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XtremeCT User Guide

1. Overview Window In this field a certain number of slices are displayed normally 16 Clicking with MB1 on an image in this field it will become the current image and is displayed large in field 4 Orthogonal Selection Overview Window Selection of orthogonal views in 2D or 3D or Scout View Brightness Scaling Changing the brightness scaling causes all images to be reloaded While being reloaded all images are displayed at a fixed brightness scale so you can compare brightness values visually Clicking the arrow pointing up makes the images brighter whereas the arrow down makes the images darker To return to the original display all images at the most possible brightness click on the button again Color lookup table Click with MB in this field to change the color lookup table for the display of the images By repeated mouse clicks with MBl you will return to the original black amp white display Pointer Histogram Profile Ruler Angle Tools and Tasks Click on a button for a tool and move the mouse pointer into the Main Window 4 Read the results in the Information Area 12 or in the Evaluation Information Win dow 13 See Pointer Ruler Profile Angle Tools on page 56 See Evalu ation 3D on page 50 for the T button 10 Slice Selection Slider LOAD to preload all images for a fast access to those 11 Image Selection Area Moving the cursor in this field and clicking with MB causes the indic
2. Figure 15 2D Evaluation vivaCT 80 1 3 Evaluation 48 vivaCT 80 1 3 The following window appears at the lower right Figure 16 2D Histomorphometry ROI Selection If you have drawn any contours before a white bounding box appears around all your objects If you have not drawn any contours a default sized box ap pears in the middle of the image The bounding box delimits the selected area for the evaluation You can move the ROI defined by the bounding box around by clicking and dragging on one of the selection points using MB or you can resize it by clicking on one of the selection points using MB2 The evaluation will only be performed inside the area of the white box If a contour is drawn the common region between the white box and the region delimited by the contour will be analyzed You can also set or adjust the position or size of the ROI by directly entering the coordinates and dimensions using the keyboard Additionally you can select the number of slices which will be analyzed With the scaler SLICES you decide how many of them will be processed With the START Z and DIM Z you select the range of the evaluation 2D evaluation will start with slice START Z and continue to slice START Z DIM Z while processing SLICES in total equally distributed Note If you set SLICES to 1 only the first slice will be processed no matter how large your DIM Z is set Segmentation Using the scalers SICMA SUPPORT
3. adaptive_threshold Using this command you can find out which threshold leads to the best seg mentation of the bone The program examines the BV TV parameter at differ ent threshold values given by first_threshold last_threshold and nr_steps It then tries to find the threshold with the least change which it DECterm Based Programs 80 vivaCT 80 1 3 considers to be the best choice At the end this value is applied to the input and written to the output object using the value in range as in threshold ipl adaptive thresh input gauss gt a output th_adp gt c first_threshold 400 gt 300 nr_steps 30 50 value in range 127 fft laplace hamming Segmentation of an object based on zero crossing of second derivative The second derivative is calculated in the fourier domain by applying a W2 filter for noise smoothing a Hamming filter is simultaneously applied To ensure that regions with high attenuation are segmented as foreground the original image is added with variable weight 1 laplace_epsilon The result is an ob ject of type float that has to be normed to short again with norm max Redim pow2 can be used to simultaneously interpolate the object to a new vox el size by fourier interpolation in powers of 2 redim pow2 2 4 times inter polation Laplace epsilon controls the weight of the curvature image the higher the epsilon the more edge enhanced the image appears Lp cut of
4. Figure 13 Color Coding in Image Selection Area erla Sequence Overview Click on 1st slide which should be included in VOI Draw object hand drawn or geometric shape Click on last slice which should be included in VOI Draw new object in this slice Open the Contouring menu as shown above C Click on RANGE selects your VOI inside of your selected slices Click on MORPH extends the shapes inside of your selected slices Click on CANCEL closes the Contouring dialog box Start either 2D or 3D Evaluation as in previous versions 1O 00r N QU pe Xo E Tip Move forwards in your slices while you are morphing and the Range BP System automatically selects the correct range Evaluation 47 The drawing below is an example of how to create a complex 3D shape if you want to create the following VOI you have to define 3 reference slices Reference Slice BP Slice 12 Incorporated Slice Interpolated Slice Reference Slice BP Slice 33 Interpolated Slice Interpolated Slice Reference Slice BP Slice 55 Figure 14 Creating a VOI Evaluation 2D The 2D evaluation is performed on one slice after the other The intension is to obtain results comparable with histology However microCT is a true To start the 2D evaluation click on menu TASKS and choose EVALUATION 2D File Edit Zoom Tasks LUT Options Scripts Print Images Distance 3D ES Contouring Evaluation 2D Alt 2 RV Evaluation 3D Alt 3
5. cooococcnccnccnccncnncnncnncnnos 25 Figure 29 Scout View Start End Position eese eee 26 Figure 30 Example relative offset mm from reference line to start of scan 28 Figure 31 Example relative offset 9o from reference line to start of scan 29 Figure 32 Example relative offset 96 from reference line to center of scan 30 Figure 33 Example relative offset 96 from reference line to end of scan 31 Figure 34 Start Measurement ANNER 32 Figure 35 Start Measurement versos ee a eiie eerie Ee E EE 33 Figure 36 Adding Tasks via iii eee e EE 34 teure 37 Task Lisbon oth A e ARR IRE REA AERE ENSE AS 34 bigare 38 Image Phantom oce en ne evan e a YR e Y EY eR 35 Figure 39 Start Evaluation Program enrenar teaa eaa E e ATN eee me me se he sene 36 Figure 40 Overview Evaluation Program eseseeeee HH e e ee eere 37 Figure 41 Evaluation Selection of Patient and Measurement eese 39 Figure 42 Select Old Measurement esses eme he he he mense he nennen 39 bueren ii EE AR SO ERA 40 Figure 44 Print Men eee teer geleed ees teg ddr eee duo 41 Figure 45 Brightness Scaling eR e eR Reha ect ads sarees BEN NENNEN ENNEN 42 Figure 46 Options Brightness Scaling oocooccoccocnncnncnncnncnncnncnncnncnnconcnnnancnncnncnnrancancnnes 42 vivaCT 80 1 3 116 Figure 47 Figure 48 Figure 49 Figure 50 Figure 51 Figur
6. 10 x 21 see Advanced Mode 22 see Advanced Mode 23 see Advanced Mode 24 see Advanced Mode 25 see Advanced Mode Measurements 23 vivaCT 80 1 3 26 The total number of slices and the resulting measurement time for the actual setting of the measurements parameters are indicated This num ber can later change when adjusting the reference lines in the ScoutView See Reference Line on page 27 27 After setting up your measurement protocol you have to test the consis tency of the protocol before you can use or save it by clicking on TEST If this is successful and your initial controlfile was not locked the buttons OK SAVE AS NEW and SAVE become available and you now can use the modified protocol for the next measurement only by clicking on OK or save it first clicking on SAVE and the clicking on OK to return to the main screen If your initial controlfile was locked the SAVE button will not get sensitive SAVE AS NEW can be used to store a modified protocol under a different name and number Modifying a Controlfile Advanced Mode Viva80 Test Figure 10 Modifying a Controlfile Advanced Mode Explanation 13 Number of Det Lines for Scout View Define how many lines of the detec tor shall be used during the Scout View Using all available lines provides faster Scout Views but some faint horizontal lines may be seen between the Stacks A stack is the set of slices that is produced during one rotation of
7. program or launch a second evaluation The batch job will run in the back ground Type QUE in a terminal session window to see if it is still running Most Evaluation scripts will use the contour saved under the default GOBJ filename i e ion Fauno C0001234 GOBJ for evaluation even if you saved your contours under a different name The evaluation will only be performed inside of both a your objects contours green red Caution b the bounding box white The bounding box in its default size contains all your objects and thus does not further limit the ROI VOI Morphometric Results Every completed 3D evaluation which produces morphometric results will au tomatically send the result sheet to a printer or create a PDF output file The output will also be written into a tabulated text file both in the measurement directory as well as in the results directory where it will be appended to pre vious results generated with the same script In the measurement directory only the results for the current dataset is written In the result directory all results generated with the same evaluation script are collected in one file The chosen project name see below is a part of those txt filenames so diffe rent projects are going into different 3D result log files You can transfer the txt file to your personal computer and open with a spreadsheet program such as Excel If you consider running multiple evaluations of the same
8. End the program and start again from new Possibly check with the archiving program whether the stor age device is still mounted Normally both optical disks and diskettes are dis mounted freeing context of libSfind file General database error get device information The specifications of a storage device could not be determined getting free luno General database error initializing device label Diskette or optical disk could not be initialized Check whether the Write Pro tect switch is correctly set Diskettes must be of the HIGH DENSITY HD format DD or ED diskettes are not allowed mounting device label Diskette or optical disk could not be mounted Check with the archiving pro gram see dismount PC formatted diskettes are not readable on your computer without format ting opening file General database error reading Scanner data General database error starting init command Initialization formatting error writing scanner data General database error vivaCT 80 1 3 Error Messages 96 vivaCT 80 1 3 Operational conditions Ambient conditions Temperature variations Caution 13 Specifications 5 to 40 C Humidity 80 for temperatures up to 31 C decreasing linearly to 5096 relative humidity at 40 C Max 8096 relative humidity non condensing 20 to 25 C 2096 8096 humidity for recom mended operation maximum 3 C h Measurements outside these temperature rang
9. last rank Kl connect boundary false value in range 127 cl extract Same as c1 rank extract but extracting according to fractional volume of components Not available with connect boundary flag ipl cl extract input seg gt output cl gt lo vol fract in perc EN ES up vol fract in perc EENS value_in_range EZ mx cl nr extract Same as c1 rank extract but extracting according to number of voxels of components Not available with connect boundary flag ipl cl nr extract input seg output Feil gt min number 10 gt max number 0 gt value in range 127 DECterm Based Programs 83 vivaCT 80 1 3 cl image Gives the component labeled image as output with value 127 for biggest con nected part 126 for second biggest etc ipl cl image input seg gt output cl gt db scanco activate Activates or deactivates the database for writing all subsequent evaluation results into it It stays activated until do scanco activate false is entered ipl db scanco activate write true iri da metric db This command triangulates a segmented object and calculates object volume and surface as well as the structure model index SMI Using the plate mod el trabecular number thickness and separation are derived Tri da metric db uses the contours of a GOBJ or AIM mask if it finds the GOBJ filename in the proceedings log Otherwise the whole box region i
10. 0 44 805 98 01 URL Wwww scanco ch e mail general info scanco ch e mail support support scanco ch e mail sales sales scanco ch 114 vivaCT 80 1 3 Appendix H Glossary Archive Move measurement data from internal hard disk to tape or external hard disks It is recommended to do this regularly to prevent the disks from getting full Always archive the RSQ and ISQ on different tapes Artifact Error in the exposure caused by for example a sample holder being too large movement of the sample during the measurement malfunction of the equipment etc Visible in the form of lines light or dark areas or stripes in the image Backup Safety copy of the databases and programs from internal hard disk to tape or local disk It is recommended that a backup is made once a week CT Abbreviation for Computed Tomography File Collection of related data in a computer for example letters a tomogram etc Harddisk Fixed internal storage device of high capacity Here are stored all the pro grams all patient data all Scout Views and all images which have not been archived Cannot be exchanged by the user LUT Look Up Table Color scale normally adjusted to the gray tone scale Optical Disk Removable storage device with large capacity The images are archived on this device A separate optical disk is kept as a safety copy of the complete system see Backup ROI Region Of Interest Scanner Measuring unit in thi
11. 3X If you select the FORWARDS or BACKWARDS range the program automatically moves to the next or previous slice after it has finished the contouring on the current slice Range Selection The following actions are performed on a RANGE You select the range by clicking on one of the options e Current image in main window only e Range start and end of range are defined by BreakPoints BPs Reference slices green objects e Forwards range starts at current slice and extends forwards e Backwards range starts at current slice and extends backwards e All entire volume The slice numbers which will be affected are indicated below the range op tions e g 17 34 See Figure 50 Contouring Subwindow on page 45 Breakpoint BP If you choose RANGE in range selection the range is defined by breakpoints Any slice containing a hand drawn contour becomes a reference slice or BP Slice 1 and the last slice of your volume are also considered as BPs You can have as many BPs as you like The whole volume is then divided into multiple ranges each extending from one BP to the next BP You choose the range by clicking at any slice in your range You can modify any slice to be a reference slice by clicking on the SET BP but ton you can remove a reference slice from the BP list by clicking on CLEAR BP and you can reset all BP by clicking on CLEAR ALL BP The range extends from the previous BP not in Note cluded in the range t
12. If it is scanning the first half it will continue immediately with the second half if you click while scanning the second half it will stop You may have to click twice to interrupt the Scout View completely Measurements 26 vivaCT 80 1 3 Reference Line Click on the REFERENCE LINE button and then move the pointer to the current Scout View at the upper right The green reference line now follows the point er As soon as the left mouse button is pressed the line is fixed You can cor rect the positioning of the line as often as you wish by again clicking on the REFERENCE LINE button As you move the reference line you also can adjust the number of slices by pressing and holding the SHIFT key Moving the pointer then adjusts the end of the scan scan length scan area By releasing the SHIFT key you can move the start line again Clicking with the mouse sets both start and end po sition line If you have chosen a locked controlfile you will not be able to adjust the number of slices To center a certain number of slices move the reference line to the top of the specimen than press the ALT key and move the mouse pointer to the bottom The reference line will be centered in between Click to fix this centered refer ence line At the bottom of the ScoutView the number of slices and size of the region mm to be measured is displayed together with the predicted measurement time Save Scout View The reference Scout View f
13. Update If you click on the SAVE button labeled UPDATE in modifying mode all input data for this sample will be saved updated Exit Sample Editing Program vivaCT 80 1 3 Click on the FILE button followed by either QUIT or EXIT This will lead you back to the main menu Using EXIT any changes will be automatically saved whereas with QUIT you can return to the main menu without saving the edit ed data File Print Quit Exit Daten Figure 5 Exit Sample Editing Program Edit Sample Data 15 Measurements Measurement Procedure To make a single scan the following work flow is used 1 2 3 Start the measurement program and wait for the warm up of the scanner Select the sample name or number See Selecting the Sample on page 18 Select the measurement parameters See Controlfiles Measurement Pro tocol on page 20 If necessary click Precalibrate and wait until ready See See Precalibrate on page 25 for when precalibration should be used Place the holder inside the scanner Perform a ScoutView and set the reference lines See Scout View on page 25 Start the scan See Single Measurement on page 33 Starting the Measurement Program To start the measurement program you must first enter your name or your number in the field OPERATOR Then on the main menu select the icon with the scanner symbol by clicking on it Figure 1 Start Measurement The
14. above will not appear for the next six months vivaCT 80 1 3 Data Management 73 Device Information Figure 8 Device Information Initialize All media data carriers must be initialized formatted before they can be used for the first time In doing this every tape will be given a label The same as above has to be performed for tapes as well but tapes are one sided media only and the label is limited to 6 letters When initializing all data which could already ion Caution be on the medium will be lost vivaCT 80 1 3 Data Management 74 Mount Dismount vivaCT 80 1 3 Before tapes can be used they must first be mounted by the system made accessible to the user and after use they will be dismounted This has to be done manually for tapes because of performance reasons Data Management 75 11 DECterm Based Programs General Guidelines To start one of the following programs you need access to a terminal session window either directly on the machine or via the network telnet rlogin set host etc You can start the programs by typing a shortcut or symbol The following ta ble summarizes the names functions and location of the programs TABLE 1 Symbol Command Program Name Location Function UCT RECONSTRUCTION UM UCT_RECONSTRUCTION EXE 2D Slice Reconstruction IPL UM IPL_SCANCO_M EXE 3D Segmentation 3D Evaluation UCT_THREEDEE_BATCH UM UCT_RAY_BATCH EXE Pro
15. an object with a GOBJ or a AIM mask needs more memory and time with AIM though Voxels outside the mask are set to Zero Peel iter gives the number of two dimensional peel iteration applied to the contours The operation is working directly on the object i e it is overwriting Zeros on it NB Gobj maskaimpeel ow may be repeatedly used on the same ob ject but using a smaller pee1 iter number does not restore the region set to Zero anymore i e while trying out different peel_iters go from small num DECterm Based Programs 81 vivaCT 80 1 3 bers upwards The relative volume of the mask is stored in the proceeding log which may be shown with examine in log afterwards ipl gobj mask input output in in gobj filename default file name gt U0001977 GOBJ peel iter 0 gt cortex maskoff Expert function Combines a GOBJ contour e g the outer bone contour with a cortex seg mentation mask The resulting AIM mask is then the region inside the GOBJ but without the cortex i e only the trabecular region The input is a GOBJ file and a volume that should represent the cortex input mask This input mask has to be produces with zeg gauss beforehand e g with a high sigma 10 0 and support 6 and an appropriate threshold 150 or 300 cortex peel iter gives a minimal cortex thickness i e the minimal boundary of the outer contour that is excluded in the mask A component labeling is per formed for every slice for the co
16. and THRESHOLD you can change the seg mentation parameters Once you have found your optimal settings keep them constant for a series of evaluations i e within a study Evaluation 49 Evaluation 3D vivaCT 80 1 3 Printing out of the 2D Histomorphometry Window The next selection affects printing Set the NUMBER OF COPIES to how many copies of each result sheet you would like to obtain The toggle buttons PRINT LIST and PRINT SHEET affect the result sheet output PRINT LIST will create a summary report for all processed slices including the mean values of all slices filename of summary report is HISTO 2D xxx DAT where xxx is the measure ment number The file is located in the directory with the logical name equiv alent UCT HISTO RESULTS see Appendix PRINT SHEET creates an individual sheet for each slice showing the main image and the 2D histomorphometric values on it Keep in mind that these sheets are very large in size and could fill your hard disk if you process all slices of your measurement 200 or more Starting Evaluation If you have checked all your settings click on START EVALUATION The evaluation will only be performed inside of the combined area between both a your objects contours green red Caution b the bounding box white The bounding box in its default size contains all your objects and thus does not further limit the ROI VOI The 3D evaluation is working on the volume defined by the 3D re
17. are carried out has a dark frame and the inactive windows have light frames You can move the windows around the screen by clicking on the top bar using MBI and dragging it to the desired position To iconize a window click on the small rectangle on the top right To restore the window from the icon double click on the icon using MB All error messages must first be acknowledged with OK or CANCEL before you can make other entries This is also the case with most of the other input windows for example fin ding a patient Scout View measurements etc Push Button Click with MB1 on the button The function which describes the button will be carried out Toggle Button Selection The button can either be pressed or not with MB1 Radio Button Selection Only one button can be pressed with MB1 Text Field Click on the field with MB1 and then enter the text Scroll Bar Click on the bar in the middle with MB1 Hold MBl pressed and move the mouse The field next to the scroll bar moves The length of the scroll bar corresponds to the whole field the length of the bar corresponds to the dis played area 100 Option Menu tg Option 2 Selection Click on the menu with MB and all the possibilities then appear You can now make your choice with MB Option 1 Option Menu Option 2 Pull down Menu Selection Click on the menu with MB and all the possibilities appear You can now make your choice wi
18. as marked in the above image Remove the power cable before changing the fuses Power requirement vivaCT 80 400 W Tape Drive about 300 W Monitor about 300 W Disk Tower about 370 W Supply 2 supplies possible HP Integrity Server rx2620 max 1350 W Hardware Source X Ray Tube with a power of 4 8 W and a peak energy of 45 55 70 kVp Mode of Operation Continuous operation Leakage Radiation Equipment is fully shielded i e radiation in 5 cm distance of housing is less than 0 5 uSv h Computer HP Ingegrity Server 64bit rx2800 Memory 16 to 384GB TFT Color Monitor LTO format Ultrium magnetic tape drives vivaCT 80 1 3 Specifications 98 vivaCT 80 1 3 Printers External Gating Ethernet animal monitoring Network PostScript printer via TCP IP raw or Ipd lpr protocol Connector BNC Input 5V 2mA Overvoltage protection Reverse polarity protection 100BaseTX PSE PoE Output 44 57V 30W max IEEE802 3at IEEE802 3u IEEE802 3x Media Cat 5 5e 6 UTP STP Specifications Mouse Operation Appendix A Additional Information MB means left mouse button MB2 is the middle mouse button Usually all actions are performed using MB1 except for scaling a ROI or VOI in the eva luation program Elements of the Graphical User Interface MERGE On off Oort On 4 on Off Off Off vivaCT 80 1 3 Window Dialog Box All windows have a frame The active window in which your switch com mands
19. click on MB1 while iterating the views you interrupt and can then change the observer settings again by click and drag By holding down the SHIFT button the coordinates of the object where the mouse is pointing are displayed 3D Display 59 By holding down the CTRL button and then move the mouse the distance is measured between the initial position and new position on the object where the mouse is pointing Light Source By changing the ROTATION and ELEVATION of the light source you change the effect of shades on the object The values are relative to the observer position Figure 7 Light Source The scaler AMBIENT LIGHT affects the shading of the object where 0 means direct lighting only and 10096 means ambient lighting only The values in be tween are a mixture of both light source types The scaler shadows affects the translucency of the shadow Other Effects By changing the SCALE FACTOR you enlarge the object or make it appear smaller The PERSPECTIVE scaler lets you change the visual effect as if you moved to the object or further away The scale hereby is modified in a way that the size is not affected n pes SS MB2 for Scaling within Window Figure 8 Other Effects Alternatively you also can click with MB2 into the main window and as you move the cursor up and down you change the scaling vivaCT 80 1 3 3D Display 60 vivaCT 80 1 3 Cutplane To perform a virtual cut through the d
20. clicking on it using MB After you have performed a copy move operation you can click on UPDATE LIST as this is not performed immediately because of performance reasons Selecting the File Type If you have selected the measurement you have to select the files you want to copy or move Click on the button RAW raw data RSQ or IMA Images ISQ GOBUJs GOBJ and VOI AIM DCM TIF etc on the left For double security do not archive raw data and images on the same tape Depending on the destination device with IMA selected you also have to se lect images AIMs or everything except RAW which are handled separately for the following operation Figure 4 Selecting File Type vivaCT 80 1 3 Data Management 70 vivaCT 80 1 3 Selecting the Destination Device Click on the DEVICE button and the list of all available devices appears Select the appropriate l Hard Disk N CD R EN DVD R p Tape Streamer Wu Waste Basket Figure 5 Selecting destination device Depending on where the source files reside you cannot choose all devices e g if the files are on the hard disk you cannot choose the hard disk as a destination device The list of devices depends on which devices are available on your system and can also include NFS FTP DEI etc If you want to delete any measurements you choose the waste basket as the destination device If you want to archive or copy some
21. com or to the measurement direc tory on the data disk The color of the output can be set to different values Choose COLOR or B W Then set the PRINT FILE to your wishes and click on OK Calculating Animated 3D Sequences vivaCT 80 1 3 Click on menu OPTIONS followed by ANIMATION The following window ap pears To save the image sequence the toggle button AUTO PRINT must be ac tivated previously in Figure 77 on page 65 To make an animation turn your 3D object into the initial position desired for the animation and click GET SETTINGS A Then adjust the settings of your object to its end position and click GET SETTINGS B When you move the object using the sliders Rotation Elevation Translation etc you need to push the button START to display the changes On the sliding bar below you can select the number of frames that you would like to create between the initial and the end position 3D Display 65 vivaCT 80 1 3 Before you click Start calculation you need to set up the auto print mode To do so go to the Print menu and choose print to TIF and to File and enter the beginning of a file name e g DKO MICROCT DATAjtest_ The program will append _0000 TIF 0001 TIF etc afterwards Click on the auto print box followed by ok Transfer those TIF files to your PC and combine the sequences in the pro gram that you are using to convert the TIF files to AVI or MOV files like Win dows Movie Maker 2 or Quick Time Pro o
22. epsilons are used for suppress ing artefacts due to rough surfaces You should usually not modify the de fault values For very coarse voxel sizes above 100 um assign epsilon 0 9 may be chosen Histogram or screen controls whether a histogram of the thickness distribution is written to a text file and or shown on the screen ipl dt obj input Cool gt DECterm Based Programs 84 vivaCT 80 1 3 output out gobj filename gobj from log peel iter 4 roi radius factor 10000 0 ridge epsilon 0 900000 assign epsilon 1 800000 histofile or screen none samp012 thickness tab dt background param Calculates the mean separation of the structure with the distance transfor mation DT method by filling largest spheres into the background of the ob ject and calculating their mean diameter volume weighted mean Mean separation and standard deviation are written to the database if activated The output object shows the spheres fitting inside the background with the voxel values being their diameter in voxel units Dt background param uses the contours of a GOBJ or AIM mask if it finds the GOBJ filename in the pro ceedings log Roi radius factor controls whether only a sphere is evaluated or the whole region default DT also works with GOBJ masked objects The epsilons are used for suppressing artefacts due to rough surfaces You should usually not modify the default values For very coarse voxel sizes a
23. files choose the tape device Selecting the Copy Move Operation If you choose the COPY function the files are copied to the destination de vice but will still be available at the original device When using the copy command for the image files it is possible to copy differ ent types of files separately By clicking on the SELECT toggle button the choice of ISQ AIM GOBJ DCM TIFF TXT COM and SCY files appear One or several of these file types can then be selected Figure 6 Selecting File Type for copying If you choose MOVE the original is deleted after successful copy operation and the database entry is updated with information about the new location If you want to delete any measurement data choose MOVE and WASTE BAS KET If a COPY of the data does exist on the hard disk original still on tape then the COPY will be deleted first If you redo the command then the data where Data Management 71 Backup vivaCT 80 1 3 the database is pointing to e g Hard Disk will be deleted and then the DB will be updated If a copy of the data already has been transferred to another device this can be seen within the parenthesis behind the name of the data General Guidelines for daily operations Archiving use MOVE to Tape Restore use COPY to Hard Disk from Tape Starting the Move Copy Function If your destination device is a hard disk just click on the START button to execute the desired function If
24. files using a text editor If you start the program by entering a measurement num ber as parameter you will get the information of that specific measurement on the screen uct list 43 Processing measurement 43 Measurement Nr 43 Measurement Date 15AUG1994 09 01 Filename C0000007 DECterm Based Programs 92 WRITE INFO vivaCT 80 1 3 Sample Name Sample Nr Date of Birth MIL BV TV BS BV TV BS BV Tb Th Public Joe sl 06 SEP 1994 5 0782 35 4409 0 3389 20 5926 0 0971 Once you have measured many biopsies you might want to have all informa tion about filenames archiving data directories tape labels etc in table form You can delimit the range of your samples being listed by entering the sample numbers and or the sample names gt write info Sample Index from 0 13 Sample Index to 0 64 Sample Name from 129 Sample Name to ECK The logical UCT DB INFO usually points to the resultant text file which is usually in sys scratch DECterm Based Programs 93 vivaCT 80 1 3 12 Error Messages The most common error messages caused by insufficient or incorrect infor mation for a measurement are self explaining Unforeseen system error messages are explained in the alphabetic list below All error messages must be acknowledged with MB If the error is only a WARNING you can continue working If the error is FATAL however the program will then be terminated as a conti
25. for Red Green and Blue to obtain the color of your choice Browser Browse through a list of colors to select a predefined color Grayscale Adjust the level of gray by using the slider 2 Select the color pallet Spectrum Pastels Vivids Earthtones 3 The color interpolator To mix two colors first select one color in the pallet above and click on the color bucket in the left corner then select another color in the pallet and click on the colorbucket in the right corner When you click Smear you will get a range of color tones interpolated between the two selected colors The range of interpolated colors can then be made lighter darker using the arrows on the left side or warmer cooler using the arrows on the right side 4 Scratch pad By clicking here you can saved the generated colors for later use 3D Display Printing of 3D Scenes After you have a 3D Display on the screen you can send it to a printer or save it as a EPS or TIFF file Choose the menu FILE and PRINT The following window appears Mm AN C0012343_SEG Y ja Pes Figure 15 Printing of 3D Scenes First choose the type of printout you want by clicking on one of the PRINT FORMAT options PostScripto EPS or TIFF if available Then choose the printer attached and the corresponding button PRINTER FILE or BOTH If saving to TIFF you can choose the location directory now e g to Scratch or Export as defined in microct setup user
26. for each mea surement is displayed By using the toggle buttons at the lower left side one can chose to display AIM files or All Files If you later need to choose other measurements click on the FILE button fol lowed by SELECT MEASUREMENT Figure 41 on page 39 Selection of Measurements already Archived Saved If you want to select a measurement that has already been archived interrupt the above procedure using the button CANCEL and click on the FILE button followed by SELECT OLD MEASUREMENT Figure 4 Select Old Measurement Enter the name or number of the sample see Edit Sample Data p 13 The input window shown in See Figure 41 Evaluation Selection of Patient and Measurement on page 39 now appears again Click the sample and the mea surement as described above You will then be asked to put the correspond ing tape with the archived images into the tape drive Evaluation 39 vivaCT 80 1 3 If you archived the data to tape you will first Note have to restore the data to the hard disk before you can re evaluate it Load Save Contours Contours that you have drawn for a measurement are saved as geometrical object GOBJ files Clicking on the menu FILE followed by LOAD GOBJ will open the window below Using the option add allows you to concatenate mul tiple GOBJ files Figure 5 Load GOBJ The menu save GOBJ AS will allow you to give specific filenames e g C0040915_CORTEX GOBJ Print Sav
27. i rN 72 Brakepoints senado 46 C Calibration Record eese 22 Case Sensitive oooccoconcnnoncnnoncnnoncncnncnnnnos 18 Color Mixing ee EE 63 Color Scale tai e 115 Component Labeling sess 83 Concatenate AIMS esee 89 Connectivity coe oet aia 86 Contouring occccoccnconcnncnncnncnncnnoncnncnncnnnnnono 48 Control BOX 0oococccncncncnnnnnnnnnnnnnonononanaroraranos 7 L tal 6 20 Creating a Volume eese 45 EE UE 61 D Data Connector Jioc abi 1 Data Entry Window eese 10 Data security esse 72 Database ACUVAUNE xS eR EE e e UR 84 query 3D values esee 92 query evaluation data 92 query measurement info 93 Deleting UE 44 Density scaling coocccccnnncccnccnnconacnncnnncnnn 41 Device Information eene 74 DIAM is 23 Dismount See also Mount 75 DISPLAYS tao 4 Distance Measurement IDEM 54 Drawing ege EE 44 ODJeCts cows 43 Drawing Icons eee 43 56 DT Distance Transformation 77 109 E Ending Program sss 12 15 E EE 41 Evaluation Starting 2D iia plas 49 Starting 3D eeu 52 Evaluation Script ooccooccnccnncnnncnnccnnconaconoss 22 15 4 UMP 12 15 Extruding dd 47 F ET 115 Fixed Threshold ers 80 Blip AIMS 2 5 lence ees 90 e e EE 74 fully automa
28. if a seg mented file is opened there are only two objects where number 0 is the background number 1 is the segmented object If the opened volume con tains pixels with different values they will be shown in bins 1 to about 255 With the sliders you can select e g 1 to 80 This then corresponds to vivaCT 80 1 3 3D Display 62 vivaCT 80 1 3 all the pixels with a relatively low gray scale value the numbers and the corresponding threshold numbers are displayed just below the sliders Once a range has been selected the display properties of those values can be altered see points below for options Display properties of object within the selected range Show Display objects in range as a solid object Transparent Join Joins all selected objects into one transparent object Transparent Separate Each object is displayed as separate objects but are transparent Transparency slider Regulates the percentage of transparency Hide Hides all objects within the range Surface Object color Each object within the given range is displayed in the color given in the colorbar below By clicking on the colorbar the color mixing window see below opens and a different color can be selected Value color Each object is colored according to its value in the AIM file The color map can be changed using Object Value interface Figure 74 Object Values on page 62 Face Colors the artificial cutfaces at the boundary of the boundi
29. is non averaging scaling of binary objects always with noipscale to maintain the binary status if the integrate flag is put on false If a GOBJ mask is used for the evaluation of an object the GOBJ mask has to be transformed into an AIM mask with gobj_to_aim and this AIM mask can then be scaled to the same voxel size as the original ob ject Use integrate false for the mask scaling to preserve the binary status of the mask alternatively after masking with integrate true perform a thresh old operation to produce a binary mask again ipl gt scale input in gt a output sca gt x down scale 2 000 2 000 2 000 up scale 1 000 1 000 1 000 integrate true ipscale elsize One constituent of scale_elsize If the new voxel grid is not a integer multiple of the original voxel grid then the new values lying between old voxels points are interpolated ip and depending on the integrate flag also averaged over the voxel volume The center flag controls whether the center of the ob ject is still in the center of the scaled object or whether the upper left top cor ner is also the beginning of the scaled object center false The computation time and memory needed is larger than for noipscale elsize ipl gt ipscale elsize input in a output sca gt b down scale 2 000 2 000 2 000 gt 1 up scale 1 000 1 000 1 000 gt 2 center false integrate true noipscale elsize Scales the obj
30. main window of the measurement program will open vivaCT 80 1 3 Measurements 16 Figure 2 Main Program Screen Initialization of the Scanner After starting up the measurement program the scanner will be initialized and the power up of the X ray tube will begin Scanned objects must be completely contained in Caution the sample holder tubes Make sure absolutely no fluid can drip on the scanner mechanics vivaCT 80 1 3 Measurements 17 Selecting the Sample When you click Other the following window will appear Enter Name or Number Figure 3 Input of Sample s Name or Number Click on the input field and fill it in accordingly with either the sample name part of the sample name or sample number Confirm your input by clicking the OK button You can also click the OK button without entering any text for a list of all available sample names Please note the spelling The program is case sen Note sitive As in the program for editing samples see Edit Sample Data a list of all samples now appears that correspond to your entry Click on the sample that you want to scan in the list and confirm with OK If the desired name cannot be found in the database the following question will appear e Sample name or number not found Enter Figure 4 Confirmation You should now click on YES if you wish to enter the sample The input page of the Edit Sample program appears See Sa
31. mat input am om output out gt gobj filename gobj from log peel iter 1 roi_radius_factor 10000 0 gt ridge_epsilon 0 900000 gt assign_epsilon 1 800000 gt histofile or screen none DECterm Based Programs 85 vivaCT 80 1 3 dt mat output Performs the mid axis transformation of the structure and saves the mid axes in the output ipl dt mat output input in output out ridge epsilon 0 900000 gt connectivity Calculates the connectivity density of a segmented object according to Odgaard and Gundersen Bone 14 173182 1993 The insure that only one connected object and one connected background is evaluated a component labeling and extraction of the dominant component is performed for both the foreground and the background Use conn noc1 and conn_bgcl if you wish no component labeling or only a background component labeling extraction e g if a component labeling is already incorporated into the segmentation The component labeling and extraction changes Note the input volume ipl connectivity in out in conn nocl Calculates the connectivity density of a segmented object without prior com ponent labeling If the object consists of more than one unconnected part you would have to add the number of components minus one to the connec tivity and then calculate the connectivity density Likewise if the back ground is made up of more than one part you would have to
32. region surrounding both objects is produced Add not overlay Controls whether voxel values of second object are added to the first object with overflow taken care of i e 60 90 127 50 127 for char images or whether non zero values are laid over the first object useful for mapping the segmented image onto the original gray scale data Make edge controls whether edges are made of second object or first if second is gray scale and first is char The second object can be shifted with shift ofin2 and turned in the x y plane with turnangle Turnpoint global is tried to be set to the original rotation center of the scan ner i e for 512x512 images to 256 256 etc The turned image2 is mapped into the same box as image2 thus for larger angles the image may be cut at the boundary if there is not enough free space left around the object to con tain the turned image2 Subtraction of two binary images can be performed by a combination of set value of input2 to 127 and then concat it with in putl flag add true Als conoat inputl in gt a input2 inl b output out gt c common region only true add not overlay true make edge false gt shift ofin2 000 gt turnangle 0 000000 turnpoint global 1 1 vivaCT 80 1 3 DECterm Based Programs 89 vivaCT 80 1 3 join uncompress This operation joins two segmented volumes directly while reading and un compressing from the disk thus only needs the memor
33. ren in alleiniger Verantwortung dass das Produkt declare under our sole responsibility that the product d clarons sous notre seule r sponsabilit que le produit Computer Tomograph vivaCT 80 ID 5800 5899 Rezeichmung Typ oder Modell Los Chargen oder Seriennummer m glichst Herkunft und St ckzahl name type or model lot batch or serial number possibly sources and numbers of items nom type ou modele no de lot d chantillon ou de s rie ventuellement sources et nombre d exemplaires 100 230V 50 60 Hz max 400VA Nennleistung Power Rating Puissance Nominale auf das sich diese Erkl rung bezieht mit der den folgenden Norm en oder normativen Dokument en bereinstimmt to which this declaration relates is in conformity with the following standard s or other normative document s auquel se r f re cette d claration est conforme la aux norme s ou autre s document s normative s EN 61010 1 2010 EN 61326 1 2013 Titel und oder Nummer sowie Ausgabedatum der Norm en oder der anderen normativen Dokumente title and or number and date of issuc of the standard s or other normative document s titre et ou no et date de publication de la des norme s ou autre s document s normative s Gemiiss den Bestimmungen der Richtlinie n following the provisions of Directive s conformement aux disposition de s Directive s falls zutreffend if applicable le cas ch ant 2006 95 EG 2
34. size is the reconstructed pixel size of the image data After de selecting the Default Size you may select another voxelsize of the reconstructed image which is achieved by an interpolation during the reconstruction It only makes sense to reduce the voxelsize if binning is 1 See Modifying a Controlfile Advanced Mode on page 24 The pixel size will be displayed in yellow if it is not an optimal setting 17 Number of Slices Choose the number of slices On the right side an indi cator shows the covered range in mm resulting from number of slices and current slice thickness Below the range in mm the number of stacks will be displayed together with the number of slices per stack The number of slices per stack will vary depending on the number of total slices so that the slices are always equally distributed over the minimum number of stacks necessary The largest possible number of stacks will be displayed after the number of slices 18 Relative position to Scout View Reference Line or the absolute position O mm if Scout disabled 19 Integration Time Adapt the integration time to the sample s density and size A longer integration time leads to a higher Signal to Noise ratio The reconstruction time is not affected by this value but the measurement time If the selected integration time appears in red it means that it has is too long and will saturate the detector 20 Average Data Multiply the integration time with the chosen factor 1
35. the sample Limit the lines to a small number to reduce the number of slices per stack and to get Scout Views without those artifacts but the time and dose of the Scout View will increase 21 Number of Det Lines for CT scan During the actual CT scan how many lines of the detector shall be used Each complete rotation of the sample will produce a stack of slices The number of slices in each stack will depend on the chosen number here Limit the number of detector lines if you see residu Measurements 24 Precalibrate Scout View vivaCT 80 1 3 al cone beam artifacts the scan time and dosemay increase If not set manu ally this number will be automatically change to optimize the use of the detector with respect to the number of slices to scan 22 FOV Scandiameter Choose the diameter of the field of view the number indicated is the size of the reconstruction area This action is cropping the area of detector which leads to smaller image matrices to save space and re construction time 23 Software binning factor of the original pixels on the detector Binning is the process of combining data from a cluster of pixels to one single pixel A binning of 2 would take 2 x 2 pixels to create one pixel This operation reduc es the noise in the image and reduces its size 24 Hardware binning factor No available options for this scanner type 25 Samples number of possibly binned pixels on the detector that are used f
36. your destination device is a tape you first have to mount the corresponding tape manually see Mount Dismount p 75 After your confirmation the images of the selected measurement will be cop ied moved to the destination device If you want to view these images later again in the evaluation program you will be asked to put in the appropriate tape If you archive or backup the images on tapes you first have to copy or move them back from tape to disk to be able to re evaluate them Under some circumstances it is possible that a hard disk can crash which makes it impossible to read sample data old measurement results or Scout Views again Such defects are extremely unlikely but are disastrous for fol low up studies as previous measurement results cannot be read any more You should therefore regularly make a copy of your databases data security preferably once a week A pop up window will open every time a weekly back up is needed Please do not ignore this warning You can backup your database to either tape or local disk If you use the tape drive you can add many backups to the same tape You should use a tape specially reserved for this purpose With tapes we recommend you to use two tapes alternating between them Use a new tape for this purpose Only tapes ini tialized with label BACKUP will be accepted Note Tapes have to be initialized with free chosen la bel name with a length of 6 letters Do not store y
37. 004 108 EG 142 EG Br ttisellen 20 Januar 2014 Bruno Koller Ort und Datum der Ausstellung Name und Unterschrift oder gleschw Kennzeichnung des Befugten Place and Date of issue name and signature or equivalent marking of authorized person Lieu et date nom et signature du signataire autorise Figure II 3 Declaration of Conformity Important Information xviii Description of Warning Symbols X Rays X Rays Caution Electric Shock Note gt bp AE Product Description Intended Use ll Safety Information X Rays may be present X Rays may be present for Canada only Caution X Rays Attention Rayons X This warning symbol defines important warning information regarding the instrument or operator action Disregarding these informations may lead to damage to the instrument or loss of data Disregarding this kind of provisions may lead to electric shock and serious health risk This symbol defines information which require elevated operator attention The vivaCT 80 is an in vivo high resolution computed tomography system to be used in research to visualize and quantify the three dimensional structure of small animals or objects especially in longitudinal studies Abuse This instrument is not intended to be mis used as a human in vivo medical device or an in vitro diagnostic device vivaCT 80 1 3 Safety Information xix User s Responsibility The user is obliged
38. 12 Scout View Start End Position Following can be done Determine start and end position for the Scout View e Set the angle of the Scout View Perform the Scout View Set the reference line e Save the Scout View this is done automatically for the first Scout View of each sample reference Scout View of reference measurement Start and Endposition With the two scalers the extent of the Scout View can be determined The controlfile defines the default values which can be changed for a specific sample The start position O is defined as the top of the sample holder Angle The gantry can be rotated using this scaler Scout View only This allows to better visualize structures which are not visible from one angle but from pos sibly another view e g growth plate of a joint Default Values Sets the scalers to their initial positions 100 mm If the ScoutView setting OFFSET was selected in the Controlfile an addi tional row on the right hand side of the Scout View GUI Set here the given length of a reference object e g arm length or object length The relative off set in of this object is calculated automatically Start Scout View Click on the SCOUT VIEW button The scanner now starts acquiring the Scout View image First it will show the half of the radiograph then continue with the second half of the image You can interrupt the Scout View at any position by clicking on the CANCEL button
39. 3 Explanation 1 2 3 6 Enter a meaningful name describing the measurement protocol Display mode of the controlfile basic or advanced see Modifying a Con trolfile Advanced Mode Sample Holder Type Choose the used sample holder type with the correct diameter Scan Mode Select Gated or Continuous rotation Evaluation Choose which evaluation script shall be preselected in the evaluation program by clicking on CHANGE Figure 8 Evaluation Script Selection Energy Intensity E kVp I uA Choose Energy and Current Settings Standard energy settings for bone measurements is 70 kVp For higher absorbing materials increase the energy and for lower absorbing and lower contrast materials decrease the energy A stronger current reduces the signal to noise but increases the spot size of the X ray tube for high reso lution measurements it should therefore be kept low Filter Choose Filter Standard filter is 0 5 mm Al Calibration Select the appropriate calibration record for the chosen energy and sample by clicking on CHANGE Figure 9 Beamhardening Script Selection 9 Choose ENABLED for measurements with a Scout View which means that the Rel Pos of First Slice is relative to the reference line set in the Scout View If you DISABLE the Scout View the position of the first slice is the absolute position of the sample holder Due to the cone beam geometry you can have a mi
40. ANCO MEDICAL AG authorized resel ler This Limited Warranty does not extend to any product that has been da maged or rendered defective asaresult of accident misuse or abuse byoperation outside the usage parameters stated in the product s user documentation e by the use of parts not manufactured or sold by SCANCO MEDICAL AG by modification of the product e asa result of service by anyone other than SCANCO MEDICAL AG or a SCANCO MEDICAL AG authorized service provider SCANCO MEDICAL AG is not responsible for damage to or loss of any pro grams data or removable storage media SCANCO MEDICAL AG is not liable for any damages caused by the product or the failure of the product to per form including any lost profits lost savings incidental damages or conse quential damages SCANCO MEDICAL AG is not liable for any claim made by a third party or made by you for a third party vivaCT 80 1 3 Warranty xi Limitations of Remedy vivaCT 80 1 3 EXCEPT AS EXPRESSLY SET FORTH IN THIS WARRANTY SCANCO MEDICAL AG MAKES NO OTHER WARRANTIES EXPRESS OR IMPLIED IN CLUDING ANY IMPLIED WARRANTIES OF MERCHANTABILITY AND FIT NESS FOR A PARTICULAR PURPOSE SCANCO MEDICAL AG EXPRESSLY DISCLAIMS ALL WARRANTIES NOT STATED IN THIS LIMITED WARRANTY ANY IMPLIED WARRANTIES THAT MAY BE IMPOSED BY LAW ARE LIMITED TO THE TERMS OF THIS EXPRESS LIMITED WARRANTY This limitation applies whether damages are sought or a claim made under this wa
41. ATA C0000372 AIM or on one line only ipl aim in DISK3 DATA C0000372 AIM isq_to_aim Reads an ISQ from disk and puts the requested volume of interest into mem ory as an aim object The volume of interest is given by pos upper left corner and dim dimension of aim object ipl gt isq aim name in a isq filename default file name DISK3 DATA C0000372 15SQ pos 00 0 150 240 0 dim 1 1 1 gt 210 210 210 write Writes an object to disk The file type should be aim You can compress seg mented files using run_length or binary compression Default is binary but for gray scale images the compress type is always switched internally to none ipl write name default name a filename default_file_name gt DISK3 DATA XYZ AIM compress type bin gt r delete This command is used to delete an internal object i e to free memory ipl gt delete name gt a examine Use this command to examine different things of an object and show the re sults on the screen Possible values are geometry histogram statistics number log and z_mean_max mean and max values of each slice along z ax is ipl gt examine input default name a item geometry dim 504 122 223 DECterm Based Programs 78 off 000 pos 266 308 0 sup divide This command is used to subdivide an object into smaller objects This is helpful in examining only a small part of the complete object or f
42. CT_EVALUATIO UCT RAY VOLUMESIZE SCANCO DEF PRINTER SCANCO BW PRINTER SCANCO COL PRINTER SCANCO PS PRINTER UCT EVALUATION SHEET UCT HISTO 2D SHEET UCT RAY SHEET UCT SINGLE IMAGE SHEET UCT ONE IMAGE SHEET UCT FOUR IMAGES SHEET UCT SIXTEEN IMAGES SHEET UCT 3D LIST SHEET UCT 3D SINGLE SHEET UCT CONTROLFILES DATABASE UCT MEASUREMENT DATABASE UCT EVALUATION DATABASE UCT SAMPLE DATABASE UCT SCANNER DATA UCT SLICE NAME FILE SCANCO PATIENT DATABASE SCANCO ZIP CODE DATABASE UCT DB RESULTS UCT DB INFO UCT_BACKUP_COMMANDF ILE vivaCT 80 1 3 Meaning SCSI Controller SCSI Controller System Disk User Disk Data Disk Data Disk Magneto optical drive Floppy Drive Streamer Tape Login Directory Scratch Directory Directory for Programs Directory for Interface and Printing Directory for Database Files Measurement Main Directory Scout View Directory Directory for 2D Hist Results Batch Measurement Script Measurement Batch Queue Slice Reconstruction Image Reconstruction Batch Queue Reconstruction Command Proce Reconstruction scaling factor Beamhardening Correction Beamhardening Correction 3D Evaluation Batch Template Min Volume Size in MB for linear Default Printer Queue B W Printer Queue Color Printer Queue PostScript Printer Queue Template for 3D Histomorph Eval Template for 2D Histomorph Eval Template for Ray Tracing Template for Main Image Template for image prin
43. Connection and Main Power Switch Only use suitable power cords for mains connection Use Main Power Switch to switch instrument on or off 1 Main Connector Current supply see specifications 2 Data Connector Patch Cat 5e Gigabit Ethernet 3 Gating input BNC for external gating Data Connector 4 Data Connector Connector for optional animal monitoring The RJ45 connection is to be used for connection to the computer only Animal BedThe animal bed should be placed properly inside the scanner The knobs underneath the animal holder should be fitted into the holes in the vivaCT 80 1 3 Startup Procedure vivaCT 80 1 rack The position of the holder should then be locked by turning the stick from the left to the right Animal bed with op tional animal monitor ing device Animal bed in scanner Computer For information on computers See Hardware on page 98 Quality Control Phantom For information on phantom See Quality Control on page 35 vivaCT 80 1 3 Startup Procedure vivaCT 80 Optical Signals 1 X Ray Indicator 2 Control panel SCANCO MEDICAL vivaCT 80 1 3 Startup Procedure vivaCT 80 Turning on Equipment 1 Turn on peripheral devices such as optical disc drive tape drive and printers 2 Turn on computer and monitor 3 Turn on the key switch front top and turn on the main switch on the back The display lights up front top To operate the equipment make sure that both ke
44. Data management Archive Delete Measurement Data Weekly Database Backup Exit MicroCT Main Program The layout of the main program well reflects the general work flow 1 2 3 Enter operator data See Edit Operator Data on page 10 Enter sample data See Edit Sample Data on page 13 Start the measurements in the measurement program The images are automatically reconstructed without any intervention of the user See Measurements on page 16 Open the reconstructed images for visualization and analysis in the evalu ation program See Evaluation on page 36 Open the evaluation results in the 3D viewer to generate 3D images See 3D Display on page 57 Archive your data See Data Management on page 68 Program Overview 9 4 Edit Operator Data Start Program Edit operator data by selecting the framed button ERI D lee A BIES BI nn Figure 1 Edit Operator Data The following data entry window appears by selecting the EDIT button ill 4 4 4 4 A E Scanco Medical i i H i Figure 2 Operator Registration Program Enter the operator data Each field can be selected directly Using the RETURN key brings you to the next field The operator number is automatically assigned by the program and cannot be changed vivaCT 80 1 3 Edit Operator Data 10 Upon finishing the data input the data can be saved by clicking the SAVE UP DATE button For a
45. IS OUI IU ECL PimikilenaM ENEE Elevation Rotation CODIES t dics etta ro E tana UCTIEIST ES viii 12 13 Appendix A Appendix B Appendix C vivaCT 80 1 3 WRITEAINEO EE 93 EXNO Ee e orale 94 ie ella ele ui TO 97 Obpbercdtioncdlcorncdlitiorns dri terit aec ler nt a Measurement Method vcs e lee Le rel E DIMENSION emer ntt v a o rtc eit sep a eve e Mains Connection vivaCT 80 sar Mains Fuses vivaCT 90 Power requirement ds ole le d ol P um Additional Information sss MOUSE ODerdtloDp ertt e oe D ee oc at d cido etn Elements of the Graphical User Interface Window Dialog BOX wo E e ET EE Toggle BulttOp ctii tdeo ab ec ect als E ER PN Radio Button Text Field oot tele Option Menu Pull down Menu SCOISH TENIS Input Change of the Header and Footer of the Print Out oo ccc 101 Files Used and Created by MOT 102 Directon Stt c Ure AA s Asien ce e p Ret e c Peer eed eb edo Ate 102 MICROCT MICROCT DATA SSSSSSSS MMMMMMMM eene MICROGCT DATASSQQOPUTS Sisi there rcr dein MICROCT DATABASE MICROCT MAIN MICROCT RESULTS MICROCT SCRATCH MICROCT TIPS MIGROCT UILbB a netiis MICROCT UTIL MICROCT XDEFAULTS Ll Logicals and SHIVA ONS suasit n trt Rr adeb unto 104 Definition of Logicals an
46. Invert Merphing eoDfTOWES iiid ep dn ERE C ER CHR URGE DORSET rra Color Coding in Image Selection Area sss eee 47 Morphing Sequence Overview EVGIUGHOR 2D reete Nh ett ROI Selection Segmentation Printing out of the 2D Histomorphometry Window sse 50 starting EVA e lee EE 50 tee euo pM 50 Selecting an Evaluctiori Task E 51 vi 10 11 vivaCT 80 1 3 Defining VOI ated tiec o ee ai edd segmentada et reo ad cen aties STONING EVOIUICITIOD E Morphornmietric Results da tree re ra ee dte Modifying Evaluation Scripts Importing Evaluation Scripts Print Ireges acr e t eq et ea acra TC re UR rU v geri s ria a Distance 9D eset nue d o O de et itv e e a AR C YR D wen Pointer Ruler Profile Angle Tools sss Pointer Ruler Profile Angle Tools RR M T 57 Starting the 3D Display Program Ee RRE Selecting the Sample and the Measurement sss eee 58 SUSO e EEN Visual Effects CDSOTVOLF etin idi rete re dern gud rerit ere rb eee br aeo diet 59 le lege lte me E 60 aerem 60 eec S 61 SUDAM EE 61 ee M EP IT 6l Object te EE 61 WI Eege REENEN 62 Colon MIXING a bee ntt enn te Orco ep a dd 64 Printing Of 3D Sceries ti ie ERG TERI GO oma ET damien 65 Calculating Animated 3D SEQUENCES sss eee emnes 65 EE 66 Datel MANI Mi id 68 OVOLIVIOW iia AD meint ENEE Starting Program Archiving Deleting Backup DOTA sese eee Selecting the Measurement sss
47. Pary in Scoult VIOW no aenean eer e e ee aera Adjusting Brightness in Scout View High Resolution Radiographs sese Single Meoasurerrnent cce ee ene inen eed a nf ee ren tele E EEN Cancel Ee re tei mte tette id SconnincMOGGOS co re E RERO EN ERE YER CRINE WC DOREFU UTERE AGING TASKS 4 EM STAN IGISKS Anata ette cot Ra e t o n ON E e p e o do Keeping Deleting Tasks sse eene enm GuUuiallb X in de EE 85 PRONTO eroe temere orerdecers Duce idad Weekly Phantom Measurement QC1 Monthly Phantom Measurement QC2 e Ee lee SE 36 General NN Starting the Evaluation Program sss Standard Evaluation Procedure ss OVSIVMISW cuccioli Selection of Sample and Measurement serrer Selection of Non Archived Measurements Selection of Measurements already Archived Saved wc 39 Esad Save Contour pite aede api eimi taa 40 Print Scive IMAGES EE Header information LOONA a AAA M Brightness SENS mimi retire reed rere eerie intact Defining the OLor MOL tia iced tetti env n re ERE RED rr qn Drawing Hee EE Drawing CORTOUIS indias darla al Modifying Contours sss Moving Scaling Objects selecting OD EE Deleting Graphical Objects Copy Cut Paste Replace Objects Creating a Volume of Interest sss seen nennen trative COOU zd c red Hee HOT RARE Range Selection Breakpoint BP A oi i Ea N ins GNU Ata rE AREAN Delete
48. Program sess e mese ensem 10 Figure 10 Select Sample A ER E e Ne NR 11 Figure 11 Select Operor eeh e ete HE NRI E I DATE IR AURA E 11 Figure 12 Exit Operator Editing Program ocooccoccocnconncnncncnncnncnncnncnncnncnncnnconcnncnncnncnnes 12 Figure T But Samples Data ia ARR RR ENEE eda GENEE 13 Figure 14 Sample Registration Program seesseseeseesee ee eene hehehe 13 Figure I5 Select Sample ia ERE AORTA RARE AERA 14 Figure lo Select Sample on List ea e a e a a e E RR RR 14 Figure 17 Exit Sample Editing Program eseseeeeeeeee e eee e emer sene 15 Higure 18 Start Meas rement israse i itni a desde dda eet da ede rap eeu pneu ip eigen ierra 16 big re I9 Main Program EEN aurere sea o eese ia Ae RB DR Re RR RR APA e conte DUE Dua es 17 Figure 20 Input of Sample s Name or Number 18 Figure zk Confirmation i3 eH e as 18 Figure 22 Information on the Measurement sample eee 20 Figure 23 Selecting a Controlled CR AR A ARMIS e one oe ln on eer dios 20 Figure 24 Modifying a Controlfile Basic Mode oocooccoccncnncncnncnncnncnncnnconcnncnncnncnncnncnnos 21 Figure 25 Evaluation Script Selection esses eene he hen hene ne 22 Figure 26 Beamhardening Script Selection ooocoocionionnocnncnconcnncnncnncnnconcnncnncnnrancnnrnnos 22 Figure 27 Modifying a Controlfile Advanced Mode sese 24 Figure 28 Scout View of a Bone Biopsy with Reference Line
49. TABASE COM Database logicals MICROCT DATA SSSSSSSS MMMMMMMM Main measurement directory where ssssssss 8 digits is the sample number and MMMMMMMM 8 digits is a consecutive measurement number unique for one database In these directories the following files can be found Cxxxxxxxx RSQ Raw Data Sinogram sequence Cxxxxxxxx 1SQ Image Data Slice sequence Cxxxxxxxx AIM VOI of Image data Cxxxxxxxx SEG AIM Binarized VOI Cxxxxxxxx MSQ Animated 3D Sequence not always present where xxxxxxx is a consecutive 7 digit number unique number for scanner 102 MICROCT DATA SCOUTS ssssssssccc SCV compressed Scout Views where ssssssss is the 8 digit sample number and ccc is the 3 digit controlfile number MICROCT DATABASE UCT CONTROLFILES nnn DAT Controlfile DB UCT EVALUATIONS nnn DAT Evaluation DB UCT MEASUREMENTS nnn DAT Measurement DB UCT OPERATORS nnn DAT Operator DB UCT SAMPLES nnn DAT Sample DB UCT SCANNER xxxx DAT Scanner calibration UCT SLICENAME xxxx DAT Slicenumber UCT ZIP CODES nnn DAT Zip Codes operator where nnn is the name of the customer and xxxx is the scanner SN MICROCT MAIN contains all programs and command procedures needed for operating the system MICROCT RESULTS Contains the summary files of 2D Histomorphometric evaluations The file names are HISTO 2D xxx DAT where xxx is the measurement number MICROCT SCRATCH All temporary files for evaluation and printing are st
50. TXT SYSSSCRATCH ARCHIVE COM 105 mmm mmm mmm mm mmm mmm Gm mm o o omg o o mom Oo U U U Type Symbols Symbol UCT UCT BACKUP UCT EVALUATION UCT LIST UCT MEASUREMENT UCT MOVIE UCT SAMPLE UCT THREEDEE UCT THREEDEE BATCH UCT UTILITIES IPL SCANCO SUBMIT COMMAND SCANCO ANSI PRINT COMMAND SCANCO PS PRINT COMMAND WRITE INFO vivaCT 80 1 3 Meaning Foreign command for Main Program Foreign command for Backup Program Foreign command for 3D Evaluation Pro gram Foreign command for DB QueryProgram Foreign command for Measurement Program Foreign command for AnimationProgram Foreign command for Sample Edit Program Foreign command for Interactive 3D Display Foreign command for Batch 3D Display Foreign command for Tools Program Foreign command for Segmentation Program How to submit batch jobs How to print text files How to print PostScript files Create Informational Report Default Value SUM UCT_MAIN EXE UM UCT B EXE SUM UCT_K EXE SUM UCT_LIST EXE UM UCT_MEASUREMENT COM SUM UCT_MOVIE EXE SUM UCT_A EXE SUM UCT_RAY EXE SUM UCT_RAY_BATCH EXE SUM UCT_M EXE SUM IPL_SCANCO_M EXE INTER SUBMIT NOPRINT QUE SYSSFAST LOG SYS SCRATCH PRINT QUE DL3500 DELETE PRINT QUE SCANCO_PS_PRINTER DELETE SUM UCT_WRITE_INFO EXE Batch Procedure Appendix D 3D Batch Evaluation As soon as you click START EVALUATION in the Evaluation Program the command p
51. a view and you do not interrupt the build up automatically a TIF file is generated numbered sequentially Get Settings A Get Settings B 200 RE T GN No of frames Start Calculation OK Figure 16 Animation Settings Presets Under the Presets menu it is possible write the currently applied settings from the 3D window to a DAT file or to open a previously written file with presets By clicking on Apply Preset A and Apply Preset B only activated if two sets of 3D Display 66 vivaCT 80 1 3 presents are defined in the file the settings defined in the opened file are ap plied Figure 17 Preset menu 3D Display 67 10 Data Management Overview e Archive RAW data and image data to tape local disk remote server via NFS or FTP or USB drives formatted for VMS e Copy files to USB disk formatted for Windows using FAT 32 Delete measurement data while keeping the sample information in data base Formatting initializing of VMS FAT32 Hard drives Determining capacity free blocks of the hard disk Backup of all databases and programs to optical disk or tape full backup Starting Program Click with MB1 on the Floppy disk symbol A Bali Figure 1 Start Archiving Program vivaCT 80 1 3 Data Management 68 Archiving Deleting Backup Data Figure 2 Archiving Program Selecting the Measurement In the upper left hand side samples are listed depen
52. add the number of background components minus one ipl conn nocl in out Lat a conn Doc Calculates the connectivity density of a segmented object with only compo nent labeling and extraction of the background If the object consists of more than one unconnected part you would have to add the number of compo nents minus one to the connectivity and then calculate the connectivity den sity The component labeling and extraction changes Neve the input volume ipl gt conn bgcl in out in DECterm Based Programs 86 vivaCT 80 1 3 voxgobj scanco param Evaluates a segmented image for the fraction of voxels set and writes result to the database if activated For gray scale original images mean attenuation coefficient is written to database The object is masked again with the given GOBJ or AIM mask By default the GOBJ filename is taken from the pro ceedings log last occurrence of a GOBJ filename If the GOBJ file is not found vox scanco param see below is applied Peel iter controls the num ber of 2D peel iterations for the mask By default pee1 iter is taken from the proceedings log ipl vox input seg gobj filename gobj from log peel iter 1 VOX Scanco param Evaluates a segmented image for the fraction of voxels set and writes result to the database if activated For gray scale original images mean attenuation coefficient is written to database If the proceedings log of the object
53. ame for the beginning and the end for one direction voxels run from off x to dim xoff x but may be different for the different directions x y and z The offset is then disregard ed in subsequent image processing or statistical examinations ipl offset add input in gt a add offset 000 gt 00 4 offset_set Changes the offset around the object independent of what it was before ipl gt offset_set input in b DECterm Based Programs 90 vivaCT 80 1 3 new offset FO 00207 9 2 727 XL Clear offset Sets all voxels in the optionally new offset to zero ipl offset set input i0 o new offset 1 1 1 22 1 fill offset mirror Fills the offset of an object with the mirrored values just to the inside of the offset May be used after operations that steal from the image e g gauss fil ter Be aware that voxel information is just duplicated and that values calcu lated afterwards can be biased ipl fill offset mirror input in in convert to type This converts objects from one input type to another e g a char image to a short image The output type is given by out type ipl convert to type input in ZS output out out type short xray Produces a virtual linear X ray image of the object along the z axis flip the object with flip_aim first for other desired orientations The output is a char image The voxel values for every x and y
54. andard evaluation Start Evaluation 3D IPL is operated in batch mode Then the two dots in the last IPL line of the batch com mand file are very important DO NOT DELETE OR FORGET THEM At the IPL start up in batch mode the whole string is read up to the two dots and then commands in the string are executed one by one Note On the other hand in interactive mode IPL executes the commands immedi ately To exit interactive IPL use quit help Gives the list of all available procedures or a short description of a procedure if ipl gt help xxxx is typed quit Quits the program ipl gt quit or q list Lists all objects currently in memory or lists all procedures optionally only items starting with beginning_with ipl gt list objects true procedures false DECterm Based Programs 77 vivaCT 80 1 3 beginning with gt read Reads an object from disk The file type has to be aim By reading an object from disk you have to give it an internal name ipl gt read name in a filename default file name DISK3 DATA C0000372 AIM type aim uncompress true gt aim read Shortcut for reading an AIM from disk The file type has to be aim By read ing an object from disk you have to give it an internal name Same function as read but type and uncompress are assumed to be aim and true ipl gt aim name in gt a filename default file name gt DISK3 D
55. are added along the z axis from startslice for number of slices and the sum is either normalized with the largest occurring voxelsum fixed norm char false or to a fixed norm for binary input volumes fixed norm char true ipl gt xray input in output out startslice 0 number of slices 16 fixed norm char true msq from aim Write an object in memory to disk in the MSQ format e g to view it with the 3D Display program ipl gt msq aim name out msq filename default file name from aim to isq Write an object in memory to disk in the ISQ format e g to produce a GOBJ with the Evaluation program again The object will be at its original global position ipl from aim to isq aim name out isq filename default file name For an extensive discussion of the obtained structural indices see Appendix see Explanation of Structural Indices p 108 DECterm Based Programs 91 UCT THREEDEE BATCH UCT LIST vivaCT 80 1 3 Use this program to recreate a 3D result sheet including the 3D image and the histomorphometry values calculated by IPL Filename Enter the correct filename of the sample measurement you want It MUST have a filename of SEG AIM The file is usually located in the following di rectory DK0 MICROCT DATA ssssssss mmmmmmm Where s is the 8 digit sample number and m is the 8 digit measurement number PrintFilename You can enter any valid filenam
56. ated image to be shown in field 4 You also can enter a slice number by using the keyboard or click on arrows to more troughs multiple slices one by one 12 Information Area Information window showing coordinates of cursor size of ROI and distance density and area calculations 13 Evaluation Information Window Printing 2D 3D histomorphometry 3D distance measurements The brightness scaling 7 does not affect any evaluation but only the display on the screen The user has to supervise the contouring and if a single or more slices are missing do not start an evaluation Wait until all slices are reconstruct ed Images are only for visual control The numbers Caution on the result sheet not the images have to be in terpreted for an analysis Evaluation 38 Selection of Sample and Measurement vivaCT 80 1 3 Selection of Non Archived Measurements After starting the evaluation program the following window occurs Figure 3 Evaluation Selection of Patient and Measurement On the left hand side you see all the samples whose measurements have not yet been archived Click on the desired sample with MB and all the available measurements of this sample will appear on the right hand side After you have clicked on a measurement and confirmed with the OK button an over view of the images belonging to this measurement will be loaded and appear on the screen Per default only the original image file ISQ file
57. bove 100 um assign epsilon 0 9 may be chosen Histogram or screen controls whether a histogram of the thickness distribution is written to a text file and or shown on the screen ipl dt back input in output out gobj filename gobj from Log peel iter zb rol radius factor 10000 0 ridge epsilon 0 900000 assign epsilon 1 800000 histofile or screen none dt mat param Calculates the mean trabecular number of the structure with the distance transformation DT method by filling largest spheres into the background of the mid axis transformed object gt mat and calculating their mean diameter volume weighted mean Mean number and standard deviation are written to the database if activated The output object shows the spheres fitting in be tween the mid axis structure with the voxel values being their diameter in voxel units Dr mat param uses the contours of a GOBJ or AIM mask if it finds the GOBJ filename in the proceedings log Roi radius factor controls wheth er only a sphere is evaluated or the whole region default DT also works with GOBJ masked objects The epsilons are used for suppressing artefacts due to rough surfaces You should usually not modify the default values For very coarse voxel sizes above 100 um assign epsilon 0 9 may be chosen Histogram or screen controls whether a histogram of the thickness distribu tion is written to a text file and or shown on the screen ipl dt
58. cept length The MIL method as implemented in the IPL module works only for a sphere within the volume of interest MIL is used to determine the surface to volume ratio BS BV and then assuming a plate model of bone trabecular number Tb N thickness Tb Th and separation Tb Sp can be derived The distribution of the MILs is taken to determine the principal directions of the MIL ellipsoid and the Degree of Anisotropy Further literature H J G Gundersen T B Jensen R Vsterby Distribution of membrane thick ness determined by lineal analysis J Microsc 1978 113 2743 TRI is used to triangulate the surface of the segmented object and calculate the volume of the enclosed tetrahedrons and the surface of the triangles It is a more direct way to get to the surface to volume ratio BS BV than with the MIL method Still assuming a platemodel of bone Tb N Tb Th and Tb Sp can be calculated To calculate the principal directions of the MIL ellipsoid and the Degree of Anisotropy the area of the surface triangles are projected onto a directional surface distribution skalar product of areaweighted normal vector with the directions of the direction distribution which is the inverse of the directional MILs Artificial boundaries at the edge of cubic or conforming GOBJ produced vol umes of interest are not counted in the calculation i e boundary problems are taken care of Further literature T Hildebrand A Laib R M ller J Dequec
59. changing Note the data and then finally using UPDATE If the changes in sample name is more than cor recting a typo create a new sample name and re import the data Edit Sample Data 13 Possibilities Find The following data entry window appears by clicking the FIND button o mea Hel Figure 3 Select Sample Click the data input field and fill write the sample name or first part of a sam ple name Confirm your input by clicking the OK button Upon entry of a number or of the complete entry of the sample s name the data will appear in the fields If only the first few letters of a name are entered then a list show ing all samples starting with these letters will appear Thus if E is entered the list will show all samples whose name starts with E such as Example 1 Example 2 etc Ok Cancel Figure 4 Select Sample on List Click on the desired name and confirm the entry by clicking OK Please note the spelling The program is case sen Note sitive vivaCT 80 1 3 Edit Sample Data l4 The possibility now exists of changing or completing the selected data Always use the same spelling Find Next By clicking the FIND NEXT button the next sample in alphabetical or numeri cal search order will appear depending on whether you entered the samples name or number while using FIND New If you click on the NEW button all fields become free to enable a new sample data to be entered Save
60. contains a GOBJ mask operation the relative volume of the masked region is incorpo rated into the calculation ipl vox scanco seg mil param This command executes the MIL calculations Mean Intercept Length Parfitt You should usually not modify the default values If the database is activated the result of the calculations are written to the evaluation data base ipl mil param input default name a ray plane scale 2 000000 roi radius factor 1 000000 t dir ortho no t dir ortho nr 8 t dir radius 2 fabric tensor yes milvl param This command executes the MIL calculations in its first version different bor der handling You should usually not modify the default values If the data base is activated the result of the calculations are written to the evaluation database ipl milvl input default name a ray plane scale 2 000000 roi radius factor 1 000000 gt t_dir_ortho no gt t dir ortho nr 8 gt t dir radius 2 fabric tensor yes histo Gives a histogram of an object With the default arguments same effect as examine in histo Optionally the histogram is shown from from_val to to val default from minimal value to maximal value found in input volume Optionally a tabulated version of the histogram is printed to a file given with fileout or screentab or the screen fileout or screentab screen in addi tion to the bar column representatio
61. d Symbols sss nnns 104 ele mE 105 SA EE 106 Appendix D Appendix E Appendix F Appendix G Appendix H vivaCT 80 1 3 3D Betrlchi Ge Re Oia var cecpenva Mencechvinetilimiban aonielen 107 Batch Procedure eee e oie eerie eee di ndn 107 Checking Status and Progress of Batch Jobs 107 Explanation of Structural Indices ss 108 Miete ld TRI Method WEE Connectivity Density Structure Model Index Distance Transformation Methods Elte 110 Checklist for Measurernents 5 enin en ere eie e iod 110 Checklist for Evaluation Checklist for Shutdown Preventive Maintenance renerrien 111 General aen a oana s 111 Maintenance 11 Accomplishment of Maintenance 1 Maintenance Te EE 11 Spare PAMS mu E 113 Disposal 13 Cleaning 13 Se E long EEN 113 Contact Information for Service and Maintenance asss 114 Ee e LN 115 Archive 15 Ataca 15 Backup 15 EL EE 15 E 15 Harddisk 15 LUT L k USTED iiber tee ee re nn eder c n ee E eds 115 Optical Disk 15 ROL eege 15 Scaner c A ER e b t TERR ORC e Pee ree 15 CEET ETS KIEM un t EENEG 115 Shutdown 15 MO os M eat mosse 15 ZOOM buses cta se re e e eO tO cac t e de van ere te 15 Warranty Limited Warranty Statement This Limited Warranty defines the restrictions and warranty period that apply to the SCANCO MEDICAL AG uCT products that you have purchased Contact SCANCO MEDICAL AG if you have questions about
62. d by the script Gauss and Threshold for your current Project Those values will be used when you then start the script unless you override them manually by Evaluation 53 Print Images vivaCT 80 1 3 entering them through the GUI in Figure 56 3D Evaluation Subwindow on page 51 before starting the 3D evaluation At the end save or save as new or cancel your changes Importing Evaluation Scripts More Evaluation Scripts are available in the menu scripts import e g Con vert to Dicom and Convert to TIF These scripts can be imported and made available in your current list of Evaluation Scripts Click on menu TASKS followed by PRINT IMAGES RW The following input window appears Figure 20 Print Images Figure 21 Print Images Details With the toggle buttons on the left side you can choose how many images per sheet you want to have printed The size of each printed image dependents on this value Then select the requested images by clicking on the button with the corre sponding number using MB Alternatively if you press the button 4 or 16 either 4 or 16 images are selec ted equally distributed over the whole range of slices The button ALL selects all images while the button NONE clears all selec tions Confirm your selection with PRINT B W The images will appear after a few minutes Evaluation 54 If you have a color printer defined you may print on that specif
63. ding on which toggle but ton has been selected Current on Disk Lists all samples that either have measurements that have not yet been archived or have not yet been deleted Current with RAW shows a list all the above samples with the additional condition that the RAW datafile of the sample is still available on the disk All Lists all samples including archived samples Information about where the samples are stored which tape or which disk is then displayed next to the sample By entering the sample name part of the sample name or the sample number in the Filter text box only sample containing the given text string will appear in the list vivaCT 80 1 3 Data Management 69 The list of samples can then be ordered according to sample number sample name or measurement number according to which toggle button is clicked Figure 3 Selecting Measurement Choose the corresponding measurement by clicking with MB1 You can now either archive these measurements or delete them To select multiple data use CTRL and select the measurements with MB1 To select several consecutive measurements use SHIFT and select the first and last sample with MB1 To get the data of archived measurements back to your local hard disk click on SELECT OLD MEASUREMENT and then you are prompted to enter the name or number of the sample you want Enter its name or number and all mea surements of that sample appear Select the desired measurement by
64. dit Menu Creating a Volume of Interest Drawing contours on all slices is very time consuming To create a volume of interest it is sometimes possible to get a quicker result by one of the follow ing graphical methods Click on the C button or click on menu TASKS fol lowed by CONTOURING for these tasks Figure 11 Contouring The following window appears Figure 12 Contouring Subwindow vivaCT 80 1 3 Evaluation 45 Iterative Contouring Once you have drawn a contour its shape can be automatically adapted to the surface of the sample The object to start from i e a hand drawn contour should approximately match the form of the scanned sample The automatic adaptation is starting by holding down SHIFT and double click inside the con tour To start the iterate contouring click on the button ITERATE FORWARDS or ITERATE BACKWARDS The finding of the contour can be influenced by 1 Object to start from The closer the hand drawn object to the real contour the better the adaption 2 The value INNER VALUE should be set to the approximate value of the object to segment i e bone see threshold setting in 2D 3D Evaluation 3 The value OUTER VALUE should be set to the approx value of surrounding material i e soft tissue see threshold setting in 2D 3D Evaluation 4 Number of Iterations Usually the ITERATION 1X is sufficient If the shape of the object changes very rapidly from slice to slice choose 2X or
65. e 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 vivaCT 80 1 3 Drawing IONS xchat ee ee Ae EE EEN 43 The Edit Mem e ee eere ENEE 45 Sess Ee ek RC EE 45 Contouring SubWindOW c est e eee AA ee AN e en NT 45 Color Coding in Image Selection Area sess 47 Creatingia VOL iia eret e eere lee deep eer levee eer rane neget 48 2D Eval ation eec pert rre E 48 2D Histomorphommetry orror eee e eR de e 49 3D Eval ation tai ARRA EE ER EAE E RR EI EA EUR 50 3D Evaluation Subwindow eese eee eene en sennene 51 Modifying Scripts Basic Mode sese eee 53 Print IMAGES Dita A TEA A AA AA day E awe A 54 Print Images Details 4 A de A e eda 54 Distance 3D roe re re mre e nen eri AAA erre e aeu waa 55 Distance Measurement enee 55 Pointer Ruler Profile Angle Tools ocrccacirncnrnirnengirnenenini ee 56 Start 3D DISplay ARS 57 Main Program TEE tn o ere eee reve e er he Peer ENEE 57 IDC o E CLP C 58 Selecting the Sample and the Measurement sse 58 Start Stop Caleulation 4 220843 4 cA Nes ed ATA Ade aia aad 59 ObS
66. e Images Clicking on the menu FILE followed by print opens three selectable options print MAIN WINDOW print overview WINDOW or print evaluation WIN DOW After selecting one of these options the Print Menu will appear For mat PostScript is used to print out paper sheets Format EPS or TIFF is used to get the image into a file When generating TIF files you can choose the di Evaluation 40 vivaCT 80 1 3 rectory e g Scratch Measurement Directory or a predefined directory for Ex port where to save your files icon48985 Pas Figure 6 Print Menu Header information By clicking on Header Information the parameters used for the scan and that were given in the controlfile are displayed Zoom If you have to correct your contour you can display part of the screen en larged To do this click on the menu point ZOOM and choose the enlarge ment factor in the submenu ZOOM 2x to ZOOM 20x In the current image a green frame appears which shows the screen section which will be enlarged and which can be moved with the mouse Click with MB1 and the section dis played will be enlarged If you wish to have another section enlarged choose the menu point ZOOM once more and so on With ZOOM RESET you will return to the normal display It is also possible to zoom by click and drag with MB2 directly in the image Click and drag with MB3 to move the view within the window SHOW LEFT WINDOW and SHOW RIGHT WINDOW open
67. e Update If you click on the SAVE button labeled UPDATE in modifying mode all input data for this operator will be saved updated Exit Operator Editing Program vivaCT 80 1 3 Click on the FILE button followed by either QUIT or EXIT This will lead you back to the main menu If not saved explicitly using EXIT any changes will be auto matically saved whereas with QUIT you can return to the main menu without saving the edited data File Print gt Quit Exit Daten Figure 5 Exit Operator Editing Program Edit Operator Data 12 Start Program vivaCT 80 1 3 5 Edit Sample Data Before starting a scan a name must be given to each sample and a unique sample number is assigned automatically This number is the key to access all scan data and evaluation results concerning this sample Edit samples data by selecting the framed button KE Ca HESEL Figure 1 Edit Samples Data The following data entry window appears by selecting the framed button Figure 2 Sample Registration Program Enter the sample data Each field can be selected directly Using RETURN key brings you to the next field The sample number is automatically assigned by the program and cannot be changed Upon finishing the data input the data can be saved by clicking the SAVE button For a measurement the program requires at least a name The data can however be completed or changed at any time by using FIND
68. e button 9 you select the Scale Move mode You can grab the objects by moving the pointer on one of the eight handles By clicking and holding MB1 you can move the object around By clicking and holding MB2 you can scale the objects By using SHIFT MB2 the scaling will be constraint Note which means that the scale factor will be equal for both horizontal and vertical direction Selecting Objects Click on the Move Scale button 9 Then use the repeated SHIFT MB to se lect the individual object you want to select This can also be done by using select child in the Edit menu By using ALT MB1 you select all objects of one slice This can also be done by using select parent in the Edit menu Deleting Graphical Objects You can delete a single object by clicking on button 6 Strike over the object you want to have deleted by using MB By clicking button 7 you delete all objects of the current active slice By clicking button 8 you can delete all graphical objects of all slices Copy Cut Paste Replace Objects To copy an object first select the object Selecting Objects p 44 then in the Edit menu click Copy or click CTRL C Same procedure is used for the Cut op tion Using Paste from the Edit menu pastes the object in a selected slice as an ad ditional object The Replace function replaces the existing object in the cur rent slice with the previously copied or cut object Evaluation 44 Figure 10 The E
69. e for the intermediate storage of the resulting PostScript File We recommend a filename like sys SCRATCH filename PS Ambient This value corresponds to the scaler of Ambient Light in the interactive 3D Display Program The value can be from O to 100 here to be entered as a value between 0 0 and 1 0 Shading A value of 1 will lead to shadows a value of O not Size This value determines the quality of the 3D image but also affects the calcu lation time Elevation Rotation These two numbers define the position of the observer relative to the object in degrees Copies Enter a value between 0 and 9 and the corresponding number of copies will be printed At the end of printing the result file printfilename will be delet ed If you enter a value of O the file will neither be printed nor be deleted af terwards but is kept on the hard disk This option can be used to print it on a different printer later Once you have measured many samples you might want to have all your re sults in table form to include them into a spreadsheet program You can delimit the range of your samples being listed by entering the mea surement number range uct list Template File UCT 3D LIST SHEET Output File SYSSSCRATCH UCT EVAL TXT From Meas 0 300 To Meas 0 400 The resulting data is written to the file given in Output File The template file input field can be used for different types of report You can modify the
70. e it sits in and twice the mean value of all structure voxels then is the mean thickness To calculate Tb Sp the same procedure is performed for the background of the structure i e object bone and background air are switched To calculate Tb N the spacing of the mid axes is calculated as for Tb Sp Then the inverse of the mean spacing is Tb N Further literature T Hildebrand P R egsegger A new method for the model independent as sessment of thickness in threedimensional images J Microsc 1997 185 67 75 T Hildebrand A Lab R M ller J Dequecker P R egsegger Direct 3 D morphometric analysis of human cancellous bone microstructural data from spine femur iliac crest and calcaneus J Bone Miner Res 1999 14 7 1167 74 vivaCT 80 1 3 109 Appendix F Checklists Checklist for Measurements Switch on Equipment 30 Minutes before first measurement Start main program Enter sample data Start measurement program Insert sample sample holder Choose Define Modify measurement protocol controlfile Perform Scout View a define Scout View region b perform Scout View measurement c if OK set reference line Perform Measurement batch or interactive mode Remove sample Checklist for Evaluation Switch on equipment printer optical disk and computer Start the main program Select evaluation program Select sample and measurement Click on EVALUATION Click on DEFINE VOI Draw volume of interest Positio
71. ects without interpolating non integer voxel locations in the scaled object but takes nearest neighbor approach Computational faster and uses less memory but nearest neighbor choice may create less accurate scaling Does not account for fractional voxels for non integer scaling even if DECterm Based Programs 88 average flag is true e g for down scale 2 6 and average true only 2 voxels are averaged per direction ipl noipscale input im Sea output sca x down scale 2 000 2 000 2 000 up scale 1 000 1 000 1 000 average true gt scale ow elsize noip Same as noipscale elsize but overwrites input Saves memory Does not Work for increasing resolution since output memory would have to be bigger than input memory ipl gt noipscale input output in gt a down scale 2 000 2 000 2 000 up scale 1 000 1 000 1 000 average true gt set value With this command you can set the value of all non zero voxels of a segment ed object to a given value and all zero voxels to another Useful for inverting foreground background of the object and for producing a negative image value object 127 ipl set val input in value object 227 value background 0 concat Concatenates two objects Common region only if two objects with unequal di mensions or unequal positions are chosen this flag controls whether the re gion common to both objects is taken or whether the box
72. ed for the measurement is allocated and then the Reference Intensity IO and dark are measured One projection after the other is then continuously measured The raw data sinograms of a measurement appear consecutively the most re cent always being shown full size at the upper right Cancel See cancel See p 27 of Scout View Scanning Modes Both Scout Views and or Scans can be placed in a task list The tasks from this list can then be started in interactive mode or in batch mode scans only The individual tasks are performed one after the other without any further user intervention This unsupervised measurement mode is similar to batch mode but still under user control through the graphical user interface To use the Scout Views that have been performed through the task list mark the task in the task list and click load scout Adding Tasks The procedure is not much different from the standard way of starting scout views or scans The add scout and add scan buttons will add the selected Scout View or the Scan to the task list for consecutive execution If you perform a Scout View and have defined a reference line you can add the task scan to the list by clicking on the add scan button This may take a few seconds as the Scout View radiography file RAD is stored to the mea surement disk at this stage Confirm the message shown in the image above Measurements 33 vivaCT 80 1 3 Figure 19 Adding Tasks Star
73. ed scripts A typical work flow when using scripts is the following Open the measurement to analyze See Selection of Sample and Measure ment on page 39 Click on the T button Figure 55 on page 50 and select an evaluation script See Evaluation 3D on page 50 e Ifrequired by the script define the region of interest drawing and saving contours or by adjusting the white box See Defining the ROI or VOI on page 43 e Start the evaluation See Starting Evaluation on page 52 The evaluation will then be started and run in batch mode Depending on the size of the image data complexity of the evaluation and the available comput er power the task will take from a couple of seconds to many hours or days To see which jobs are running open a Terminal Session Windows and write que Evaluation 36 Most scripts produce a series of results that can be found in the measure ment folder or will be send directly to the printer See Morphometric Results on page 52 for example of results Overview With the evaluation program you can perform the following functions view slices XY XZ YZ view enlarge zoom document print convert EPS TIFF DICOM distance measurements measure angles display histograms view profiles linear attenuation coefficients along lines examine linear attenuation coefficient at cursor position define and analyze ROI Region Of Interest 2D ROI with different shapes rectangle ell
74. erVer sss EEG EEG EE E I Y E d I Y XY EN CENA 59 Light SOUTO e rre e vite side den ID ID CI LACE CISCO I E 60 Other Effects see aki eee Oeo o de eere een 60 EE EE 61 Subditnensioning ii Ie tot e EGG d ex x e xen x uera 61 Display modes es toe t ee E 61 eje elo ID NEE 62 Object Properties e dcn cede dee eed dd dice E ede ec 62 Color Mixing for color model Dicker 64 Printing Of JDsScenes esse edet eere TO pe ve TRE EE E EAE AE 65 eege ue 66 Preset menu E dd eto deci dude deve Ns 67 Start Archiving PrOgTafQ ee re A RN NR A EM 68 Archiving Protan deeg n IC ERES ase E use sen o e ts 69 Selecting Measurement 5 3 nne ea eee 70 Selecting File LP TENA e eda died asta NER NEN ERE REPRE REIR NRI 70 Selecting destination device erario tote BETATT ATOE OR ATPAREN 71 Selecting File Type for copying carrar rana tena tana Te EEE emere 71 Backup Options euer a 73 Device Informatioti 4 Sr Sie cens o 74 GAUSS MT I 80 117 Numerics 2D Evaluation eege en 48 2D Reconstruction ococcccncnnoncnnoncnnoncnnnnos 76 3D Result Sheet ee EE 92 3D Effects LightSource ou E e casdn 60 OBSEVE ee 59 Perspective coccoccncnncnnncnncnnonccncononnnnno 60 e TE 60 3D Evaluation esee 50 3D Histomorphometry eseesss 77 A ACCUTLAGY ee ca a 97 Adaptive Threshold oococcoccncnccnccnccncnnccnos 80 Adjusting Scan Range esee 27 Animation Sequence Calculatide andador 65 B e tetetdiu
75. ersons should access to the inside of the housing Do not manipulate the system Be aware that the scanning of a live animal exposes the animal to radiation Safety Information xxi vivaCT 80 1 3 Electrical Installation and Damaged Cables Electric Shock Touching electrical connections inside the instru ment or damaged cables may lead to electric shock and serious health risk In case of dam aged cables disconnect the equipment from the power supply and call SCANCO Medical AG for service Safety Information xxii Safety Measures Caution Only original spare parts should be used Only nonflammable gas for anesthesia should be used e g Isoflourane 1 I Caution When using narcotic gas the room must be suffi ciently ventilated and national and local regulations must be taken into account Emergency stops and switches vivaCT 80 1 3 Safety Information xxiii 1 Capture Key The scanner works only if the capture key is present and both main switch and capture key are activated green lamp is lit 2 Emergency Stop Pushing the emergency stop button will immedi ately interrupt the main power 3 X Ray Indicator 4 Control panel SCANCOMEDICAL eent ooi Zum T When the power needs to be disconnected the appliance coupler is the dis connecting device that cuts both power supply phases vivaCT 80 1 3 Safety Information xxiv 1 Startup Procedure vivaCT 80 Connections Mains
76. es can cause inaccuracies Dust smoke Pollution degree Vibrations Placement Altitude Over voltage category Measurement Method Measurement type Measurement area Accuracy Slice Thickness Image Matrix Resolution Archiving Tomograms Dimensions Scanner Computer Operate the system in a clean environment Accumulations of dust or other particles can damage sensitive parts SCANCO Medical AG recommends a smoking prohibition in the area of the MicroCT 2 Vibrations can have negative influence on results Place the instrument on a flat and sta ble surface free from vibrations The equipment is to be used indoor only Max 2000m II Computed tomography small angle cone beam Y max 80 mm scan length max 145 mm 5 156 um 512x 512 to 4096 x 4096 pixels 5 156 um nominal pixel size to tape Streamer 1750 2030 x 1230 x 910 mm HxWxD with x ray warning lamp 750 x 580 x 390 mm HxWxD approximately value depending on individual configuration Specifications 97 Weights Scanner approx 300 kg Computer 25 kg approximately value depending on indi vidual configuration Mains Connection vivaCT 80 100 230 V AC 50 60 Hz 400 VA Mains supply voltage fluctuations must not exceed 10 of the nominal supply voltage Mains Fuses vivaCT 80 2xT6 3A Replacement of fuses The fuses can be changed by the user and are placed in the back of the scanner
77. ety tests for the purpose of preventing hazards and the necessary settings for optimum image qual ity and minimum exposure to radiation is performed in order to meet reg ulatory requirements After Service and or e Perform a weekly and a monthly test with QC phantom see above Maintenance Visits vivaCT 80 1 3 112 Maintenance and repairs must be entered in the medical device logbook in cluding the following data Spare Parts Disposal Cleaning Type and scope of work If necessary details of any change to settings or the working zone Data person performing the work signature The replacement of spare parts not supported by SCANCO MEDICAL AG or the replacement of spare parts by unauthorized people could negatively af fect the functionality of the XtremeCT II and leads to the loss of the CE conformity according to the Medical Device Directive 93 42 EEC and may no longer be conform to relevant standards Caution Replacement of computer should be made in agreement with SCANCO MEDICAL AG The equipment contains low quantities of several materials which may be hazardous to the envi Caution ronment if not disposed correctly Please consider local regulation and contact SCANCO MEDICAL AG before disposal of equipment or X ray tube Equipment For outside cleaning use soft materials moistened with water only vivaCT 80 1 3 Equipment must be turned off before making any cleaning action Clea
78. f freqis the Hamming filter lowpass frequency in units half the Ny quist frequency 0 5 is a filter rolling off to O just at the Nyquist boundary Hamming amp is the amplitude of the Hamming filter its default is best not var ied ipl fft laplace input in gt in output 1h gt out redim pow2 0 0 0 gt laplace eps 0 900000 lp cut off freq 0 400000 hamming amp 1 000000 norm max Norm max has to be applied after ft laplace hamming to convert the float val ues to short again max in the input will be set to the maximal possible value of the chosen data output type type out 32767 for short as will all values above max The values from zero to max will be scaled to the data range avail able for the output data type With examine 1h histo the histogram of the fft laplace output can be viewed and a suitable max can thus be chosen normally a value at the upper end of the main distribution The range of the fft laplace output can vary greatly for different types of objects since the curvature can be very different It is advised however to use the same value for max for one type of sample i e within one study population The value is not very crucial as long as it is above the respective value that is thresholded afterwards to produce a binary image ipl gt norm input 1h output norm max 50000 000000 type out short gobj maskaimpeel ow Performs a masking of
79. facturer Hamamatsu Photonics K K Model U I L8602 70kV 0 18mA AA X CE Figure II 1 Type Plate vivaCT 80 1 3 Important Information xvi 2x T6 3A H 290V Figure II 2 Fuses to be Used Disposal Waste Electrical and Electronic Equipment WEEE The symbol shown left is marked on the product type plate which indi cates that this product must not be disposed of with other waste The instrument contains low quantities of several materials which may be hazardous to the envi ronment if not disposed correctly Please contact SCANCO Medical AG before disposal of instrument Caution or X Ray tube Disclaimer SCANCO MEDICAL AG will not accept any claims for compensation for any damages incurred in connection with this instrument and software SCANCO MEDICAL AG will not be liable for technical or editorial errors or omissions contained herein nor for incidental or consequential damages resulting from the furnishing or use of this material Declaration of Conformity With the CE marking SCANCO MEDICAL AG confirms compliance with the European directives stated below vivaCT 80 1 3 Important Information xvii vivaCT 80 1 3 SCANCO MEDICA EU UE KONFORMITATSERKLARUNG DECLARATION OF CONFORMITY DECLARATION DE CONFORMITE Wir We SCANCO Medical AG Nous Name des Anbieters supplier s name nom du fournisseur Fabrikweg 2 CH 8306 Br ttisellen Anschrift address adresse erkl
80. g sample etc or if the Scout View is not optimal and you need to Measurements 27 Relative offset mm from reference line to start of scan The absolute offset is set to 22 0 mm vivaCT 80 1 3 reposition the sample you can use this function to return to the main win dow Correct the errors and start again with the Scout View Examples of Scout View modes In the examples below cases of Offset given in mm or 96 from the reference line to the start center and end of the stack are shown Figure 13 Example relative offset mm from reference line to start of scan Measurements 28 Relative offset 96 from reference line to start of scan The off set is set to 496 of 420 mm 16 8 mm vivaCT 80 1 3 Figure 14 Example relative offset from reference line to start of scan Measurements 29 Relative offset 96 from reference line to center of scan The offset to the first slice is 296 of 420 mm e g 10 2 mm total scan length 2 3 3 mm vivaCT 80 1 3 Figure 15 Example relative offset Y from reference line to center of scan Measurements 30 Relative offset 96 from reference line to center of scan The offset to the first slice is 2 of 420 mm 10 2 mm total scan length 2 18 6 mm vivaCT 80 1 3 Figure 16 Example relative offset 90 from reference line to end of scan Measurements 31 Measurement Click on the SCAN button The follow
81. gion if inter est created by the contours and or the white box To start the 3D evaluation click on the T button or click on menu TASKS followed by EVALUATION 3D Figure 17 3D Evaluation Evaluation 50 vivaCT 80 1 3 The following window appears at the lower right Figure 18 3D Evaluation Subwindow Selecting an Evaluation Task By clicking on SELECT an Evaluation Task can be chosen from the list of cur rently available scripts See below for more information about the Evaluation Scripts Defining VOI If you have drawn any graphical objects before a white bounding box around all your objects appears on the screen If you have not drawn any contours a default sized box appears in the middle of the image The bounding box de limits the valid area for the evaluation You can move the VOI around by clicking and dragging on one of the selec tion points using MB1 or you can resize it by clicking on one of the selection points using MB2 By clicking on Default VOI the bounding box will automat ically be placed around the contour You can also define or adjust the position or dimension of the VOI by directly entering the coordinates sizes using the keyboard Segmentation For most Evaluation Scripts choose Sigma and Support of the Gauss filter and lower and upper THRESHOLD to binarize segment your image If the script is not locked the proposed segmentation values can be modified After clicking on Prev
82. gram to print 3D Result Sheet UCT LIST UM UCT_LIST EXE DB Query 3D Histo UPAT_LIST UM UPAT_PRINT_LIST EXE DB Query 3D Histo WRITE_INFO UM UCT_WRITE_INFO EXE DB Query Sample Info Reconstruction vivaCT 80 1 3 If for any reason e g insufficient disk space the slice reconstruction was not successfully finished or you have destroyed the reconstructed Slice data ISQ but still have the RAW data RSQ you can reconstruct the missing slices with this program Start it using the following command UCT_RECONSTRUCTION Raw Data File DISK3 MICROCT DATA 00000033 00000680 C0000372 RSQ SliceSelection N 1 slice or N M from to or A all SliceNr 0 222 Neg to stop 17 34 You first have to enter the input filename which is the RSQ file Then you define which or how many slices to reconstruct You can give the following values e AThis means reconstruct ALL slices e N Enter one value then this slice will be reconstructed and you will be asked again To end the program enter a negative value e N M Reconstruct a range from slice n to m so enter e g 5 19 Most programs operated in the terminal start counting the slices at O while the standard user programs start counting at slice 1 You might have to adjust for this difference of 1 Note DECterm Based Programs 76 IPL Image Processing Language vivaCT 80 1 3 This program can be used as a supplement to the scri
83. he contour remains square Draw Ellipse Circle Contour By holding down the SHIFT button while drawing the contour remains a circle Delete Contour Deletes one contour of the current image by crossing over it with the MB1 Delete A11 Contours Deletes all contours of the current image slice Delete Contours of All Images Deletes all contours of all images Move MB1 Scale MB2 contours Open Contouring Subwindow Also possible with double click on main window or via menu TASKS Figure 9 Drawing Icons Drawing Contours Choose the slice where you want to draw a contour by clicking on the appro priate field or by entering its number Then click on one of the drawing options CONTOUR CIRCLE ELLIPSE or SQUARE RECTANGLE Button Button 1 4 or 5 You can get circles squares by using SHIFT MB1 Note Without the SHIFT modifier you can also draw el vivaCT 80 1 3 lipses rectangles Evaluation 43 vivaCT 80 1 3 Drawing a contour has to be performed counter Note clockwise to analyze its interior A clockwise con tour excludes its interior Modifying Contours You can modify contours by clicking on button 2 or 3 Then draw over the contour you want to modify You have to keep the same drawing direction counter clockwise The original object has to be crossed at least twice The part between the first and last crossings will be replaced by the new drawing Moving Scaling Objects By clicking on th
84. he same way as with the QC1 mea surement If you have a deviation of more than 596 to Rod Volume please contact SCANCO MEDICAL AG Quality Control 35 General 8 Evaluation 2D and 3D evaluations can be performed on either a rectangular cubic vol ume or any irregular shaped ROI VOI Region Volume Of Interest The ROI VOI is defined by a set of Graphical Objects GOBJs which can be contours or geometric objects such as rectangles or ellipses The ROI VOI has to be drawn on a slice based method The 3D shape can be defined by either drawing objects on all consecutive slices or by creating a hull between any two slices interpolating the intermediate contours mor phing The defined ROI VOI is saved to disk and will be reloaded once the measure ment data is being reloaded Exactly the same VOI thus can be re evaluated at a later time For fully automated contouring scripts are available that work for certain types of scans Please contact SCANCO MEDICAL AG Starting the Evaluation Program Enter your name into the operator field See p 11 and click with MB1 on the button with the evaluation symbol in the main program vivaCT 80 Operator I Edit 4 BE e B Figure 1 Start Evaluation Program Standard Evaluation Procedure vivaCT 80 1 3 The evaluation program offers numerous possibilities of analyzing and evalu ating the data either directly in the Graphical User Interface or by using pre defin
85. he user must be sure that the unit and its accessories are in good working order and the appropriate accessories are present Inspection by the user Defective indication lights damaged components labels and warning signs Inspection by the user Irregularity of the display flickering breakdown Inspection by the user e System start up test with QC phantom Weekly QC See Weekly Phan tom Measurement QC1 on page 35 e Incase of operational defects or other deviations from normal opera tional behavior occur switch off the equipment and inform the Service Organization Monthly Tests QC2 test with QC phantom Geometry QC See Monthly Phantom Measure ment QC2 on page 35 Oncea week the system should be turned off so that the shutter fail save test will run during the next start up Monthly Performance fno scans were made over a longer period please perform a test with the QC phantom as described in weekly tests at least once a month to conserve the stability and the durability of the X ray tube Oncea month the main switch should be turned off so that the safety relay will be tested during the next start up vivaCT 80 1 3 111 Table 1 Interval Operation Yearly Maintenance Have the X ray unit serviced by SCANCO MEDICAL AG at least once a year Heavily used X ray equipment might need maintenance more fre quently All the necessary maintenance including the saf
86. ic printer by clicking on the PRINT COLOR button Do not switch off your computer SHUTDOWN be Note fore you have received all the print outs Distance 3D To measure the distance between two points in 3D click on menu TASKS fol lowed by DISTANCE 3D Figure 22 Distance 3D The following window appears Figure 23 Distance Measurement Select the 1st slice where you want to set a marker Then click on GET POINT A using MBl and move the cursor to the main window As you move the cur sor the coordinates appear in the window at A If you have found your Posi tion A click using MB Proceed the same way for Point B You also can manually enter coordinates using the keyboard The distance from Point A to Point B is displayed in the window every time you click in the main window or enter coordinates using the keyboard Two green markers indicate the positions vivaCT 80 1 3 Evaluation 55 Use CANCEL to terminate 3D Distance measurements Pointer Ruler Profile Angle Tools vivaCT 80 1 3 Pointer Ruler Profile Angle Tools By clicking on the buttons shown alongside you can 1 2 Show Image Values at Cursor Position Show Histogram of image within the region of interest Show Profile along a user defined line The start and end point of the line can be moved using MB1 Determine Distances between two points in the image along a line The start and end point of the line can be moved
87. iew the Main Window shows the result of the segmenta tion and the Evaluation Window shows the histogram of the gray scales and the volume fraction of the segmented object s Toggling between preview and grayscale allows you to fine tune the segmentation parameters The histogram and the volume fractions that are shown in the Evaluation Window are computed Note on what is visible in the Main Window and inside of the contour if you zoom in on a region only the histogram of the zoomed region is shown Evaluation 51 vivaCT 80 1 3 If your chosen script can handle multiple objects click on the radio buttons numbered 1 to 4 Object 1 to Object 4 to change the settings for the different objects The unit selector to the right of the radio buttons allows you to spec ify in which units the threshold is given Order of Precedence in most scripts if multiple objects are selected and their thresholds are overlapping object 1 wins then object 2 then object 3 then object 4 Starting Evaluation The green objects indicate the VOI which will be used for the 3D evaluation The VOI is further delimited by the white bounding box The volume inside of the white bounding box will be written to disk as an aim file Everything out side the bounding box will not be evaluated nor be displayed in 3D If you have set your VOI click on START EVALUATION and the evaluation im mediately starts as a batch process this means that you can now exit the
88. ing window will appear BEEN paraa Figure 17 Start Measurement Start Measurement Click on the START MEASUREMENT button with MB1 The computer system first allocates the disk space needed for the measurement and then starts the measurement The raw data sinogram of a measurement appear progres sively Cancel See cancel above of Scout View Zoom Pan in Scout View Once you have performed a Scout View interactive or reloaded via task list you can zoom in in the upper window using MB2 Dragging downwards will zoom in dragging upwards will zoom out For panning use the right mouse button and drag the image in any direction Adjusting Brightness in Scout View If you use the SHIFT MB button and drag the mouse upwards or downwards within the Scout View window you can increase or decrease the brightness of the currently loaded image High Resolution Radiographs The Scout Views are stored in low resolution SCV In addition to this for mat a high resolution image RAD native scanner resolution is stored in the directory of the corresponding measurement The image can be viewed in the Evaluation program V6 5 vivaCT 80 1 3 Measurements 32 Single Measurement Task List vivaCT 80 1 3 Click on the SCAN button The following window will appear Camel Start Measurement Figure 18 Start Measurement Start Measurement Click on the START MEASUREMENT button First the disk space need
89. into two sections One section is designed for testing the stability of the density measurement and the other for the stability of the geometric parameters For scanning the two sections a corresponding locked controlfile is provided for each of them The evaluation of the phantom mea surements is performed by an automated procedure that is started in the Evaluation Program Evaluation p 36 Figure 1 Image Phantom Weekly Phantom Measurement SCT It is very important to regularly run the QC1 measurement and to compare the results with the reference values Turn on the system and start the measurement program Select the controlfile for the weekly phantom measurement Insert the phantom Check the proper positioning of the phantom Start the measurement Q ug up Start the evaluation program and load the QC1 Check that all slices have been reconstructed Then start the evaluation Task button T and then click Start Evaluation button and you will get a printout Compare the measurement results with the reference value If you have a deviation of more than 16 mg HA ccm to Mean 5 please contact SCANCO MEDICAL AG Monthly Phantom Measurement QC2 vivaCT 80 1 3 Use the same procedure as with the weekly phantom measurement but select the controlfile for the monthly phantom measurement QC2 The reconstruction of the measurement will take longer than that from the QC1 measurement Start the evaluation t
90. ipse contour analyze ROI attenuation coefficient determine area histomorphometric evaluation 2D amp 3D create data set for 3D Display Animation 3D Histo BCT Evaluation Program V 5 1 File Edt Zoom Tasks UT Options Scripts ei mp sv E 2 N go bee EG A k 3 PI X Y lpk Value Dk o F2 X V bok m oo Well od Distance mm 0 Area rsch 9 9 Angle tk 0 IN E V le ES jr Figure 2 Overview Evaluation Program 1 Drawing Symbols Icon Box By clicking on these symbols the function which will be applied is selected These functions can only be used in the Main Window 4 See Defining the ROI or VOI on page 43 2 Orthogonal View Selection Main Window Selection of orthogonal view in the Main Window Note as per default only 16 slices are loaded first the XZ and YZ views are interpolated It is recommended to use LOAD 10 in XY mode first to load all the slices first before switching to XZ or YZ For large data sets this can be a rather time consuming operation 3 Image Information Controls Temporarily hide the contour the scale bar or the sample info for printing e g vivaCT 80 1 3 Evaluation 37 vivaCT 80 1 3 Caution Caution Main Window In this field the image being operated on current picture is shown As soon as the mouse pointer moves in this field and MB is pressed and or is held down the drawing function selected in field 1 takes place
91. irst measurement is automatically saved when the scan is started and is shown for every follow up measurement of the same sample The function SAVE therefore is only used if the reference Scout View for some reason should be replaced The Scout View is saved as a SCV file low resolution and a RAD file high resolution Print Scout View Use this button to make a hardcopy of the image on the top right of your screen You can choose between PostScript sheet including sample name number etc or Encapsulated PostScript and TIFF format image data only file only Add Scan Batch Measurement This button will put the measurement you have just defined into the task list You can define multiple measurements Add Scan Power Down Same as above But the X ray tube is powered down after the scan You can do either a single interactive scan by set ting the reference line then just clicking on OK and then clicking on START SCAN on the main Note screen Or you can perform multiple scans by clicking on ADD SCAN for each scan to be per formed and then clicking either on SUBMIT SCANS or going via the task list OK When you have positioned the reference line as prescribed See p 25 click on the OK button to start an interactive measurement This button also saves the Scout View to disk if it is the first Scout View for that specimen Cancel If you notice an error in your inputs for example wrong measurement proto col wron
92. is a part of the MicroCT and may not be copied onto a computer other than that delivered with the instrument The operating system software OpenVMS DECwindows Motif is licensed for this computer only and may only be copied for safeguarding purposes Installation of the equipment may only be carried out by SCANCO Medical AG or SCANCO Medical AG authorized personnel To assure adequate circulation of air for cooling make sure that the instrument is located at least 10 cm away from the wall on the back of the in strument Caution For the radiation safety the customer is responsible that national regulations are followed The equipment may only be moved by SCANCO MEDICAL AG or SCANCO ME DICAL AG authorized personnel Crate Your equipment was delivered in a specially designed crate This crate en sures that your instrument is protected against physical damages while transportation Please retain the material in case the instrument should be moved for any reason Maintenance of the equipment transportation and re installation in a diffe rent place may only be carried out by SCANCO MEDICAL AG or SCANCO ME DICAL AG authorized personnel Never remove or open any covers or parts of the equipment and do not manipulate the system A yearly maintenance by SCANCO MEDICAL AG or SCANCO MEDICAL AG authorized personnel is rec ommended For more information about preventive maintenance See Preven tive Maintenance on page 111 Impo
93. isplayed object align the scaler be tween 100 and 100 96 O is an exact cut through the middle of the object parallel to the monitor layer Figure 9 Cutplane Subdim Click on menu subdim to open the following subwindow Changing the scalers allows you to perform virtual cuts through the object along the principal axis of the image volume Figure 10 Subdimensioning Mode There are five different display modes available as are listed in the figure be low Figure 11 Display modes Object Values Click on menu OPTIONS followed by VALUES to open the following subwin dow You can change the brightness of the displayed image and the color lookup table You may want to enter Zero for Min for better contrast To fur ther increase brightness enter a lower Max value than proposed Click on the color bar to toggle between different colors Click on OK and click into the 3D Display 61 main image for a new image build up To change the color look up table click on the colorbar Datamin we object mm w Figure 12 Object Values Object Properties Click on menu OPTIONS followed by Object display properties to open the following subwindow This allows you to show or hide objects to change its colors etc Find a more detailed description on our Webpage FAQ Figure 13 Object Properties 1 The two sliders at the top selects different objects in the aim file
94. ker P R egsegger Direct 3 D morphometric analysis of human cancellous bone microstructural data from spine femur iliac crest and calcaneus J Bone Miner Res 1999 14 7 1167 74 Connectivity Density vivaCT 80 1 3 Connectivity density Conn D is calculated with the Conn Euler method of Odgaard et al Their boundary edge problem suppression is applied on the surfaces of cubic AIMs but not on the possibly artificial surface of contoured GOBJ determined volumes Usually conforming volume of interests are much larger than cubic ones so the boundary problem has a much smaller effect For measurements of intact bones we propose to calculate the connec tivity of the complete bone incl cortex or to put an artificial cortex around the spongiosa again with the help of the GOBJ create mask aim from GOBJ with gob to aim concat with segmented object with concat inputl seg input2 mask output shelled seg common true add true make edge true Cl shelled seg then gobj maskaimpeel ow shelled seg again to calculate re lative masked volume then calculate connectivity with conn nocl shelled seg Further literature A Odgaard H J G Gundersen Quantification of connectivity in cancellous bone with special emphasis on 3 D reconstruction Bone 1993 14 173 182 108 Structure Model Index With this index the structural appearance of trabecular bone is quantified The triangulated surface is dilated in normal direction by a
95. lfiles define all measurement parameters for the scan There are two types of controlfiles e Pre defined with fixed measurement protocols e User defined types can be altered by user Selecting a Controlfile Select the desired controlfile by clicking on one item of the list Modity Delete New _tock Figure 6 Selecting a Controlfile After the controlfile is selected you can perform a scan or a Scout View by clicking on either SCAN or SCOUT Creating a new Controlfile If you want to define a new controlfile click on NEW and the controlfile de finition box appears Measurements 20 vivaCT 80 1 3 Deleting a Controlfile If you have selected a user defined controlfile you can delete it by clicking on DELETE You have to confirm the deletion of a controlfile Locking a Controlfile If you have created or modified a user defined controlfile you can lock it and hereby prevent its further modifications or deletion Click on LOCK for this purpose and confirm your action Locked controlfiles can not be modified anymore except for the number of slices to be scanned Note Modifications of a locked control file has to be saved as a new controlfile using the save as new button Modifying a Controlfile Basic Mode You can alter a controlfile before starting the measurement by clicking on MODIFY Iviva80 Test Figure 7 Modifying a Controlfile Basic Mode Measurements 21 vivaCT 80 1
96. measurement the program requires at least a name The data can however be completed or Note changed at any time i e address change change of name because of marriage etc by using FIND changing the data and then finally using UPDATE Possibilities Find The following data entry window appears by clicking the FIND button o mea Heb Figure 3 Select Sample Click the data input field and fill it in as required Confirm your input by clicking the OK button Upon entry of a number or of the complete entry of the operator s name the data will appear in the fields If only the first few let ters of a name are entered then a list showing all operators starting with these letters will appear Thus if O is entered the list will show all opera tors whose name starts with O such as Operator 1 Operator 2 etc 06 cancel Figure 4 Select Operator Click on the desired name and confirm the entry by clicking OK vivaCT 80 1 3 Edit Operator Data 11 Always use the same spelling because the search Note SC is case sensitive The possibility now exists of changing or completing data Find Next By clicking the FIND NEXT button the next operator in alphabetical or nume rical search order will appear depending on whether you entered the opera tors name or number while using FIND New If you click on the NEW button all fields are cleaned to enable new operator data to be entered Sav
97. mple Registration Program on page 13 Enter the corresponding data See Measurements on page 16 After you have chosen or entered a sample name the main measurement window appears If the sample is not being measured for the first time its vivaCT 80 1 3 Measurements 18 vivaCT 80 1 3 measurements history will be displayed with date and number of slices You can now mount the animal bed Caution The animal must be placed in an appropriate holder Be extremely cautious about putting only animal beds which fit into the bore Be aware that the animal bed will be moved into the bore Caution Be extremely cautious that the whole animal fits into the bore when moving the animal bed into the scanner Caution Caution Before closing the door make sure that the ani mal bed is aligned and locked Make sure that absolutely no fluid is dripping Caution into the scanner The instrument can be seriously damaged Before use check the animal bed for leaks Measurements 19 Figure 5 Information on the Measurement sample If you selected NO in Figure 21 Confirmation on page 18 or would like to change or modify the sample name or number this can be entered by clicking on Other Modify or New in Figure 22 on page 20 Controlfiles Measurement Protocol vivaCT 80 1 3 After choosing the sample name now select a pre defined controlfile or set up a new controlfile for your scan Controlfile Types The contro
98. n with the number of bins given with nr bins in tab The number of bins in the bar column representation is not affected by nr bins in tab DECterm Based Programs 87 vivaCT 80 1 3 ipl histo input in rat fileout or screentab none my histo tab from val 1 gt 1500 to val 1 3000 nr bins in tab SL gt scale_elsize Using this command you can change the voxel size of your object down_scale enlarges the voxel size reduces the resolution up_scale makes the voxel size finer Non integer scaling can either be given directly e g with down_scale 1 5 or with a combination of down_scale 3 and up_scale 2 The effect is exact ly the same the latter may just save you a division by hand The integrate flag controls whether averaging of voxels is done in down scaling and poten tial interpolation of partial voxels and whether interpolation is done in up scaling It is suggested to use integrate true for gray scale images but integrate false for binary segmented images to preserve the binary status Otherwise a subsequent thresholding operation may be needed to ensure a binary image again Scale_elsize automatically selects among the below described procedures ipscale_elsize and noipscale_elsize according to whether there are frac tional voxels who may then be interpolated gt ip For integer down scalings noipscale is chosen for non integer down scalings and any up scalings ipscale is chosen The exception
99. n VOI using MB move or MB2 scale or enter values directly with keyboard Check Dimensions of VOI should be equal Rectangles indicate VOI for 3D Display Circles indicate VOI for 3D Histomorphometric Evaluation Click on START EVALUATION Exit program Checklist for Shutdown vivaCT 80 1 3 Exit from the main program click on EXIT button optional End Session using Session Manager Enter Shutdown as Username press RETURN twice Wait approximately one minute Switch off equipment 110 General Maintenance Plan Appendix G Preventive Maintenance Maintenance Due to use of the equipment and environmental influence the equipment needs maintenance in regularly intervals By entering into a service agree ment with SCANCO MEDICAL AG you maintain the value and safety of your X ray equipment The user is responsible for the adherence of maintenance schedule Implication of Lack in Maintenance The lack of preventive maintenance may lead to reduced instrument perfor mance of your instrument or falsification of results Accomplishment of Maintenance Maintenance consists of tests which the user can perform and maintenance which is performed by SCANCO MEDICAL AG or by persons explicitly autho rized by SCANCO MEDICAL AG For continued reliable and safe operation of your equipment yearly mainte nance is strongly recommended Table 1 Interval Operation Weekly Tests QC1 Before each use t
100. n either SEGMENTED ALL FILES or ANIMATION Then click on the sample you want to display If there is data of the corresponding type available it appears on the right side Click on the measurement you want to display The data is loaded after you confirmed your choice with OK To display the data click on the START button at the bottom left of the screen vivaCT 80 1 3 3D Display 58 Start Stop Visual Effects vivaCT 80 1 3 Start the calculation of the 3D Scene by clicking on the START button You can interrupt the calculations by clicking on the STOP button Eed Figure 5 Start Stop Calculation Alternatively you also can click with MB into the main window to start stop the calculation and the display In ANIMATION mode they start stop the animation Observer By changing the ROTATION ELEVATION and ROLL of the observer you change the angle from which you look at the object You can also move the object horizontally by changing the value for Translation H and or vertically by changing the value for Translation V Figure 6 Observer Alternatively you also can click with MB into the main window and as you move the cursor up and down you change the ELEVATION if you move left or right you change the ROTATION If you release MB1 the calculation starts If you click with MB3 into the main window and as you move the cursor up and down you can change the Translation H and the Translation V If you
101. n infinitesimal amount and the new bone surface and volume is calculated By this the de rivative of the bone surface dBS dr can be determined The SMI is then dBS BY dr BS SMI 6 and relates the convexity of the structure to a model type Ideal flat plates have an SMI of 0 no surface change with dilation of the plates whereas ideal cylindrical rods have an SMI of 3 linear increase in surface with dilation of rods Round spheres have an SMI of 4 Values below O can come from air bubbles within the bone concave structure gives negative dBS dr Artificial boundaries at the edge of the volume of interest are not included in the calculation and thus suppressed Further literature T Hildebrand P R egsegger Quantification of bone microarchitecture with the structure model index Comp Meth Biomech Biomed Eng 1997 1 15 23 Distance Transformation Methods By distance transformation the calculation of the metric distance of every bone object voxel to the nearest bone air background surface is under stood These distances can be imagined as the radius of a sphere with centre in this voxel that fits inside the structure Then redundant spheres are re moved big sphere eats small encompassed spheres The result is the mid axes transformed structure with the centres of maximal spheres filling the structure completely To calculate Tb Th each voxel then gets the value of the radius of the maxi mal spher
102. n it by using cotton cloth and don t use abrasive detergent Do not use organic solvent or any kind of detergent containing any kind of organic solvent Do not utilize spray it can penetrate into the equipment and damage the electronics inside Ensure that no water or other liquids can enter the X ray equipment This precaution prevents electrical short circuits and corrosion forming on components To disinfect the equipment we recommend using water based solutions connecting cables by wiping only We recommend to not utilizing aggres sive detergent based on Alcohol If you perform room sanitation with an atomizer you must first switch off the X ray equipments capture key When the X ray equipment has cooled down cover it carefully with a plastic sheet When the mist of disinfectant 113 has subsided you can remove the plastic sheets and disinfect the X ray equipment by wiping Shut down properly and turn off capture key before 1 Caution cleaning Never spill liquids on or in the equipment Never use any corrosive solvent or abrasive deter ion Caution gents or polishes If you use disinfectants which form explosive mix Caution tures of gases these must first have evaporated be fore you switch the X ray equipment on again Contact Information for Service and Maintenance vivaCT 80 1 3 SCANCO Medical AG Fabrikweg 2 CH 8306 Bruettisellen Switzerland Telephone 41 0 44 805 98 00 Telefax 41
103. ng box or along the defined cutplanes Like surface Uses the same surface color as for the rest of the object Object color Uses the same surface color as for the rest of the object Face color Uses a user defined color for the face This color can be changed by clicking on the colorbar that appears when you select this option Value color The face is colored according to the value of the object that is saved in the file The color lookup table can be changed using the Object Values interface Figure 74 Object Values on page 62 Change the color of the ambient and direct light using left and middle color button Change the color of th background by clicking on the right color button The slider is active for transparent objects where it regulates how many transitions between objects or object air that are displayed Printing options Clicked toggle buttons are information that will be printed in the 3D window Options Print Name Print LUT Look up table Print Scale Print Company 3D Display 63 vivaCT 80 1 3 Color Mixing Clicking on a color bar in the object properties subwindow opens the color mixing subwindow which allows you to toggle between different colors Figure 14 Color Mixing for color model Picker 1 Color model Picker Use the interface as described in the points 2 4 HLS Adjust the sliders for Hue Lightness and Saturation to obtain the color of your choice RGB Adjust the sliders
104. nor inaccuracy of the vertical position you select on the Scout View and the volume which will be scanned To enhance the positioning accuracy with the Scout View you can reduce the number of detection lines on the detector used for the ScoutView 13 Measurements 22 vivaCT 80 1 3 10 Start Position of Scout View This value appears in the Scout View Dialog Box as the default value and can be altered for each measurement individ ually 11 End Position of Scout View This value appears in the Scout View Dialog Box as the default value and can be altered for each measurement individ ually 12 Angle Scout View Mode only rotating the object for a better visual pre sentation of the object 13 see Advanced Mode 14 There are 4 modes of the resolution option TABLE 1 Resolution Acquisition Reconstruction vivaCT 80 Standard 250 Projections 1024 x 1024 Medium 500 Projections 1024 x 1024 High 1000 Projections 2048 x 2048 Custom up to 1500 Projections up to 4096 x 4096 Scan Mode Number of Projections 180 Image Matrix 15 FOV Diameter Choose the diameter of the field of view the number indi cated is the size of the reconstruction area FOV sizes not marked possible Marked Yellow possible FOV smaller than diameter of sample holder for local tomography Marked Red not possible 16 Voxelsize When Default Size is selected the voxelsize is shown in the slider The chosen voxel
105. nuation is impossible can also oc cur by ERROR Italic text shows what you can do yourself against the error If there is no italic text after the error message contact SCANCO MEDICAL AG Creating directory Write error on the hard disk Creating operator logical Operating personnel cannot be registered Try starting the program again Decoding Measurement Nr Measurement number invalid Decoding Sample or Patient Nr Sample or Patient number invalid Decoding Site Measurement site invalid Decoding Slice Number Image number invalid Deleting indexed Record An entry in the database cannot be deleted Disk must have a name Diskette was not initialized formatted Initialize the diskette Encoding Slice Number Image number invalid End of file No more records available There are no further entries to be read in the database as you have reached the end File Read Error A tomogram cannot be read Usually appears only when a measurement was interrupted or if the images belonging to a measurement have been deleted Freeing logical unit number General database error Getting Binary Time The time cannot be determined Getting current date time The time cannot be determined Getting free logical unit number General database error Getting number of free blocks Free space on a storage device cannot be determined Getting volume name The label of a storage device cannot be determined Keyword not f
106. nventions Within this manual special text formates will appear Below you find the for mate related meanings Action performed by the operator Text which is entered by keyboard SOFTWARE BUTTONS ON THE COMPUTER SCREEN Cross references Hyper links Abbreviations e MBl Mouse Button 1 i e left Mouse button MB2 Mouse Button 2 i e middle Mouse button e MB3 Mouse Button 3 i e right Mouse button User s Guide Updates The latest release of this document may be obtained contacting SCANCO MEDICAL AG Target Group and Users Qualification These instructions are intended for users who have been instructed by SCANCO MEDICAL AG or their authorized representatives This equipment must be handled only by qualified people and in accordance with the operating instruction Only trained and qualified personnel should have access to the equipment Manufacturer and Contact for Service or Support SCANCO Medical AG Fabrikweg 2 CH 8306 Bruettisellen Switzerland vivaCT 80 1 3 Important Information xiii Telephone 41 0 44 805 98 00 Telefax 41 0 44 805 98 01 URL www scanco ch e mail general info scanco ch e mail support support scanco ch e mail sales sales scanco ch User s Responsibility The user is obliged to the read safety instructions before operating the instru ment Software Licence Agreement Installation Transportation Maintenance vivaCT 80 1 3 The software described in this document
107. o the next BP included Global Scaling You can scale objects in the selected range by setting the range the X and Y Scale factor and then clicking on the APPLY button vivaCT 80 1 3 Evaluation 46 vivaCT 80 1 3 Delete You can delete objects in a range by setting the range and then clicking on the DELETE button Invert You can invert objects in a range by setting the range selecting an object and then clicking on the INVERT button Morphing contours To create a VOI you can morph or interpolate the missing contours between two reference contours The program interpolates the contours on the slices in between To create complex shapes repeat the morphing step for different ranges Hand drawn objects are automatically taken as BP s but you may use the SET BP CLEAR BP and RANGE functions for to alter the proposed rang es Morphing only occurs between matching number of objects If you have two objects in the first slice you also need 2 objects in the last slice of Note your range The first drawn object in the first slice is morphed to the first drawn object in the last slice The second drawn object to the second drawn object and so on Color Coding in Image Selection Area The color coding helps you in the process of morphing objects Breakpoints are marked green morphed slices are marked red If slices are marked yellow a re morphing is necessary because one of the reference objects was modi fied
108. oCT Shutdown of Computer T rning Off EGulprient sot dr nne ed REOR Oen 8 3 Progr De EE 9 Standard WOrkflOW iieri nion ere e ien eee inten ide 9 4 Edit Operator e te DEE 10 Start Program POSSIDIIMES isaac aaa PG RR RE ER A FRO ccrte MR REA MA bito o cad ia la a Ll e o Find Next VIE Se Ve e EE 12 Exit Operator Editing Progi AM EE 12 5 Edit Sample DATO asista Ea AA 13 Star Progra yamma ea ete ities cp ob RETE o EE 13 ee UU l4 Find Fina Nex EE 15 IER 15 So Klee e EE 15 Exit Sample Editing Giele Te 15 6 PVT CAS UIST NSA E 16 Measurement Procedure sse nennen nnne Starting the Measurement Program Initialization OFTHE el Selecting RSS Mp Sami Controlfiles Measurement Protocol Controlle Types x t e ee Me Ea des Selecting a Controlfile sss Creating a new Controlffile sss Deleting a Controlfile AA Locking a COnmroltiles oi ee p eee cin nent ee remit a c Rd Modifying a Controlfile Basic Mode 21 Modifying a Controlfile Advanced Mode eee eene 24 ee lire c e EL 25 SEUS WA A AAA ORIOL 25 CEN lira aaa 25 Stark and Gelee ia SS 26 AA id a do a do ON 26 Print SCOUT VIS Wait Add Scan Batch Measurement ele Kee elt eg DOWN EE Examples of Scout View modes sss eene MEGSUrFEMEAT iio IL On URP ERE X EU d EE HE ER vivaCT 80 1 3 vivaCT 80 1 3 Start Measurernetit oc o Rage cte Roo ar tuo e daa ele meet eee bie rU eO aa Zoomy
109. old adaptive dese semper gerere rd 80 fixed ET 80 TRI Triangulation Method 77 108 Turning On Equipment sess 1 U UCT LIST i 4535haaGGo dada sas 92 V bo 43 115 Defining s ever eed 51 Volume of Interest 43 W Window A A NEEN NES 100 X X Ray Tube ew e nee re ed 4
110. or each slice note this number is given for the whole FOV regardless of what is entered in 22 Proj 180 number of projections taken per 180 degree turn of the sample Precalibration is necessary if your sample or animal holder is so long that it enters the Field of View in its initial placement It is also possible to use the precalibration option when doing in vivo scans to minimizes the time spent inside the scanner for the animal The precalibration is done by clicking the Precalibrate button The precalibra tion is valid 20 minutes and within this time you must start the scanner General The Scout View comparable to a conventional radiograph is used to deter mine the measurement area On the Scout View a reference line has to be set This reference line determines the position of the first slice or a fixed off set from this position in mm or 96 depending on the controlfile settings and must therefore be selected very carefully Figure 11 Scout View of a Bone Biopsy with Reference Line The ScoutView can either be started by selecting SCOUT VIEW or be put in the task list by selecting ADD SCOUT The task list groups prepared scans and ScoutViews to be performed in a list that will be executed unsupervised one after the other either in interactive or in batch mode Measurements 25 vivaCT 80 1 3 Select SCOUT VIEW with MB1 If the Scan Offset has been set in mm the fol lowing window will appear Figure
111. or halfaxes x y otherwise to the given size may overlap the bound ary cutborder controls whether the border of the shape is set to zero true or not false The operation is overwriting i e the input object is altered ipl cut2d shape input output in type of gobj circle halfaxes x y 3121 gt midpos x y 1 1 gt cutborder false gt DECterm Based Programs 82 vivaCT 80 1 3 cl ow rank extract Component labeling CL of a segmented image Faces have to touch for voxels to be considered connected i e a voxel can have 6 connected neighbors Ex tracts the regions with the given rank in the size ordered table Overwrites the input Usually used with rank 1 to 1 to remove any small noisy speckles not connected to the main structure connect boundary controls whether the whole boundary of the box containing the object acts as a connector of sur face points iplo el input output seg gt a first rank 1 gt last rank 1 gt connect boundary false value in range 127 cl rank extract Same as above but not overwriting the input Uses more memory ipl cl rank input seg gt output ex gt first rank 1 gt last rank 1 gt connect boundary false value in range 127 cl26 rank extract Similar as above but also voxels only touching by an edge are considered connected ipl c126 rank input seg gt output cl gt first rank 1 gt
112. or segment ing the whole object using small subobjects to save memory You can either define the subvolume s by entering the number of subvolumes supdin in all directions or their size in pixels subdim suppos is the offset of the object in pixels in local coordinates If you leave the value at 1 the object s will be centered testoff is used for overlapping the small subobjects in case of a procedure such as a gauss filter If supdim numbers is not a divisor of the orig inal object s dimensions a few voxels may be discarded at most subdim number voxels per direction x y or z ipl gt sup divide input in gt a supdim numbers 1 1 1 gt 4 testoff pixels 0 0 0 gt 2 suppos pixels local 1 1 1 gt subdim pixels 1 1 1 gt vivaCT 80 1 3 If you plan to subsequently use a gauss filter on the object testoff must be equal to the support in the gauss filter Note sub_get Extracts a sub volume that has the position and size as entered by pos and dim The flag global_pos_flag controls whether pos is the global position giv en by the original measurement or the local position in the input object ipl sub get input in gt a output sub gt s pos 0 0 0 gt 10 30 10 dim 0 0 0 gt 120 global_pos_flag false gt sub_pick Is an older version of sub_get that needs previous execution of sup_divide to enter the positions and sizes in the grid subpos_numbers is the 0 based posi tion in n
113. ored to this directory Content can be deleted at any time MICROCT TIPS Sample documents describing OpenVMS tasks as well as actions to perform interactive segmentation etc MICROCT UIL User Interface Description Directory Files define the look of the programs If available subdirectories for different language variants The template files for printing PS also are located in this directory MICROCT UTIL This directory contains Utility Programs mainly used by Service Personnel MICROCT XDEFAULTS Directory containing settings for X Windows Environment vivaCT 80 1 3 103 Appendix C Logicals and Symbols Definition of Logicals and Symbols The logicals and symbols used by MICROCT are defined in the following files e SYSSSTARTUP SCANCO SYLOGICALS COM Systemwide DISK1 MICROCT LOGIN COM Process Job DISK1 MICROCT MICROCT_SETUP COM Process Job DISK1 MICROCT MICROCT_SETUP_USER COM Process Job e DISK0 MICROCT COMMON MICROCT SETUP COMMON COM Process Job vivaCT 80 1 3 Logicals Logical MICROCT SCSI UCT ACQ LINE DISKO DISK1 DISK2 DKO MOO FDO TPO SYSSLOGIN SYSSSCRATCH UM SCM UU SCU UCTD SCD UCT MEASUREMENT DATA SCANCO SCOUT DATA UCT HISTO RESULTS UCT BATCH MEASUREMENT UCT MEASUREMENT QUEUE STRUCTION STRUCTION QUEUE UCT RECO UCT_RECO UCT_RECONSTRUCTION_FILE UCT_RECONSTRUCTION_SCALING UCT_BEAMHARD_FACTOR UCT_BEAMHARD_POWER U
114. ound An entry in the database cannot be found for example when looking for a sample or patient who has nof yet been registered or whose name has been spelt incorrectly Error Messages 94 vivaCT 80 1 3 Name contains a wrong character Names of data media can only use the letters A Z or the numbers 0 9 but no spaces or special characters No Controlfile selected You have not yet selected a controlfile Measurement site and cast No Sample or Patientname You have not yet entered a sample s or patient s name No Sample Patientnumber You have not yet selected a sample or patient No images available The pictures for the measurements cannot be read Have you selected a valid measurement Have you possibly deleted its images No logical unit number free General database error No operator selected For measurement and evaluation the field OPERATOR must be filled in with a valid name Check in the sample or patient registration program whether the operator has been accidentally entered as a patient or as a physician op erator must be a member of the staff No scout scans performed Number of slices O is not allowed Not enough disk space left Hard disk is full First delete or archive other measurements Not enough space on disk Optical disk is full Use new optical disk Not more than 15 characters The label of a diskette or an optical disk may not be longer than 15 charac ters In addition no special character
115. our backup disks or tapes in the Caution same room as the equipment better still not in the same building Danger of fire water damage etc Before you start a backup procedure you should terminate all other pro grams or applications such as measurement program evaluation program etc Otherwise some files might be locked by those applications and there fore not be saved Data Management 72 To start the backup operation insert the optical disk or the tape and click on the DB BACKUP TO DISK DKO or DB BACKUP TO TAPE button EA es es Figure 7 Backup Options Then confirm the following question whether you inserted the appropriate disk or tape A safety copy of all databases will then be made The procedure can be done in interactive or in batch mode Operating System Backup Every six month a pop up window occurs with a reminder to perform a back up of the operating system The backup should then be made as soon as pos sible In order to perform the backup make sure that no jobs are running or pend ing in the queue before starting and that all other users are logged off Log in to the calibration account Type in the DECterm window set proc priv bypass r um uct b Push either the button OS Backup to Disk DKO or mount the specific OS back up tape and push the OS Backup to Tape button Exit the Backup Program and log out of the calibration account After a successful OS backup the message
116. pts started in the Eval uation program to execute the 3D segmentation and different morphometric evaluations e g MIL Mean Intercept Length DT Distance Transformation TRI Triangulation SMI Structure Model Index etc The concept of this program is You work with multiple objects in memory One object is usually the input for a procedure whereas the result will be the next object You can delete objects internally in memory only You can also read and write objects from to disk Each object has to be given an internal name such as input output segmented or just a b c etc Once launched in interactive mode you can execute the commands below Each command takes a few arguments which usually have a default value By pressing the return key the value is entered If you have to enter values for all coordinates x y and z you can either give all three values separated by a space or just enter one value which is then applied to all coordinates If the order of the arguments is known by heart you can supply them in the correct order together with the command e g gauss in out and then press return to be asked the next arguments IPL commands may be abbreviated The procedure name list is searched against your input and IPL takes the first command that matches the abbre viation execute he1p to see the list and search order There is no ambigu ous command warning Note IPL only accepts lower case input In the st
117. r 121 eig eir Por Exe aea 10 16 Optical Disk eee 115 P Password cocooconoccnncnnnconccnncnoncnnncnnronnconaconoos 5 POSITION donde eee EE ORO ROUEN RESO ats 23 Print Images eese 8 54 Printing 2D Histomorphometry 50 PrintOUL tee 101 Program Overview 9 10 13 16 Q QUIT M 12 15 R Radiation Dose c ooccocccnccnnccnnccnnconacnncnnncnnns 98 RANGE Pe rererere rE E rA E bes ier SS 46 Reconstruction geesde 76 Reference Line eege oe ee Dee ed e sedo 27 Region of Interest sees 43 RESOMMIION esit occ eene eee e eee eh 23 ap EEN EE AEN 1 io 43 115 Defining eege EENS 49 S Safety COPY Ree ee 72 Sample E 13 Scaling Voxelsize eese 88 SCAN Range EE 27 Segmentation 49 51 80 81 Apt ME 49 A 51 Segmentation Program sss YT Selecting Objects 20 eee eee eens 44 Session Manager sss 6 SBHU tdOWLD ii 8 Shutting Down 6 7 9 10 13 16 Slice Reconstruction eeeess 76 SMI Structure Model Index 77 108 Specifications eee 96 97 Starting MicroCT Programs 5 Startup eese 1 7 9 10 13 16 SUD rere ee ees 61 Symbols in IPL 0ocoocccncnncccnnccnnconccnncnnncnnn 92 T Tape M 75 Task Dist oer RENE ee RR 33 Terminal Programs eee 76 Thresh
118. r Adobe Premiere etc The order in the above list can also be reversed You can first set up the auto print and then go into the Animation menu choose start and end settings and hit start animation The positions A and B can be freely chosen e g with subdim you can first take everything A then slide it back to nothing B You can even slowly change the color of an object Or slowly hiding objects in the Object Properties choose Transparent Separate for object but change the Transparency from 0 0 A to 1 0 B If you want to create a movie with different sections e g first rotate the object around then slowly make the object transparent then cut in Do this in mul tiple sections with the 3D program e g first create Auto Print files rota tion 0000 to rotation 0200 then transp 0000 to transp 0050 and then cut 0000 to cut 0100 Make sure ALL the settings from the last view of the previous section match those of the first view of the next section so you get smooth transitions To save the settings A and B for the film to reuse on another sample click Save Presets File A dialog box will open where you can define folder and file name for the file The file should be saved in DAT format The auto print box can also be used without the Animation Menu Activate it like above with sys scratch test only the beginning of filename Click oK Then whenever a 3D image is completely built up so when you are happy with
119. rocedure OCT EVALUATION logical name see above for current file specification is submitted using the symbol sCANCO SUBMIT COMMAND After having selected an Evaluation Script a job with name EVAL PRO JECT SSSSSSSS MMMMMMMM is started where PROJECT is the project name as defined in the Evaluation Script e g Bone Morpho The batch job also creates a LOG file in the Scratch directory with that name If the Evaluation is started without having selected any scripts a job with name UCT EVALUATION is started The batch job also creates a LOG file in the Scratch directory with that name Checking Status and Progress of Batch Jobs vivaCT 80 1 3 To check whether batch jobs are running enter one of the following com mands QUE or to see more details SHOW ENTRY SHOW ENTRY FULL SHOW SYSTEM BATCH To check the progress or status of a batch job you have to take a look at the batch log file in svs scnRATCH Either double click on the log file in the Session Manager or use the following command TYPE PAGE SYSS SCRATCH UCT EVALUATION XXXX LOG with correct xxxx log filename You also can omit the PAGE qualifier and use Fl toggle for Hold Screen to check the file 107 MIL Method TRI Method Appendix E Explanation of structural Indices With the original MIL method test lines are traced through the segmented volume and the intercepts are counted The test line length is then divided to give the mean inter
120. rrant by or as a tort claim including negligence and strict product lia bility a contract claim or any other claim This limitation cannot be waived or amended by any person This limitation of liability will be effective even if SCANCO MEDICAL AG or an authorized representative of SCANCO MEDICAL AG has been advised by you of the possibility of any such damages This li mitation of liability however will not apply to claims for personal injury Warranty xii Il Important Information Purpose of this Document The purpose of these instructions is to inform the user about the technical functioning of the equipment for the intended purpose its safe operation ad justment and user based maintenance All the equipment manufactured and supplied by SCANCO MEDICAL AG has been tested and examined to ensure as far as reasonably practicable that it is safe and without undue risk to the health when properly used The condition under which our equipment will operate safely and without un due risk to health are specified in this User s Manual and users should en sure that they fully understand the technical conditions regarding safe operating of the equipment and are conversant with and observe regulations and codes of practice which relate to X Ray equipment It is also the duty of the employer to ensure that this employees fully under stand the regulation and operating instructions Typographic Conventions and Abbreviations Typographic Co
121. rtant Information xiv Cleaning For outside cleaning use soft materials moistened with water or ethanol only Shut down properly and unplug instrument before cleaning Never spill li quids on or in the instrument Make sure that absolutely no fluid is dripping Caution into the scanner The instrument can be seriously damaged Before use check the animal bed for leaks Sample Holder Compattibility The sample holders are made of PET Polyethylene Terephthalate vivaCT 80 1 3 Important Information xv Thermal and Chemical Compatibility TABLE 1 Resistance Properties PET Temperature Range 40 C 100 C Sterilisation Steam Autoclave N Water lt 65 C R Inorganic Acids r Inorganic Bases r3 Ketone R Aldehydes Formaldehyde R Alcohols R Ether r Ester e g Ethyl Acetate r Aliphatic Hydrocarbons R Aromatic Hydrocarbons r Chlorinated Hydrocarbons r R resistant r limited resistance N non resistant 1 not possible 2 limited resistance only in diluted form 3 limited resistance only in diluted form Labels Attached to the Instrument Informative Labels Attached to the Instrument SCANCO MEDICAL AG Model Vivat T80 CH 8306 Bruettisellen Switzerland SN 13092700 www scanco ch Made in Switzerland ID 5802 Manufacturer SCANCO Medical AG Manufactured September 2013 Input 100 230V 50 60Hz max 400VA Fuse T6 3AH 250V X ray Tube Manu
122. rtex c1 cortex in percent and then for the inner mask c1 inner in percent in the example below fro every slice only parts of the cortex that take up more than 50 are considered for the slice wise exclusion and then only parts making up more than 60 are taken for the mask ipl cortex mask input mask in gobj filename default file name gt u0001234 GOBJ output out cortex peel iter 5 cl cortex 10 000000 gt 50 cl inner 10 000000 60 gobj to aim Produces a solid filled volume from a GOBJ file i e the inside of the GOBJ mask This function is needed if the element size voxel size of the original volume or segmented volume has been changed with scale el size e g to make the voxels cubic Then the GOBJ produced on the original ISQ file does not match anymore but the AIM mask produced with gobj to aim can be scaled to the appropriate voxel size scale with integrate false written to disk and then used in gobj maskaimpeel ow Also any other IPL commands can be applied to the AIM mask like to any other binary volume ipl gobj to aim gobj filename default file name gt U0001977 GOBJ output out gt out peel iter 0 cut2d shape ow Cut a two dimensional ellipse circle or rectangle extended along the z axis from an object and set all points lying outside to zero The size of the shape type of shape is adjusted to the biggest size lying within the x y plane if 1 is chosen f
123. rtup Procedure vivaCT 80 6 2 Shutting Down Exiting Main Program MicroCT To exit the Main Program click on the EXIT button Kat me 8398 Figure 1 Exiting Main Program MicroCT To exit completely click on the SESSION menu and select END SESSION in the Session Manager Figure 2 Exiting the Session vivaCT 80 1 3 Shutting Down 7 Shutdown of Computer Enter sHUTDOwN as USERNAME and click on OK simo A x ea Figure 3 Login Box for Shutdown The computer closes all databases and programs so that you can use all the programs again without having problems the next time Never switch the computer off without performing a correct SHUTDOWN Only in this way it can be guaranteed that all data can be read again with out problems Note Wait approximately one minute then you can turn off the equipment as fol lows Turning Off Equipment 1 Monitor Computer Tape Drive Printer Uic de O Scanner vivaCT 80 1 3 Shutting Down 8 Standard Workflow vivaCT 80 1 3 3 Program Overview ES Pt 3 88 2 Figure 1 Main Program MicroCT With the program MicroCT the following can be done 1 Sr Ei Entering or Changing Operator Data Editing 2 Entering or Changing Sample Data Editing 3 4 Evaluating Measurements Performing Measurements Slicewise Evaluation 2D Histomorphometry 3D Histomorphometry Image Documentation 3D Display and 3D Documentation
124. s evaluated The results are written into the database db if the database was activated see db scanco activate You should usually not modify the de fault values of the arguments ip sigma ip support ip threshold interpolate nrave iter t dir radius epsilon The output is an object with nr views different 3D views of the triangulated object This output may be written to disk with msq from aim and viewed with the 3D Display program ipl gt tri input th gt seg output tri gobj filename gobj from log peel iter 1 gt ip sigma 2 000000 ip support 1 5 ip threshold 64 interpolate true nr ave iter 0 t dir radius 2l epsilon 1 200000 size image SL ALT gt scale image 0 700000 edges false nr views 0 dt object param Calculates the mean thickness of the structure with the distance transforma tion DT method by filling largest spheres into the object and calculating their mean diameter volume weighted mean Mean thickness and standard deviation are written to the database if activated The output object shows the spheres fitting inside the structure with the voxel values being their diam eter in voxel units Dr object param uses the contours of a GOBJ or AIM mask if it finds the GOBJ filename in the proceedings log Roi radius factor controls whether only a sphere is evaluated or the whole region default DT also works with GOBJ masked objects The
125. s a window and shows the image from the main window or the overview window in 1024 x 1024 pixel resolution Click on CANCEL to close it Brightness Scaling Usually all slices are shown at the slice wise maximum brightness However this can lead to a difference in brightness between slices which prevents you from visually comparing the bone values to other bone measurements By Evaluation 41 vivaCT 80 1 3 clicking on the button above the color scale the images will be displayed in a unified norm fixed scale maximal normal Figure 7 Brightness Scaling You can achieve the same effect with the menu OPTIONS followed by Bright ness Figure 8 Options Brightness Scaling Evaluation 42 Defining the ROI or VOI Drawing Icons By 10 clicking on the buttons shown alongside you can Draw Contour Draw contours in the counter clockwise direction All contours are automatically closed A contour drawn clockwise excludes the region inside the contour Correct Contour The contour to be corrected must be crossed at two points The part lying in between these crossing points will be replaced by a new contour segment counter clockwise drawing direction Correct with Straight Line The contour to be corrected must be crossed at two points The part lying in between these crossing points will be replaced by a new segment Draw Rectangle Square Contour By holding down the SHIFT button while drawing t
126. s case a tomograph Scout Scout View Overview image comparable to a radiograph Shutdown Program for ending the operating system Ensures that all data and programs in the computer can be read again without problem at the next operation VOI Volume Of Interest Zoom Magnify 115 List of Figures Figure LE Type Plate 5 eet e e ig ie e d ERES xvi FigureII 2 Fuses to be Used orita iii e en Henr eaae xe eae weeds NONE xvii Figure II 3 Declaration of Conformity asserire eea e aE E T AA AAA xviii Figure TIT d Caution X RAYS ina dolia e ATI ee re Cepek eee T XX Figure III 5 Caution X Rays for Canada only sese eee XX Figure III 6 Caution X Rays On Attached to the X Ray Indicator Lamp XX Figure III 7 Emergency Stop Attached to the Emergency Stop Button xxi Figure III 8 Caution Animals must be Contained in the Bore eee xxi Figure 1 Turning On Equipment EE 4 Figure 2 LOSin BOX hice C C 5 Figure 3 Session Managern aeeie e E E E E E A E 6 Figure 4 Exiting Main Program MicroCT cece ccc ee eee seen eee heme eene 7 Figure 5 Exiting The SESSION yes Sie Ree ele e das do 7 Figure 6 Login Box for Shutdown ocooccocnncnncnncnncnncnncnnonncnncnncnncnncnnonno hee hehehe nennen 8 Figure 7 Main Program Micro CT oiae dae cioe ree Site ad Des tte Eege 9 Figure 8 Edit Operator Data ive edd ee 10 Figure 9 Operator Registration
127. s or spaces may be used Opening database file General database error Opening filename General database error Opening scanner datafile Scanner calibration data cannot be opened Opening slicename file Slicename file cannot be opened Reading Slice Number General database error Reading filename General database error Reading indexed record An entry in the database is not found for example when looking for a sample or patient who has not been entered or has been spelt incorrectly UM FULL BACKUP COM General error by weekly backup Selected operator is not an operator You have attempted to enter an invalid person as the operator for example a patient or doctor If this is not the case check with the sample or patient re cording program whether the STAFF button is pressed Unable to translate logical General program error Unknown error Error for unknown reason Error Messages 95 Unlocking indexed record General database error Updating indexed record General database error Error Messages 83 Writing Slice Number General database error Writing data General database error Writing filename General database error Writing indexed record General database error Wrong Volume label Wrong diskette or optical disk has been loaded copying files General database error deleting filename General database error dismounting device Error while dismounting a diskette or optical disk
128. scan you must wait until the current evaluation is finished before you can start the next one Note Evaluation 52 vivaCT 80 1 3 If your evaluation does not end successfully or ends with unexpected results go to the scratch directory and check the eval XXXX log file with XXXX being the Project Name sample and mea surement number Look through the log file for information why the evaluation was not success ful e g look for error messages at the end of the log file Note As part of the result the morphometric analysis will also generate several aim files that can be visualized in the 3D viewer See 3D Display on page 57 Modifying Evaluation Scripts In the menu scripts MODIFY the available Evaluation Scripts can be modi fied E gt Bone Trab Morphometry 3D Seg 3D Calc Print Sheet Pas SR be E DELL IL n Figure 19 Modifying Scripts Basic Mode Name of Script Enter a meaningful name for your Evaluation Script Help Text Enter a short help text for the script Project Name Enter a short Project name less than 15 letters for your eval uation script This project name will also be used in the filename of the result txt file in disk1 microct results Eval IPL User Script Filenames Enter the names of the programs that you wish your evaluation script to call Changing them is recommended for ad vanced users only Object 1 to 4 Enter the default segmentation parameters if require
129. seems Selecting the File Type wcities Selecting the Destination Device sss Selecting the Copy Move Operation Starting the Move Copy Function sse BACKUP E D A Operating System Backup sese Device nformatiohi s mee ecc NNAS e EE leg Tag RI EE vii vivaCT 80 1 3 UCT THREEDEE BATCH aim read isq to aim ULTRAM eim MEM Gelle sup divide Cue e UI SUD DICK d M GOUSS Mop TT ic NET gauss seg and seg gauss sssssss sese eee 80 adaptivethresholdi a eda ce labe e ihn dO 80 fft leplacezharnifg icc eat ran re fame n aen tee i re 81 gobi rmeskaimpeelt OW odd eie A n E dedere ied 81 GOD eX EYOISKOff Coki d ete tte Uu v ORAT D tn Ede TEENS FUE AS eaaet 82 00l SM LOO gap 82 eg nee e EE 82 AA MS ra eT 83 CLC SAMA NA URE cl26_rank_extract LOA o oia NS Te SE CISIMOGS EE le elei e E ele e EE 84 tri da metric db dt object param dt background param OLMO TS ed cede ttai e eire etie ai to dar qnas outputs aede aet A CONMEGTIVITY LN COMO CU mE CONN BOC WEE voxgobj_scanco_param vox_scanco_param ALOITIN o EE ENET REEE MIV er Ia EE histo scale elsize ipScale EE Wee ee EE scale ow elsize nolp E Ee UNTER El e LEE JOIN Dieren el EE DOUNGING E ee EE le Be on WEE Offset e EE Offset EEN eeler IN BEE Hl OffSetcmmilltOLU ettet t E te convert to type o ET MSA IOM OI EE from aim to isq alten men AN TU
130. ted contouring 36 G Gauss Eilter iie Ine PIS 80 Global Delete tata ANAL 47 Global Scaling esens nseries s a res 46 gob Mask ir ee eee 81 Graphical User Interface 100 Usina estes eed edie EE 100 H Harddisk td di dass 115 Header and Footer c occocccccccnncnccnccnccncnneno 101 LHistogramJs 052 d AA ATUS Ados Aqu 87 Histomorphometry elle in e ose Sete ES PUE 50 I eg 74 Integration Time sees 24 Interactive Measurement 32 33 Interpolating ageet aee hen ees 47 Pla 77 Iterative Contouring eese 46 K Key Switch UICE DE INSURERS 4 L Load GOBS ia 40 LOSiN EN 5 RENE 115 M Main Switch cocoa 4 MRT ere ege A Eed 100 Measurement eese 15 16 Add SCA Ee 27 Interactive Mode 32 33 Measurement time ossessi eoio sste 24 MIL Mean Intercept Length 77 MIL Calculations oococcoccnccnccncnnnnnnncnncnncnnos 87 Modifying Objects eee 44 Morphing tere Re ee EORR 47 Morphometric Results ees 52 Mount See also Dismount 75 Moving Scaling eee 44 O Object Properties ueteri 62 Object Values eet tete enne ene canas 61 Objects Deleting xoxo eet esee ete eun 44 Drawing eee 43 eeh 44 Moving Scaling o c 44 Eelere 44 Operational conditions 97 Operato
131. th MB Pulldawn Option 1 Option 2 Scaler D Click on the scaler with MB1 Hold the key pressed and move the mouse ES The input values change If the scaler is surrounded by a rectangle click on it to make it active you also can use the LEFT and RIGHT ARROW keys to change the value By using CTRL ARROW you can change the values in larger steps Scaler Input Change of the Header and Footer of the Print Out On the result sheets the name of the operator or sample appears at the top and bottom of the sheet You may have either the default output sheets or customized ones If you have the standard sheets you can change the header and footer Choose the operator registration program and find the number 1 At the top of the sheet appear the fields Name and Address 1 at the bottom of the sheet the fields Address 2 Zip Code and City vivaCT 80 1 3 101 Directory Structure vivaCT 80 1 3 Appendix B Files Used and Created by MicroCT The directory structure is as follows MICROCT DATA 00000001 00000048 00000049 00000050 00000051 00000005 00000065 00000066 00000067 00000007 00000129 00000130 SCOUTS DATABASE MAIN RESULTS SCRATCH TIPS UIL UTIL XDEFAULTS The directories MICROCT DATA reside on DISK2 all other directories are lo cated on DISK1 MICROCT LOGIN COM User definitions MICROCTXXXX COM MicroCT definitions MICROCT DA
132. this Limited Warranty Terms of the Warranty SCANCO MEDICAL AG warrants that the product you have purchased from SCANCO MEDICAL AG or from a SCANCO MEDICAL AG authorized reseller is free from defects in materials or workmanship under normal use during the Warranty Period The warranty period commences on the date of installation or three months after delivery whatever occurs first and ends 12 month lat er Your installation protocol showing the date of installation of the product is your proof of the date of installation This warranty is transferable to any one who subsequently purchases the product from you This Limited Warranty does not include expendable parts Should the product require service during the term of the Limited Warranty SCANCO MEDICAL AG will repair or replace the defective part s with new part s or at SCANCO MEDICAL AG s discretion a used part s that meets or exceeds the performance specifications for new parts In some cases SCAN CO MEDICAL AG will ship a new user replaceable part s directly to you or at SCANCO MEDICAL AG s discretion a used part s that meets or exceeds the performance specification for new parts All exchanged parts and products re placed under this warranty will become the property of SCANCO MEDICAL AG SCANCO MEDICAL AG is not responsible for any handling fees import duties or tariffs This Limited Warranty extends only to products initially purchased from SCANCO MEDICAL AG or from a SC
133. ting 1 Template for image printing 4 Template for image printing 16 Template for Listing of 3D parame Template for Display of 3D param Controlfiles DB Measurement DB 3D Evaluation DB Samples DB Scanner Calibration Data Current Slice number OperatorDB Zip Codes DB operators Result File of DB 3D histo query Result File of DB Infor query Command Procedure for offline Default Value DKB100 MICROCT_SCSI DKAO DKAO DKA100 DKA100 WDB200 DVAO MKC500 DISKI DISK1 DISK1 MICROCT MICROCT SCRATCH MICROCT MAIN DISK1 MICROCT UIL DISK1 MICROCT DATABASE DK0 MICROCT DATA DISK1 MICROCT DATA SCOUTS DISK1 MICROCT RESULTS UM UCT BATCH MEASUREMENT COM SYSSBATCH UM FAN RECONSTRUCTION EXE SYSSSLOW UM UCT RECONSTRUCTION COM 4096 System dependent System dependent UM UCT EVALUATION V4 COM 500000000 2500 MB L3500 PS L3500 PS EK PS CANCO DEF PRINTER U UCT EVALUATION EN PS U UCT HISTO 2D EN PS U UCT RAY EN PS D D T S U U U U U UCT SINGLE IMAGE EN PS UU UCT ONE IMAGE EN PS UU UCT FOUR IMAGES EN PS UU UCT SIXTEEN IMAGES EN PS UU UCT 3D LIST TXT UU UCT_3D_SINGLE TXT UCTD UCT_CONTROLFILES_cust DAT UCTD UCT MEASUREMENTS cust DAT UCTD UCT EVALUATIONS cust DAT UCTD UCT SAMPLES cust DAT UCTD UCT SCANNER xxxx DAT UCTD UCT SLICENAME xxxx DAT UCTD UCT OPERATORS cust DAT UCTD UCT ZIP CODES cust DAT SYSSSCRATCH RESULTS TXT SYSSSCRATCH INFO
134. ting Tasks Click on the Task List button in the main program to open the list You can click on individual tasks check the parameters sort the list using the ar rows remove them or make them inactive task remains in the list but will not be performed Once you have all tasks ready you can start executing all active tasks ACTIVE by clicking start interact tasks If you click submit batch Scans only scans and not the Scout Views will be started in batch mode un attended batch jobs program will close Figure 20 Task List Keeping Deleting Tasks Scout View tasks are kept in the list and once they are all done you will have to reselect them load the corresponding Scout View image and then define the reference line to be able to add a scan to the list Therefore these tasks have to be deleted manually once you do not need them any further Scan tasks get the keep flag cleared by default This means that the tasks are deleted automatically from the list if they were executed successfully Should an error occur during the scan e g sample holder too big calibration error x ray tube error power loss etc the scan will reside in the list and can be re started easily next time you launch the measurement program Measurements 34 Phantom Quality Control Each system is delivered with a quality control QC phantom which is used to check the functionality and the stability of the system The phantom is divided
135. to read the following safety instructions before operating the instrument Not respecting the instructions for a safe use of the equip ment can be dangerous for the user Safety Precautions Warning Labels Attached to or Displayed on the Instrument The following warning labels are attached to the instrument Figure III 1 Caution X Rays Figure III 2 Caution X Rays for Canada only Figure III 3 Caution X Rays On Attached to the X Ray Indicator Lamp vivaCT 80 1 3 Safety Information Xx vivaCT 80 1 3 Figure III 4 Emergency Stop Attached to the Emergency Stop Button CAUTION The animal bed will be moved into the bore Make sure that the animal will fit into the bore Figure III 5 Caution Animals must be Contained in the Bore Safety Provisions Caution Your instrument is equipped with various safety pro visions It is prohibited to modify suspend or remove these safety provisions under all circumstances lonizing Radiation X Rays This uCT instrument generates X rays The system was tested for radiation leakage at the factory and conforms with regulatory requirements under normal operating conditions Do not operate your instrument if it is physically damaged The damage of the scanner housing may lead to emitted stray radiation In this case the system must be inspected by SCANCO Medical AG authorized personnel prior to using it again Only authorized p
136. umbers in the suppos grid ipl sub pick input in gt a output sub gt s subpos numbers 00 0 DECterm Based Programs 79 vivaCT 80 1 3 gauss Ip This is the command to gauss filter an object The shape of the filter can be given using sigma and support You have to give an internal name for the out put object 2 sigma 2 support 1 K _ _ Figure 1 Gauss ipl gt gauss input in o a output gauss b sigma 1 000000 1 2 support 2 gt threshold Using this command you can binarize an object All voxels below lower in perm and above upper in perm will be set to value O the rest the object will be given a value of value in range usually 127 The values for the lower and upper threshold are given in 1 1000 covering the whole range of the data values 0 to 32767 for gray scale AIMs 128 to 127 for char AIMs ipl thresh input gauss gt b output th gt c lower in perm 300 220 upper in perm 1000 value in range 127 gt gauss_seg and seg_gauss Use this command to do the gauss_lp and the threshold in one step This saves memory and reduces the computing time However you have no access to the intermediate object ipl gt gauss seg or seg input in a output seg gt b sigma 1 000000 1 2 support 2 lower in perm 300 220 upper in perm 1000 1000 value in range LAY gt
137. using MBl Determine Angles The angle between two edges of a triangle The vertices of the triangle can be moved using MB1 Open 3D Evaluation window Figure 24 Pointer Ruler Profile Angle Tools Evaluation 9 3D Display Starting the 3D Display Program Enter your name into the operator field See p 11 and click with MB1 on the button with the 3D symbol in the main program Figure 1 Start 3D Display Figure 2 Main Program Screen vivaCT 80 1 3 3D Display 57 General 3D Scene The 3D Scene is as follows Light SS 3D Object Rotation Observer Figure 3 3D Scene There is an observer who moves around in the scene and looks at an object which is positioned at the origin The observer is at a specific elevation angle and looking either from above below or straight on the object He also moves around the object which is given by his rotation angle The light source is given relative to the observer So if the observer moves the light source also moves Standard values are 20 higher and 20 to the right from the observer position Selecting the Sample and the Measurement If you start the program the selection window appears automatically If you want to choose another sample after displaying the first one click on the menu FILE and then OPEN This following window appears Figure 4 Selecting the Sample and the Measurement First choose the type of data by clicking o
138. vivaCl 80 User s Guide Revision 1 3 TD 327 Rev 1 3 Date of Release June 19 2015 O all rights reserved SCANCO MEDICAL AG Fabrikweg 2 CH 8306 Bruettisellen Switzerland vivaCT 80 1 3 vivaCT 80 1 3 vivaCT 80 1 3 Content o A xi Important ui ter Le inacci n xii P rpose of this DOCUMENT steel ista xiii Typographic Conventions and Abbreviations sss eee xiii User s Guide Updates cedente iei iter ied de aa jii Target Group and Users Qualification Manufacturer and Contact for Service or Support sse Xiii Users RESPONSIDI Y EE i Software Licence Agreement i ASTANA ON E i INANSDOMOTION ites EE i IMG te ee i Labels Attached to the Instrument sss eene pee EE Waste Electrical and Electronic Equipment WEEE DISGIGIIMOER EE Declaration Of Conforrnlly nica Sen Safety INFOrMOAHON TE xix Description of Warning Symbols Product Description uere t Redes User s Responsibility seseemn Safety ee e cct RERO ELTE UR LEBER ERI PR tee E EE Emergency stops and switches Startup Procedure vivaCT 80 1 CONNECTORS Jette ND b RR e ba TA TUER LA ERR RE RI ERIS 1 COMPUTER i e ether iens Quality Control Phantom OpticalSignals EE TUPMINGOR EQUIPIMENT x tot b e P comes re Xe hp ne era Control Panel onsite rene e nere nene lo n de diee Starting Main Program MicroCT SIMIC DOWN sa ua teo m ume Meno du tud 7 Exiting Main Program Micr
139. y of the output volume once It may be useful if concat does not work because of too small virtual memory The compressed files are read from disk and the uncompressing is done directly into the correct memory location in the output The volumes may be overlapping but then the respective part of file2 is overwritten in cluding zeros onto filel Join uncompress only works for compressed files Note on disk and only works for volumes with the same dimensions in x and y direction ipl gt join filel filel rat seg partl aim file2 file2 gt rat seg part2 aim output out shift ofin2 z 0 bounding box cut This operation determines the smallest box around the object of non zero voxels An additional boundary can be chosen with border z only controls if only the bounding box in z direction is determined and cut out with a given border ip1 gt bounding box cut inputl in gt output out gt z only false border 0 0 0 gt flip aim Flips an object to a side i e x y and z direction are switched according to new xydir NB it is not necessarily a proper rotation of the object in 3D space The new x direction is the first letter given in new xydir the new y di rection is the second letter the new z direction is the remaining direction ipl flip aim input in gt a output out gt f new xydir yz gt xz offset add Changes the offset around the object The offset is the s
140. y switch and main switch are turned on Figure 1 Turning On Equipment It takes about 5 minutes before your computer is ready to start The power up of the scanner warm up of X ray Note tube may take from a few minutes up to hours de pending on how long the system was switched off vivaCT 80 1 3 Startup Procedure vivaCT 80 Control Panel Indicators SCANCO MEDICAL vivaCT 80 1 X ray indicator 2 X ray tube param XRAY OFF 4 okv o va eters 3 Door Open Close DOOR OPEN ACCESS 3 Touch screen active icons 4 Light e o 5 Camera E 6 Heater Starting Main Program MicroCT vivaCT 80 1 3 Enter mICrRocT as USERNAME and press the RETURN key Then enter the re quired password and press the RETURN key again or click on the OK Button Figure 2 Login Box After logging in three windows are visible The Main Program a terminal ses sion window and the Session Manager The Main Program is described in de tail in the following chapters From the terminal session window a number of operations can be performed including running IPL and manual slice recon structions More information about the DECterm based programs can be found in chapter 11 Startup Procedure vivaCT 80 5 The Session Manager helps you to browse your files and access other avail able applications such as web browser calculator new terminal session win dow etc Figure 3 Session Manager vivaCT 80 1 3 Sta

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