the Run button RFPulse calculates the effects of these changes in all 12 transformation tabs downstream from the transformation tab changed Note as of this writing there is no undo functionality in the transformation tabs in the application Although for existing pulse projects that have been loaded into a tab changes to that project are not saved to the database until you select the PulseProject Save menu manually 13 3 The RFPulse Main Window This is a view of the main Vespa RFPulse user interface window It is the first window that appears when you run the program It contains a tabbed window into which pulse projects can be loaded a menu bar and status
39. oughout the program It also reports short messages that reflect current processing while events are running On the Menu Bar Pulsebrolect New Opens a new pulse project tab PulseProject Copy Tab to New This will open a new pulse project tab and populate it with the same values that are listed in the current pulse project This is a short cut for varying design parameters to get different results while retaining the ability to compare back to a previous results set without having to save them both to the data base PulseProject Open Runs the pulse project Browser dialog from which you can choose a pulse project to open from the database to open PulseProject Save Saves the pulse project in the current tab to the database Note pulse project results are not automatically saved to data base after a Run button is hit PulseProject Third Party Export Opens a dialog that will export the final result of the active pulse project into a file suitable for import to various MR manufacturers platforms PulseProject Exit Closes current pulse project tab Will prompt for save if necessary Add Transforms Create SLR Appends an SLR create transformation tab to current pulse project 14 Add Transforms Create Hyperbolic Secant Add Transforms lInterpolate and Rescale Management Manage Pulse Projects Management Manage Machine Settings Templates View lt various gt Help User Manual Help RF
40. p an imaginary pulse project Each transformation contains the parameters used in its algorithm a set of results from running its algorithm and a reference to the results in the previous transformation step used as an input Transformation List Transformation 2 Transformation 3 Results Results Previous Results Previous Results Transformations can be added or removed from the pulse project typically by closing the associated tab in the GUI with a few caveats New transformation steps can only be added to the end of the current project Any general transformation can be closed removed however this triggers an automatic recalculation of the steps downstream of that transformation The create transformation can not be removed unless all general transformations have been previously closed removed This is due to the fact that the general transforms would have no results on which to act without an initial create transformation The take home lesson from this section is that the Vespa RFPulse application provides a modular design platform for optimizing RF pulses Various steps in RF pulse creation and modification can be included in a given design or not In the appendix that follows we will specify what each transformation step included does are and how they are typically used Other useful information 24 e Anytime a tab s GUI is out of sync with the parameter values used for the last Run of the tra
41. p angle at the center of the profile may be different from the tip angle used for the design of the pulse This however does not invalidate the initial design which provides for the correct average tip angle over the profile for which the pulse was created 34 Appendix C Third Party Export This section describes the Third Party Export dialog launched by selecting the PulseProject ThirdPartyExport menu item This dialog converts RFPulse waveform results into various third party formats and exports the converted results to a file At the moment RFPulse supports three formats 1 Siemens IDEA single RF pulse ASCII format 2 Siemens Vision single RF pulse ASCII format 3 Generic ASCII magnitude phase representation The same dialog is used to output all formats an example is shown below Third Party Export x M Output Format and Location Format eut dd Output Location Browse c tbsoher simple_ 4pt_H5 pta Siemens IDEA Pulse Description Name Simple_64pt_H5 Comment Exported from Yespa RFPulse project name a Simple 64pt HS UUID 14c8fd9c 36ec 4be1 9336 d6811cb581b0 and pulse duration 2 048 ms e m Siemens IDEA Pulse Characteristics Min Slice Thickness mm 1 0 Max Slice Thickness mm Ja OK Cancel C 1 General Functionality The third party export dialog acts on the pulse project that is active when the dialog is launched The GUI reformats itself depending o
42. pectral resolution than for the non extended profile This allows you to view out of band excitation Ext Absolute Profile checkbox Selects the RF extended absolute frequency profile to be plotted This is the magnitude plot of the extended frequency profile plot described above Waveform checkbox Selects the time domain RF pulse waveform to be plotted The Usage Type drop list widget requires a more careful explanation For any given RF pulse running the complex time waveform through the Bloch equations results in a description of the magnetization along the Z axis as well as in the X Y plane Depending on what the pulse will be used for you may want to check the pulse performance of either the Mz or Mxy and sometime both directions Changing the Usage Type widget allows you to specify what is plotted along the vertical axis a k a the y axis in each plot in the figure Usage Type effects on Y axis Choice Excite The M real part and My imaginary part if turned on magnetization is plotted in all profile plots with the assumption of initial magnetization along the z axis Inversion The Mz magnetization is plotted in the real part and zeros in the imaginary part if turned on in all profile plots with the assumption of initial magnetization along the z axis Saturation The Mz magnetization is plotted in the real part and zeros in the imaginary part if turned on in all profile plots with the assumption of initial magnetization a
43. rable when creating graphics in PowerPoint or other drawing programs At the time of writing this only the EPS files were readable into PowerPoint The Vespa RFPulse View menu lists commands that only apply to the active transformation tab in the active pulse project tab Select the View Output option and further select either the Plot to SVG or Plot to EPS menu item You will be prompted to pick an output filename to which will be appended the appropriate suffix 22 Appendix A RFPulse Design A 1 What is under the hood A 1 1 Vespa RFPulse Basic Concepts This is a combination of logical concepts and constraints that determine how RFPulse works These rules are enforced through the application and to some extent the database The main objects in the system are pulse projects transformations machine settings and master parameters There are two types of transformations create and general which will be described in more detail later Pulse projects are the primary objects everything else is secondary Here s how they re related e Each pulse project has one or more transformations Transformations are the building blocks of a pulse project design The pulse project object contains a list of all transformation objects that are part of the RF pulse design The pulse project also contains the machine Machine Settings Object settings and master parameter settings used e Each transformation step of the design contains t
44. required include Name text This value defaults to the pulse project name but can not contain spaces or periods so these are replaced by underscores automatically This value is also used as the default filename for the output location Comment text The default comment contains the pulse project name UUID and pulse duration as reminders to you once it is imported into IDEA This also allows the Name header variable and or filename to be changed without losing provenance regarding the pulse project origin of this result This comment is contained on only one line in the output file so don t hit return in entering your comment Min Slice Thickness float mm See the Siemens IDEA manual for additional description of this parameter Vespa RFPulse defaults this value to 1 0 Max Slice Thickness float mm See the Siemens IDEA manual for additional description of this parameter Vespa RFPulse defaults this value to 40 0 C 2 2 Example Siemens IDEA Output File Here is a short example of the data output to a Siemens IDEA format output file Note that the COMMENT parameter is typically all on a single line but formatted here for easier reading PULSENAME Simple 64pt_SLR COMMENT Exported from Vespa RFPulse project name Simple 64pt SLR UUID alcec249 446c 4le2 a2fd 578a3894ad7d and pulse duration 8 0 ms REFGRAD 0 000003670 MI NSLI CE 1 000000000 MAXSLI CE 40 000000000 AMPI NT 8 436948615 POWERI NT 7
45. rojects name is double clicked on the program loads the information for that pulse project from the database into a pulse project object in memory Pulse Project Browser l Pulse Projects Hyperbolic Secant Example SLR Example x Name Hyperbolic Secant Example Creator Philip Comment This is an example of a 64 point Hyperbolic Secant pulse with an additional transformation that rescales the pulse This object then creates a pulse project tab and sets up the transformation tabs that describes its creation You might notice a delay when opening larger pulse projects 5 2 When you select the Pulse Project New menu option a new pulse project tab is created in the pulse project window and the Basic Info transformation tab loaded This tab requires you to type in a project name before the project can be saved A project investigator and or a comment can optionally be added Is public True Created 20 April 2011 16 41 07 et Running a new pulse project A list of available transformations is on the Add Transformations menu Create transformations are found under the Add Transformations Create sub menu All the other transformations directly under the Add Transformations menu are general transformations A detailed description of each transformation and its general usage can be found in Appendix B As noted previously a pulse project object consists of one or more transformation objects
46. s Duration ka milliseconds Bandwidth fio kilohertz Seperation p10 ighierte Mx My normal Absolute Frequency Profile m Single or Dual Band Ze Single Band Dual Band M Non Coalesced Phase Type Linear Filter SLR Remez Least S5Squares Extended Absolute Profile Passband Ripple ba Percent Reject Ripple fi Percent E CN Mx My normal E CN Mx My normal Run RF Pulse Waveform M Plot Control IV FreqProfie IV Abs Freq Profile T Ext Profile IV Waveform Usage Type Excite e BasicInfo SLR x EEN KENE Value 0 00001 On the Plot Control Panel Freq Profile checkbox Selects RF pulse frequency profile to be plotted This result comes from running the RF waveform through the Bloch equations to calculate the complex RF profile at 1 times the Nyquist frequency and at the calculation resolution set in the Basic Info tab Abs Freq Profile checkbox Selects RF pulse absolute frequency profile to be plotted The magnitude plot of the frequency profile plot described above Ext Profile checkbox Selects the RF extended frequency profile to be plotted This result comes from running the RF waveform through the Bloch equations to calculate the complex RF 18 profile at 4 times the Nyquist frequency and at the calculation resolution set in the Basic Info tab This allows you to check a wider bandwidth range albeit at a coarser s
47. the SU 2 representation offers considerable mathematical simplification and as a result is used in the SLR algorithm The second important conceptual component of the SLR algorithm is the hard pulse approximation Pauly et al 1991 which is useful in particular in the case of non adiabatic pulses The hard pulse approximation states that any shaped or soft pulse B t can be approximated by a series of short hard pulses followed by periods of free precession The larger the number of hard pulses used combined with the resultant decrease in the duration of the free precision periods the more accurate the approximation 29 By describing rotations in the SU 2 representation and using the hard pulse approximation the effect of soft pulses on the magnetization vector can be mathematically described by two polynomials with complex coefficients The mathematical process that converts an RF pulse into the two polynomials is called the forward SLR transform It is important that the inverse SLR transform also can be calculated The inverse transform yields the RF pulse given the two complex polynomials corresponding to the desired magnetization In digital signal processing DSP these polynomials are filters for which there are well established and powerful design tools available In the SLR algorithm the inverse SLR transform is used in conjunction with finite impulse response FIR filter design tools to design RF pulses directly Pauly et a
48. the total tip rotation of the pulse by rescaling the amplitude of the pulse Net angle is calculated as integral of the waveform gamma Total rotation is calculated as integral of the absolute value of the waveform gamma The choice of net tip angle or total tip rotation is determined by this rule e H the sum of the absolute values of the imaginary components of the waveform B1 is greater than 0 01 then it uses the total rotation otherwise it uses net angle For analytic pulse types e g the Hyperbolic Secant rescaling can be used to change the amplitude of the pulse for various magnetic fields by changing the total rotation significant amounts if needed Amplitude modulated pulses e g SLR pulses can only be adjusted by a few percent before they start to degrade in performance In this case rescaling can be used to see how much it degrades so one can see how it performs under various intensities that may be caused by susceptibility issues limitations in the field coils etc Note For amplitude modulated pulses such as an SLR pulse the tip angle specified on the interpolation and rescaling transformation widget the on resonance tip is the tip angle at the center of the profile However due to ripples in the passband the tip angle at the profile center is usually at an extremity either maximum or minimum of the allowed tip angle as specified by the ripple amplitude set by the user when the pulse was designed Thus the ti
49. tomatically calculated header parameter User set header parameters that are required include Name text This value defaults to the pulse project name but can not contain spaces or periods so these are replaced by underscores automatically This value is also used as the default filename for the output location Comment text The default comment contains the pulse project name uuid and pulse duration as reminders to you once it is imported into IDEA This also allows the Name header variable and or filename to be changed without losing provenance regarding the pulse project origin of this result This comment is contained on only one line in the output file so don t hit return in entering your comment Family Name text This value is used to group related pulses in the Siemens Vision pulse libraries It may not contain spaces or periods Min Slice Thickness float mm See Siemens Vision documentation for additional description of this parameter Vespa RFPulse defaults this value to 1 0 Max Slice Thickness float mm See Siemens Vision documentation for additional description of this parameter Vespa RFPulse defaults this value to 40 0 C 3 2 Example Siemens Vision Output File Here is a short example of the data output to a Siemens Vision format output file Note that the Entry_Description parameter is typically all on a single line but formatted here for easier 37 reading Also the waveform results are entered seq
50. tting tool 5 Compare side by side results from one or more pulse projects 6 Output results in text or graphical format including MR manufacturer platform formats 7 Export Import Vespa pulse projects to from other users 8 Bean open source test bed for your own algorithms and transformations What is an RF pulse project A pulse project consists of one or more design steps Each pulse project has a single creation step You can further refine the pulse by adding additional general transformation steps Each step of the design process creation plus other transformations contains time and frequency domain results for the RF pulse up to that point These results can be visualized in plots to the GUI at any time Changes to any given step in the design process trigger a downstream calculation of all subsequent transformations You can open multiple pulse projects and compare them side by side Any pulse project tab can be copied into a new pulse project tab This allows you to make minor changes to a copy of an RF pulse in order to see the effects on the final results RFPulse can create and expects to work with four separate vectors which you will see mentioned and explained in more detail in later sections The first B1 represents an amplitude modulated RF pulse The second B2 represents a re mapped pulse reshaped for use with shaped gradients The third G2 represents the shaped gradient waveform for use with B2 Th
51. u may want to consider creating your own RF pulse designs Case 1 Improved Selectivity Many MRI pulses are designed with short TE sequences in mind and the pulses are designed with a reduced length at the expense of increased transition bands which creates some loss in selectivity and sensitivity to accommodate short TEs Somewhat longer pulses that provide for shorter transition bands may provide improved S N for signals with longer T2s In addition pulse profiles with minimal transition bands are helpful for slice selection without slice gaps RFPulse provides menus for designing longer RF pulses to reduce the transition bands Case 2 Reduced Contamination Especially for spectroscopy contamination from signal from outside the excitation bandwidth can be a problem e g leading to lipid or water signals from outside the voxel interfering with spectroscopic signals from within the voxel Selective pulses designed for improved out of band stopband suppression can reduce this problem The SLR pulse design tab in RFPulse allows users to select the amount of stopband reject band suppression and facilitates exploring the tradeoffs involved between increased stopband suppression increased transition band and increased pulse length Case 3 Observation of Spectroscopic Signals Close to Water Most MRI instruments use Gaussian pulses for water suppression However Gaussian shaped pulses generate large transition zones leading to
52. uentially one value per line all magnitude values first followed by the phase values Begin_Entry VESPA_RFPulse_ Generated Pulse En T ry_Type 6 Pulse Name Simple _64pt_SLR Entry Description Exported from Vespa RFPulse project name Simple 64pt SLR UUI D alcec249 446c 41e2 a2fd 578a3894ad7d and pulse duration 8 0 ms Num Points 64 Family _ Name vespa Slice Thick Min 1 000000000 Slice Thick Man 40 000000000 Reference Grad 0 000003670 Power Integral 7 329981263 Amp Tntegral 8 436948615 Envelope Mode 1 Entry Values 0 043329947 0 026630458 0 029410526 0 027636394 0 020032857 0 006048280 0 014027609 0 038877678 0 066164780 0 092508011 0 114093901 0 127025923 0 127717372 0 113967653 0 085044517 0 042370597 0 010457088 0 067715754 3 141592654 3 141592654 3 141592654 3 141592654 3 141592654 3 141592654 0 000000000 0 000000000 0 000000000 0 000000000 0 000000000 0 000000000 0 000000000 0 000000000 0 000000000 0 000000000 3 141592654 3 141592654 38 C 4 ASCII Magn Phase Format This is a very simple ASCII output format that basically writes the waveform to a text file as a pair of magnitude and phase terms expressed as floating point numbers One time point is written per line The magnitude term has been normalized to 1 0 and phase is expressed in radians There is no header information in this file format so you are encouraged to name each file descriptively as a remi
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