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VivoQuant Manual

1. Function function blub 4 function Dar ol Pr P2 4 return pl p2 pZs J var res bar 1 2 3 Array var array new Array arrayl0 foo arrayl1 Dart var array2 new Array foo bar var array3 foo bar var last array2 pop remove and get last element array2 push burp add element Other array functions are for instance concat join reverse sort unshift shift Hash The VQScript Toolbar Adding Script Shortcuts to the Toolbar Shortcuts for commonly executed VQScripts can be added to the Quick Scripts menu on the VQScript Toolbar To add a Quick Script shortcut e Go to Tools amp gt Configuration and click on the VivoScript tab VQScript 168 VivoQuant Manual 11 12 2015 Display Data DICOM Network VivoScript Registration Nickname Full Path MergeROl C Program Files inviCRO VivoQuant VivoScript MergeROl vqs Cancel e Select a script for which quick access is desired by clicking the button and navigating to the directory where the script is saved e Add a nickname for the script in the dialog box that appears e The script will now appear in the configuration window as well as in the Quick Scripts menu on the VQScript Toolbar e Sm a 0000 08 O y Oop Bove ae pi Mu Slice View Navigation Quick Scripts gt 4 D e Quick Scripts can be edited directly from the VQScript Toolbar by clicking on the pencil b
2. CT CTReco s bed removed DEMO a Y NM NM Reco Co Registered DEMO amp 0 03 11 12 2015 One of the most powerful features of the distance annotation tool is the built in capability of performing landmark based co registration With two data sets loaded use the distance annotation tool to draw at least one line that connects corresponding locations 1 e locations which should be registered between the reference and input data sets The line should start on the reference image and be dragged to the input image For example if using a CT image as a reference and a SPECT image as input 1 left click on the CT drag to the corresponding location in the SPECT image and left click again to end the line It may be useful to use the arrow line type to make clear the direction the input image will be reoriented The user should perform landmark based co registration on one view at a time to optimize registration results Profile 86 VivoQuant Manual 11 12 2015 Click on the Landmark based Co registration icon 6 to perform the registration Once registration is complete the shifted input data set will appear in the Main Window as Input 2 Landmark based Co Registration 87 Checkerboard In Checkerboard mode the reference and input data set s are arrayed in a pattern of alternating squares resembling a checkerboard This mode is especially useful when checking image registration Getting There Th
3. Function Upon selection of the Modeling Tool the Modeling operator window is display Modeling 99 VivoQuant Manual 11 12 2015 Operator ax 2TCM v Read Times Voxel wise e ROI Isotope Decay Corrected E background 0 1000 1 min E lt thetat lt 6 0000 1 min 0 00100 1 min theta2 lt 0 10000 1 min z Compute IF Input Reference Custom Image Input Ref Function Unit Time min Iw Ref Show ROIs Y Run Appropriate data should be loaded into VQ in correct order with the reference image if any loaded first Use the Data Manager to sort the datasets as necessary From within the Modeling operator drop down the specific mathematical model applicable to your analysis may be chosen Once chosen the operator window will fill with the model s parameters and settings Descriptions of each model as well as model specific instructions for usage are given below Note Access to models is dependent on your specific VivoQuant license key Models Two Tissue Compartment Model 2TCM The 2TCM is a three compartment model that includes two tissue compartments one tissue compartment represents free and nonspecifically bound tracer within the tissue referred to as nondisplaceable and the other tissue compartment represents specifically bound tracer within the tissue The third compartment represents tracer within the arterial plasma arameter Description Co Concentration in F NS c
4. 99M 0 gmg t 8 ope MM Min Max Min Reference 1000 Input 1 0 Input 2 0 alt Hist 0 Tool de min Operator DM MM Max 9360 56 0 00101808 0 00101808 te 0 f max Downloading Annotations took 0 0 sec Unit HU uCi uCi e aX Display SI AN Look in C Users lkgoettler Desktop DEMO A My Computer TEST gif R kgoettler File name Files of type Image type Colorbar options Storage Type Magnification Ne o __ 11 12 2015 DEMO DEMO CT DEMO NM DEMO NM DEMO a Mu Slice View v Filtering Save Image 7 Q 00608 demo png A Save Image files png jpg bmp gif tif All images separately smart labels Local image file 1 v Cancel 4 Quick Scripts gt 4 D Y Use the Slice Control or appropriate Keyboard Shortcuts to toggle between visible data sets and save the appropriate images After collecting the images for the first three frames use the Data Manager to save these processed frames 1f desired and then unload these data sets so that the next three frames in the queue will become visible data sets All operations Cropping Quantification Smoothing etc that were applied to the original three data sets have also been applied to the queued data sets with the exception of the Min Max tool How to make a dynamic movie 226 VS VivoQuant Manual 11 12 2015 Mw i VivoQua
5. Display Palette Saving Image took 0 4 sec Transverse only 162 Zoom The zoom function allows you to alter your viewpoint of the images by zooming in and out and also provides the option of a full screen view Getting There Three different methods exist for operating the Zoom function The first method to view the various zoom options for the images 1s to go to View under the select Zoom File View Tools Advanced Modules Heip ony Unde Ctrl Z los E O B ose ee ee EA ed o Ctr h fi Z a Mp Slice View v Navigation Dis e Show Reference F2 e Show input 1 F3 ee Show Input 2 F4 eee RGB data gt Slice number Cross hair E Position labels Patient name Layout ee O Zoom gt Advanced In 25 Ctrl Out 25 Ctri Normal size Ctri 0 Full screen Ctri F Ctri U ee 8 DS Auto zoom The second method to execute the different zoom options is to use keyboard shortcuts Function Shortcut Zoom in 25 Zoom out 25 Cntrl Normal size Cntrl 0 For more on keyboard shortcuts in VQ please see Keyboard Shortcuts The third method is to click on the zoom thumbnails in the Main Window Zoom In 9 Zoom View menu and 163 VivoQuant Manual Zoom Out 9 Function Zoom In The zoom in option allows you to zoom in by 25 increments ecem oF Bm PsOr ae Dow Display In 25 Saving Image took 0 4 sec
6. Operator ax Data Rendering compressed E E Quality High v Segmentation Y Crop range Smoothing Iterations 5 Multiplier 2 5 4 4 4 4 Time Step 0 125 Neighborhood 2 ROIs ix wm F RightKidney Dashed red lines will appear on the image indicating the boundaries of the selected region Display 1007 96 SegmentationExa 5 When the desired thresholding method is performed see Segmentation Tools to learn how to use the Segmentation panel of the 3D ROI Operator only the region within the crop range will be segmented Expert Settings 58 Undo Redo Functionality To undo redo operations performed in the 3D ROI tool go to View gt Undo or View gt Redo The operation being undone or redone will appear in the View drop down menu as seen in the image below Keyboard shortcuts are also available for undoing or redoing an operation o di ee ee wa A AA File View Tools Advanced Modules Operator Undo Add ROI Ctrl Z O po 0 Redo Paint ROI 1 Ctrl Shift Z Oner The undo redo function is applicable to all functions performed on 3D ROI data itself 1 e operations performed to actual volume image data cannot be undone or redone For example performing a cut on an image using an ROI cannot be undone since it is applied to actual volume data and not just 3D ROI data Important Notes e The input ROI will be set to background whenever the undo function is applied e To un
7. Resampling images to reference image took 0 1 sec Using docks Display its iu Mu Slice View Reorientation Registration v VivoQuant 2 50alpha9 64bit DEMO DEMO CT DEMO NM DEMO _ El Quick Scripts gt 4 DO Y Palette VC ax Sliders xX 78 4 gt 4 4 K qh 64 4h 64 a Y 79 Z 236 Color Controls Palette Inv Scale Intensity Y Ref gray 0 0 100 0 100 Inp1 nih_firez _ 0 0 100 0 100 v Inp2 hotgree 0 0 100 0 gt 100 E Magic Triangle Voxel Values Ref 43 5283 HU Inp1 4 01118e 05 uCi nos Inp2 128 Displays VivoQuant offers various display styles to enhance viewing and aid image analysis onal slices e Slice View Showing ortho e Tile View Showing a matrix of slices of one type e Multi View Showing side by side slices of one type side slices of one type Displays 129 Slice View The Slice View default simultaneously displays images of single slices for the MIP sagittal coronal and transversal views of the loaded data sets Getting There The Slice View is available via a pull down menu on the Main Window File View Tools Advanced Modules Help SY SY M Ege oa 0000 05 o AOO D co V oi MM Slice View y Navigation R Quick Scripts 7 4 D CG TT Slice View Display Tile View A i n Multi View MPR View Using the Slice View Display O DE VivoQuant 250alpha9 64bit DEMO DEMO CT DEMO NM DEMO
8. Whole Body Atlas Crosstalk removal Atlas NM CT analysis Split Projections fMRI Tool Install Atlas EKG split Save Calibration txt Split ROI to DICOM Show user data Sum projections Average body calculation Specify ROI center Specify ROI center 2 Upload tumor ROI Append projections Semi Stationary Data Processing TumorPK Model Dosimetry Calc Function The Near Field Uniformity tool is meant to analyze NFF QC data for monitoring detector uniformity To begin the procedure use the QC SPECT Near Field Flood NFF protocol to collect NFF QC data Place 0 5MBq of Tc 99m in as small a volume as possible in a PCR Eppendorf tube Place this tube in the NFF phantom a specially designed holder for the Minerve bed Center the point source in the object space as well as possible using the images and countrates as a guide Run the NFF Protocol rotate 90 degrees and run the NFF Protocol a 2nd time Now that data are collected they may be analyzed using the Near Field Uniformity tool The initial NFF panel shows gray areas for each head and an array of buttons To load the data press the Open button Near Field Uniformity 325 VivoQuant Manual 11 12 2015 The data for each head will appear in the appropriate box To run the analysis press Calculate Head 4 N A As the data are analyzed the screen is grayed out Progress can be monitored in the Results panel shown on the left Function 326 VivoQuant
9. a Libraries Documents a Music Pictures gra mE Videos bag 2 Homearouo Folder Customer ABYZ Select Foider Cancel To load the compressed zipacs folder later go to File gt Open Reference The session GUI displays the name and date of each study and allows for easy sorting of files when loading a previously saved session Users can click on any session to see a Preview of that session in the window 1 Mouse tumour study 1 2013 01 24T13 10 17 Mouse tumour study 2 2013 01 24T13 11 32 3 L O 2013 01 24713 13 03 Right clicking on a session in the Session Manager allows the user to delete that session export it as a compressed zipacs folder to a local storage location or create a Public Link to the session Public Links can be copied to the user s cliboard and pasted into a report email etc HOTS eis i Date Q inviro pas Export 3 18 K Delete Copied to your clipboard https invicre ipacs invicro com publiclink dl 8d03976702883003 Session Manager 350 Help The Help Menu provides access to important information like registration and the manual e Registration e Debug e Manual e About Help 351 Debug At the time of installation the Debugging option may be selected This option allows the maintenance of a logfile that may be used to help troubleshoot problems that occur while using VQ Getting There To enable debugging go to t
10. 3D ROI Tool Opens Configuration window 177 10 logout saveSession loadSession name exportSession updateGUIFromOptions handleLockScreen toggle VCView toggleMCView toggleMCView toggleDM View toggleMinMaxTool toggleWorkflow Widget VivoQuant Manual 11 12 2015 Forgets all passwords in memory does not change DICOM Rep configuration Opens Save Session dialog box Opens Load Session dialog box Opens Export Session dialog box Toggles Visual Control Toggles MIP Control Toggles Data Manager Toggles Min Max Tool Toggles Workflow Widget minimizeFloatingDock bool topLevel dataManager Object Function openDat id files getMinMax int 1 float amp min float amp max getMin int 1 getMax int 1 getMinMaxCached int 1 float amp min float amp max getMinCached int 1 getMaxCached nt 1 setMinMaxCache id min max getDataTypeString int 1 0 voxelSize id 0 voxelSizeX Y voxelSizeX int 1 0 voxelSize Y int 1 0 voxelSizeX Y int 1 0 voxelSizeZ int 1 0 getDesc id key setDesc id key value getDcmString int 1 const QString key dataManager Object Description Opens data id O Ref 1 Impl contained in list of files files Returns minimum value of image at index i Returns maximum value of image at index i Returns cached minimum value of image at index i Returns cached maximum value of image at index i Sets cached minimum and maximum val
11. DEMO DEMO CT DEMO NM DEMO NM DEMO CEN File View Tools Advanced Modules Help se 99M0 28m 40 48 90 Pe Mu Muti view Layout JiR gt Operator xX Display Use the data manager to drag and drop images into your layout Sag Sag Tra Tra y Sag Cor Layout 2 rows 2 cols Data 1 CTDEMO 2 NMDEMO None a C Show ROIs Show ROIs All Operator DM MM Resampling images to reference image took 0 1 sec ROIs may also be displayed in Viewports To show ROIs in a Viewport simply select the desired Viewport by either clicking on it in the Display or clicking on its box in the 5x5 grid and check the Show ROIs checkbox ROIs will then be displayed To show ROIs in all viewports simply click the Show ROIs All button ROIs will then be visible in all viewports Setting Up the Multi View Display 140 VS VivoQuant Manual 11 12 2015 MY VivoQuant 2 50rc10 64bit DEMO DEMO CT DEMO NM DEMO NM DEMO DOES File View Tools Advanced Modules Help mM Ss S50 5p te 2 e YD es ee MM Multi view Layout gt Operator x Display Use the data manager to drag and drop images into your layout Sag Sag Layout 2 rows 2 cols Data 1 CT DEMO vy 3 NMDEMO None Y Show ROIs Hide ROIs All Operator DM MM _Eroding Dilating took 1 6 sec Using the Multi View Display Navigation To use the Multi View as you would other Displays simply close out
12. Display _Palette_ If this function is not selected and the size of the VivoQuant window is increased the image slices will stay the same viewing angle and will not automatically fit the larger window size Saving Image took 0 4 sec Mw VivoQuant 2 50alpha9 64bit DEMO DEMO CT DEMO NM DEMO OF File View Tools Advanced Modules Help is es DO a m e M Slice View Navigati y i ipts e e S m OO 0000 08 O PASS Mu tO bn ee El Quick Scripts 7 4 O Display Auto zoom _Palette_ Saving Image took 0 4 sec Auto Zoom 166 Tools The Tools Menu contains a wide range of tools available for a variety of post processing applications e VivoScript e View Control e MIP Control e Data Manager e Min Max Tool e Workflow Assistant e Histogram e Preprocessing e Resample e Image amp Movie How To Make Dynamic Movies Split Movie into Frames Join Frames to Movie 4 Change Delay Image to Poster Image to Capture e DICOM e Update Check e Configuration Display Configuration Data Configuration DICOM Configuration Network Configuration Y Registration Configuration Tools 167 VQScript VQScript or VivoScript is an implementation of ECMAScript aka JavaScript that allows you to access large parts of VivoQuant JavaScript structures VQScript syntax is identical to JavaScript syntax Loop for var i 0 i amp lt 10 i
13. e SY SY M A rate 0000 08 O tO SB ove LA ue Ma Slice View Reorientation Registration y El Quick Scripts gt amp DO 0O Y Operator 8 xX Display _Palette_ Ref inp1 np 2 ne C ROI v vtk e e Ov Interpolator Linear v _ Quick Preview 03D O20 A Ra M3 M20 Rotation X axis Y axis Z axis 0 00 E 0 00 1 0 00 E Translation 0 000 mm 0 000 mm 0 000 mm C Uniform Scaling 100 100 100 Reorienting Images took 0 3 sec At the top of the operator window there are options to select which images and or ROIs will be subject to reorientation Checking Ref Inp1 or Inp2 will select the Reference Input 1 and Input 2 respectively To select all inputs beyond Input 2 in the Data Manager check Inp ROIs can be selected by checking the ROI box By default all ROIs will be subject to reorientation when the ROI box is checked If you wish to select only specific ROIs click the icon and select the desired ROIs from the menu You may also choose to simply view the ROIs while performing a reorientation without performing the reorientation on the ROIs themselves by selecting View Only from the menu Operator aX Display Ref Inp1 np 2 inp VIRO v gt vtk e l View Only ROI 1 interpolator Linear gt Quick Preview E ROI 2 93D 02D R30 A2 B32 M20 ROI 3 Rotation Y All X axis Y axis Z axis 0 00 0 00 0 00 Translation 0 000 mm 0 000 m
14. 11 El d mm 35 9 mm Distance Annotation Tool 84 VS VivoQuant Manual 11 12 2015 Goto with in the object Since a single left click sets a new point you have to use a single middle mouse button click to go to the given position in the two respective other slices Removing Distance Measures Right click on any of the distance measures and click Remove to delete the distance measure completely Operator Xx Line magenta EAS AE Sn x vtk input Label 1 d mm 16 2 mm 21 32 5 mapa Edit Label Hide Go To End Show on ail Link label Type gt Color Es Remove Operator Xx sfe Line v E magenta A kK 6 9 x vtk input Label 1 E 9d mm 16 2 mm 2 amp d mm 0 9 mm Profile The Profile tool available in the Distance Annotation operator plots the values in each voxel through which the line passes Values are displayed for both Reference and input data sets and given proper calibration the plot values will be in Houndsfield units and MBq for CT and NM data sets respectively The File menu provides an option to save the Profile data as a PDF Goto with in the object 85 VivoQuant Manual Landmark based Co Registration 0 07 CT CTReco s bed removed DEMO a NM NM Reco Co Registered DEMO 0 06 l CT CTReco s bed removed DEMO i NM NM Reco Co Registered DEMO E CT CTReco s bed removed DEMO ES 0 05 NM NM Reco Co Registered DEMO
15. A Settings Help Load DICOM data Load local data Sawe data Transfer to IYS Algorithm Exact Cone Beam FBP v FEF filter typejcut off Frequency SheppLogan vw fi 100 2 Identical to the function of amp apos Ctrl D amp apos this option opens the Data Browser window from where a set of CT projection data may be loaded Note that the Browser opens with the amp apos CT Projection amp zapos data filter set Identical to the function of amp apos Ctrl L amp apos this option opens a Windows Explorer browser window A properly chosen CT projection data set is then loaded into the CT Reconstruction tool File Menu 288 VivoQuant Manual 11 12 2015 Sane Allows the user to save the data in DICOM format both into the selected repository and a local folder The reconstruction is opened in the VQ If the reconstruction is allowed to finish this transfer occurs automatically Transfer to VQ Settings Menu CT Reconstruction r1 140 File ete Help Save Settings Re Hounsfield Threads Thread priority gt Alt Advanced El Auto Bed Removal FBP filter Eypefcut off Frequency SheppLogan vy flio lt Save Settings Saves the current CT Reconstruction Settings The Hounsfield Calibration uses the linear response of the detector at each of the x ray operating voltage to calculate dose to an object in terms of Hounsfield units For more information
16. CT Reconstruction 2007 10 08 14 09 88x88 0001 UN CT Reconstruction 2007 10 08 14 09 88x88 0002 UN CT Reconstruction 2007 10 08 14 09 88x88 0003 UN CT Reconstruction 2007 10 08 14 09 88x88 0004 N CT Reconstruction 2007 10 08 14 09 88x88 0005 Data 339 VivoQuant Manual 11 12 2015 Ctrl click and Shift click options are also implemented to simplify data selection This feature is useful both for selecting subsets of studies to load into the Main Window and also for selecting large groups of studies to Export Study Browser Repository SECURE Q Demo iPACS B 030810 veh ab_Em 18F 5min_em_v1 pet 030810 RX ab_Em 18F 5min_em_v1 pet _ testsync gt cr RE TR se 030810 RX ab_Em 18F 5min_em_v1 pet y F 022610 veh ab_Em 18F Smin_em_v1 pet alilo 022610 Rx ab_Em 18F 5min_em_v1 pet Srana 022610 Rx ab_Em 18F 5min_em_v1 pet A La 022410 veh ab_Em 18F Smin_em_vl pet Patients Name fa 022410 Rx ab_Em 18F Smin_em_v1 pet Patient ID Description Study Date All 65 0 Right Click function The right click function of the Data Browser is used as a shortcut for opening exporting CT or NM data and sending it to a batch job HiSPECT or BatchCT for SPECT and CT data respectively reconstruction or DICOM dump Finally when working in a local repository 1 e a local folder as opposed to data from a database or iPACS server the right click option may be used to delete data To use this function highl
17. Create a schedule for when a Sync job will run Watch Job Yi Active Jobname New foide PACS Folders Schedule Messaging Advanced Autosync changes takes precedence over schedule Mon Tue Wed 7 Thu Fri E Sat EU Sun Running every 1 lt gt week s startingon 6 26 2012 7 Only during scheduled scan interval Setting Specify how often a Sync job runs while the Scan interval eat ew application is open A Sync job will automatically start whenever a new folder is added to the top level folder Only during scheduled A Sync job will automatically start at the time specified on the days selected Autosync changes Notifications Directory Setup 11 12 2015 366 VivoQuant Manual 11 12 2015 Watch Job Yi Active Jobname New folde PACS Folders Schedule Messaging Advanced Off Aljobs Failed jobs only SMTP Server Port 465 F WM SSL Username testliser Password eseese i From Recipients comma separated support invicro com T E on Message Notifcations and specify what type of Notifications messages are sent Contact your IT department for the server address SMTP Server Normally can be found in the settings tab of your Email Client Contact your IT department for the server address Port Normally can be found in the settings tab of your Email Client Recipients Advanced Include or exclude files by specifying their extension e g dcm 1mg h
18. EEEL Expert settings E ata Resolution Algorithm Exact Cone Beam FBP v FEF filter typejcut off Frequency SheppLogan v flio a The primary feature of the Help Menu is the Expert Settings panel This panel is only for advanced users and allows several key parameters in the CT reconstruction to be overwritten including voxel size voxel volume both axially and transaxially Z offset sampling threads and Up scaling Mc Expert Settings 5 Voxel size 0 40 0 40 mn volume 10 2 10 ox 4 0 E 4 0 2 mm z offset 0 00 2 mm i A Sampling 1 gt Allows the user to choose a voxel size in either the X Y transverse or Z axial directions that differs Voxel Size from the 3 options Fast Standard Fine offered in the main CT Reconstruction panel NOTE Changing y the voxel size may slightly alter the voxel volume Allows the user to modify the reconstructed volume oxel either in terms of voxel number or total reconstructed Volume size in mm Modifications may be made in either the X Y transverse or Z axial directions Allows the user to shift and restrict the reconstructed volume to better center features of interest enabling disabled more reasonable resolution times for high resolution images Sampin Sets the number of rays used by the Exact Cone pang Beam Algorithm during the reconstruction Sets the number of threads used during reconstruction The optimal valu
19. IPACS Projectie A O 23 How to contisure the NanoSPECT s DICOM Servet ci AA 25 Addis Tasa DICOMC HE tada 27 VivoQuant Manual Table of Contents SCO A tense cn ce sented ee tole A oat debate scueasesoncaenaaees ANN E A O A A nen veer eer tere aer enanen Cem Tn ne Sen eM NOL erent eenes eae orem ame eTt event Nene er aeana enn ears et RESCUING VIGW DOTA O alae eat MIP Specitie A a a a a N A A A E A E A Classicinon Y TK MI lola IRA RA A SI UI Era RANTS ASS NTE NOCH MO PneT A ONT Pe aE OTE CDV CIV SW ah os etn lia II Sadi tn Ae Pamina TOONS io si fa acl vail et cor olores DADA WAS O A NO SIS os AA e O 0 sed awecndaaiscuctiasssaatapsesedal Getasbescusssesondadeesesl PEC Be ULI ii losa 34 37 47 VivoQuant Manual Table of Contents Reorientation Registration Tool Dand 20 Manta ODHON Sesia iii 73 Dand 21 A tomate OPUS ai 74 IN MT A a Po PO vo y EA 76 Automatic Non Einear RESTA A A dis 77 Automatic Slice by Slice Non Linear RegistratlOD ooocccccccccnnnnnnnnnnnnnnnnonnnnnnnnononnnnnnnnnnnnnnnnnnnnnnnnnnononss 78 Howto seta Default mas eS NItt shee terrae caidas 79 TIME SETS iii aaa ita 82 CA A earn eae an yr Teer 82 MS A A A sali cece tens aouesaeaaa ena aua ed eelacteconeen 82 A on au soucetaucsaatagseasde deus scecasescncatearael 82 Distance Annotation TO ds 84 Gretel UO ate ap rewire setenv eames 84 NISMO NE WOO CEPA o A A E T E E ET 84 GOO WAG LNG 0D CCE ss O dectanebeeaancdaceAcan 85 Removins Di
20. 2008 05 05 07 23 54 Job started batch 0505072353640 __ Li The BatchCT tool may be given different priority levels Lower priority means that the tool will run only when the computer is completely idle A higher priority means that the tool will continue to run even when other processes are occurring Information bubbles pop up in the task bar as jobs are added completed etc This switch controls whether or not these bubbles appear 294 Hounsfield Calibration Hounsfield Units are a powerful tool for assessing attenuation of biological materials The following calibration procedure will result in NanoSPECT CT reconstructions generated with VQ to consist of voxels having proper Hounsfield units Open the Hounsfield unit panel found in CT Reconstruction VivoQuant File Help 600 Save Settings 1 23stable 39 g7435b45 CTR 0 05 Color Panel Reconstruction Parameters Resolution Threads Thread priority Fast Standard Advanced Auto Bed Removal Algorithm m Fast Cone Beam FBP a FBP filter type cut off frequency Butterworth i gt 50 gt Study Details Patientname Volume 66 4x66 4x37 6 mm Voxel Pixel size 0 40 0 400 mm Memory Volume 14 8 MB Progress Filter Butterworth 50 0 frequency Estimated time 00 00 00 Controls autostart Reset the HU values in the panel so that each Slope 1 0 and each Intercept 0 0 Hounsfield Calibration 295
21. 3D 920 A2 B30 Aj2o Basic Settings Transform Translation ql Rigid Affine Quality Fast Standard Fine Expert Settings _ Crop Range Register Inp1 to Ref All to Ref The default options for registering data include Translation Rigid and Affine The Translation registration is a rigid registration which will shift the input data set in the x y z directions The Rigid registration will rotate and translate the input data set The Affine registration 1s a linear transformation which will rotate translate shear and scale the input data set The expert settings are intended for experienced users only and provide access to a variety of transform optimization interpolation and metric figure of merit schemes User configurable fields are also provided for the number of sampling bins minimum and maximum step length maximum number of iterations percentage of voxels to be used for registration and a relaxation factor A crop range can also be defined which when enabled will perform the registration optimization calculations based solely on the voxels within the crop range This can be useful when images have noise regions of little to no signal or other artifacts that may affect optimization calculations For information about setting a crop range see Crop Range under Expert Settings on the 3D ROI Tool page 3D and 2D Automatic Options 74 VivoQuant Manual 11 12 2015 Operator a x Re
22. 5 VivoQuant 1 05 Setup Choose Install Location Choose the folder in which to install VivoQuant 1 05 Destination Folder IC Program FilestinviCROWivoQuant Choose Install Location 11 VivoQuant Configuration The VivoQuant Configuration window has several panels providing access to customizable features as well as important registration and set up information Configuration Panels The Configuration window consists of six panels including e Display e Data e DICOM Settings e Network e Registration e VivoScript Getting There The Configuration window is available in the Tools Menu on the PC On the Mac it is available in the VivoQuant menu under Preferences File View Advanced Modules Operator Help u A Operator E BOMDSAE HSB iis EEE 0 8 gt R Q m o cu mn Ve o View control F5 MIP control F6 av voQuant File View Tc Data Manager F7 A About VivoQuant las Min Max r Histogram Ctrl Shift H oo Services E Workflow Assistant Data Pre processing Hide VivoQuant 36H Resample data f Load Hide Others xH DICOM 5 Show All Image amp Movie gt Quit VivoQuant Q Update Check Ctrl Shift U Configuration Ctrl Shift C Another method for reaching the Configuration window to use the keyboard shortcut Ctrl Shift C For more on keyboard shortcuts in VivoQuant please see Keyboard Shortcuts VivoQuant Configuration 12 Dis
23. Download Sample Library install Atlas Split ROI to DICOM Average body calculation Specify ROI center Specify ROI center 2 Upload tumor ROI TumorPK Model Dosimetry Calc 208 3D Brain Atlas Tool Overview The 3D Brain Atlas tool is used to perform brain region analysis The tool can handle CT or MR data as the input and MR PET or SPECT for the input functional data Instructions for the use of the tool are available through the Workflow Assistant VivoQuant 1 23rc9 64bit 012610 Saline File View Tools Help ICT CT recon stand FBP She Hu aw 22m 304 48 VC mc DM Mm Sice View Navigation Workflow a xX Workflow Assistant Atlas NM CT Brain Analysis Tool Introduction Install Atlas Prepare Image Data Prepare MR Image Data Atlas NM CT Settings GUI Basic Settings Atlas NM CT Settings GUI Advanced Settings Manual Correction 1 2 3 4 5 6 7 Introduction The Atlas NM CT Brain Analysis Tool is designed for automatic segmentation of brain image data Automated fusion routines register an application specific brain atlas to pre dinical image data or vice versa and advanced statistical analysis methods are employed to provide rapid and thorough region specific volume and uptake quantification NOTE PLEASE USE CAUTION WHEN SCALING DATA IN THIS TOOL AS THIS CAN LEAD TO ERRORS IN QUANTITATION FOR MORE REFER TO THE TREATMENT OF QUANTITATIVE DATA PAGE 3D
24. L Zoom Out The zoom out option allows you to zoom out by 25 increments Getting There v El Quick Scripts gt 4 O gt Palette 11 12 2015 164 VivoQuant Manual 11 12 2015 w VivoQuant 2 50alpha9 64bit DEMO DEMO CT DEMO NM DEMO i de Eb File View Tools Advanced Modules Help SY SY M Y 88 0000 o8 O ASEA se 1 Mu Slice View v Navigation y ll Quick Scripts gt 4 OD gt Display Ata zoom _Palette _ This 1s the default angle selecting this option will bring the images back to their original viewing angle Saving Image took 0 4 sec Normal Size Y VivoQuant 2 50alpha9 64bit DEMO DEMO CT DEMO NM DEMO SE E File View Tools Advanced Modules Help W oo 0000 08 O en O 9 eee ee 1 Mu Slice View v Navigation El Quick Scripts a O E gt Display pe This options displays VivoQuant in full screen mode Re highlighting the full screen option will revert VivoQuant back to its original size Saving Image took 0 4 sec Full Screen Auto Zoom Autozoom is a useful function which automatically increases the viewing angle of the images if the size of the VivoQuant window is increased Zoom Out 165 VivoQuant Manual 11 12 2015 w VivoQuant 2 50alpha9 64bit DEMO DEMO CT DEMO NM DEMO CES File View Tools Advanced Modules Help 2 Qm ep og 0000 08 O Aoo Be Y Mu Slice View Navigation Quick Scripts 4 gt
25. Local folder 8 DICOM server Y Pacs Local DICOM folder DICOM Server Calling AET INVIVOSCOPE Called AET NSxx_DCMSRV Hostname manoospectxx Port 104 Use localhost lower case for optimized local access Test OK Cancel Name preference Port where xx is replaced with the NanoSPECT number typically no leading O for numbers lt 10 In place of hostname i e nanospectxx it is also possible to use IP addresses 1 e 192 168 1 1 for local WS ACQ computer connections Please verify that the hostname resolves by using ping hostname in a Command window Also in order to access the ACQ computer from the WS computer you must configure the DICOM Server on the ACQ computer How to configure the NanoSPECT s DICOM Servers 246 VS VivoQuant Manual 11 12 2015 Adding VQ as a DICOM Client Start C Program Files Mediso DICOM Server DICOMServerMegr exe On the main panel you see the name of the database NSxx WS _DCMSRV where xx is the NS number and WS is present on the workstation which should be used as the Called AET DICOM Server Manager v1 00 077 0000 2JE3 Database dicom NS17wWS_DCMSRV v Regi lient Application Entity Title Host Port ANY SCP 192 168 200 136 5555 HELICT LOCALHOST 4104 HISPECT LOCALHOST 3104 HISPECT_BATCH LOCALHOST 3105 INVIVOSCOPE LOCALHOST 23104 PS _AnyName NANOSPECT27W S 23104 l S_LACKAS 10 8 0 10 23104 Add Client Edit Client Delete Client Click on the Cl
26. M NM SPECT NanoSPECT gt Multi Pinhole SPECT y FT Cr CT d Spec Act Calculator A NFF Uniformity QC Bed removal SUV Calculator i Data List QuantiCalc Whole Body Atlas A E Crosstalk removal Loaded 2 Atlas NM CT analysis 9 Split Projections fMRI Tool EKG split Install Atlas gt Type CT CT Rec Save Calibration txt Name Segmentat Split ROI to DICOM Show user data 1 CT Date 2010 05 19 1 Desc CTReco s b Dim 192x192x380 Sum projections Average body calculation Specify ROI center f Type NM NM Re Specify ROI center 2 Name Segmentat 2 WM Date 2010 05 19 1 Upload tumor ROI Desc NM Reco Cc Dim 192x192x380 TumorPK Model Dosimetry Calc gt Append projections Semi Stationary Data Processing Function Please visit How To Guides on the VivoQuant website to download a stand alone PDF guide for performing Crosstalk Removal Crosstalk Removal 277 Biodist Visualization The Biodistribution Visualization tool creates an atlas representation of measured mouse biodistribution values Getting There Biodistribution Visualization 1s available in the Advanced Modules Menu in SPECT Tools VivoQuant File View AS F5 abit STUDY1A2B3C CT CTReco s bed removed NM MC A 5 iY os GE omData Manager F7 A ME DE Sica View lt fig Navigation Display v Link MIP Slice control v Global scale per mod Y Apply default shift t SPECT QuantiCalc CT Spec
27. Manual manipulation using a mouse is described below Another tool the Viewer Control offers a wider array of options for controlling the Navigator window Function Navigation through the viewports includes scrolling through slices zooming and panning Navigation 33 VS VivoQuant Manual 11 12 2015 Scrolling To scroll through the individual slices move the mouse cursor up and down or to the side on the different viewports sagittal coronal or transverse A mouse wheel may also be used to scroll through slices or to rotate the MIP When in Slice View or in Multi View with Link Views checked scrolling is not independent across viewports scrolling in one viewport will affect the other viewports Zooming To zoom in or out within a viewport hold the Shift key and move the mouse wheel forward or backward respectively Zooming is independent across viewports zooming in one viewport has no affect on others and all viewports may be zoomed to different amounts Panning To pan within a viewport hold the Shift key and click and drag the mouse Panning is independent across viewports panning in one viewport has no affect on others an all viewports may panned to different amounts Resetting Viewport At any time the zoom and pan within viewports may be reset to their default positions To do this click the amp icon located on the toolbar MIP Specific Function The functions for controlling the MIP are slightly
28. The default options include 1 DICOM dem dicom 1 2 TRaster ras res bin 3 Raw raw 4 Image Files png tif tiff jpg jpeg bmp 5 Other img nii mhd mha fdf dc3 vol There also exists an option for displaying All Files and not just those with the above formats Function 343 Append Data The second data set loaded into VQ is termed the input data and refers to the SPECT data When loading multiple data sets into VQ e from the Data browser VQ recognizes SPECT PET data and automatically sets it as the input file For dual isotope imaging two input data sets can be added simultaneously The VivoQuant software is capable of handling several file formats Getting There Three different methods exist for appending data Please note An initial data set must be loaded into the Data Manager prior to Appending Data The first method is to use the Open input thumbnail in the Main Window 2 90M os 890 pe Display The second method is to go to Append Data under the File menu File View Tools Advanced Modules Help amp Data Browser Ctrl D O mm OT 7 q lo bi Open Local Data gt HB Replace Data Ctrl O E3 Save image Ctrl i hd A an E Save Movie Ctrl M DICOM i Save Data gt Bruker MR de Bon gt Multiple Images E VivoScript Ctrl Shift V Exit The third method is to use the keyboard shortcut Ctrl N to load input 1 and Ctrl Shift N to load addi
29. Type CT CT Reconstruction 2 Manual Fl Name SegmentationExample 1007 W About 1 CT Date 2010 05 19 18 34 03 series 2010 05 19 Function After selecting Enable Logfile a dialog box will appear prompting you to restart VQ and providing the location of a new vivoquant log file la y Thanks for enabling the logfile C Users KGOETT 1 AppData Local Temp VivoQuant log Please restart VivoQuant now to enable logging Upon the next restart of the VQ this logfile will record all of the operations performed This record is useful when attempting to troubleshoot or debug problems that arise in the software Debug 373 Saving 3D ROI Images Movies Known issues with graphics card On Windows 64 bit there is a known issue with the Intel G45 43 Express Chipset graphics card 3D ROI renderings will save as blank images or movies To download the fix please download the driver here Saving 3D ROI Images Movies 374 VQ Keywords e Patlak Analysis Patlak Plot e 3GB e 2D Drawing Tools e 2nd Capture e 3D and 2D Automatic Options e 3D and 2D Manual Options e 3D Segmentation Tools e About e ACO NSxx DCMSRV e Adding to Reference Library e Adding VO as a DICOM Client e Alpha version e Anonymizer e Append e Append Projections e Apply default shift e Automatic Non Linear Registration e Automatic Slice by Slice Non Linear Registration e Axial Sliders e Batch Mode Reconstruction e BatchCT Too
30. VivoQuant Manual e Projects e PSF Manager Quantification Database Quantification Options Quantification Table Options Quantification Tables e Raw e Reconstruction Parameters e Registration e Relabel Study e Release candidate e Rename DICOM Files e Repositories e Repository e Repository Type e Reset an ROL e Right Click function e ROI Creation and Deletion e ROI Loading Saving and Quantification Tools e Run DicomProxy e Run the Tool e Run Tool and View Log e Running a Batch Job e Sagittal e Save as default e Save Calibration txt e Saving e Saving 3D ROI Images Movies e Secondary Capture e Segmenting With The Tool e Select an Output Repository e Select Images e Server Options e Settings e Settings Menu e Show data type e Simplified Reference Tissue Model SRTM 11 12 2015 380 VivoQuant Manual e Simplified Reference Tissue Model 2 SRTM2 e Slice View e Slice View e Slice Viewer Object e slice Viewer Object e slice Viewer Object e slice Viewer Object e slice Viewer Object e slice Viewer Object e slice Viewer Object e slice Viewer Object e slice Viewer Object e Sliders e SPECT e SPECT reconstruction e Split Movie Into Frames e Stable version e Study Browser e Sum Projections e Sync Pos e Templates e Templates e The Calibrations e The Calibrations e The Quantification Table e The VOScript Toolbar e Tile View e Transversal e TRaster
31. Y Input 1 K Input 2 Input Append data Force 2D Smoothing Gauss T FWHM mm e OK Cancel Operator DM Downloading Annotations took 0 0 sec One of the most critical steps is the application of the Min Max Tool To begin with the tool use the Re Calc button to display the current minimum and maximum values being used for color scaling Choose common Min Max values across all three data sets Use the Apply button to adjust the color scaling accordingly The three visible data sets are now color consistent In other words the same colors represent the same voxel values across each data set How to make a dynamic movie 224 VivoQuant Manual 11 12 2015 w PA VivoQuant 2 50beta8 64bit DEMO DEMO CT DEMO NM DEMO NM DEMO e File View Tools Advanced Modules Help e SY SY W ES ata 0000 os o aS Oo Bove meee Me Mu Slice View v Filtering y Quick Scripts D Y MM xX Display Min Max Min Max Unit Reference 1000 9360 56 HU Re calc Input 1 0 0 00101808 uCi Reset Input 2 0 0 00101808 uCi di Hist 0 0 Tool k min max Y Apply Operator DM MM Downloading Annotations took 0 0 sec Save images for each data set using the Save Image option The All images separately option automatically saves five images sagittal coronal transverse MIP all in one simultaneously How to make a dynamic movie 225 10 VivoQuant Manual VivoQuant 2 50beta8 64bit
32. _ Store data Format CT 0 NM 0 Storage Options Repository Project Protocol The Preprocessing Tool is divided into three sections Resample data DICOM Image amp Movie Update Check A Configuration Ctrl Shift U Ctrl Shift C Information Loaded 2 datasets Dim 176x176x452 Vox 0 20x0 20 mm e CT DEMO DEMO DEMO Unit HU OrigVox 0 20x0 20x0 20 e NM DEMO DEMO DEMO Unit uCi OrigVox 0 20x0 20x0 20 Storage e CT Multi Frame MF module e NM Multi Frame MF module Cancel The first section is the Preprocessing Options section which includes the preprocessing operations that may be included in the protocol Preprocessing Tool 202 VivoQuant Manual 11 12 2015 Automatically detects the bed position within the image and removes the CT voxels which constitute the animal bed Only supports Minerve beds Performs automatic image co registration of all inputs to the Reference If Fast or Full 3D are not checked then Standard and Translation are used Performs automatic cropping Search for boundaries starts at the end slices of the image and moves towards the center of the image until a non background voxel is detected from all 6 faces Apply a scalar multipication to NM data PET SPECT Please pay attention to the formatting of the input cell Note Calibration factors per modality comma separated in format Mod 1 0 Unit Example PT 13456 7 BQML The ca
33. set to whatever the window was set to last Checking this box enables support for PRONTA DICOMDIR files Folder Filter Allows users to dictate the type of dicom files loaded into VQ Users can configure loading extensionless dicom data by adding a space and to the end of the default settings DICOM Settings 240 VS VivoQuant Manual 11 12 2015 Folder Filter dom dc3 dicom IM_ S_ DICOM Cache DICOM Cache Current size 0 0 MB 0 Max size 1000 MB gt free 870422 3 MB Life Time 14d 5 Clear The DICOM cache allows the storage of frequently used data sets locally thus improving load time into VQ Every time the VQ is started it checks the current size of the cache against the maximum cache size If the currect cache size exceeds the maximum cache size then older files those opened least recently in the VQ are removed i Size in Mb of the data currently stored in the DICOM Cache The percentage to the right of the field indicates how close the cache is to capacity Maximum amount of memory that can be made available for the DICOM Cache ZE default 1000 0 MB Length of time over which data will be stored in the DICOM Cache default 14 Life Time lear Empties the DICOM Cache Captures Defauit Repository Default Format Not yet implemented please check back soon Data Browser Repository Panel The DICOM Repository panel in the Data Browser is the most convenien
34. setPatientsName const QString amp text setMPRPlanes int planes setOpacityPoints int imgIdx QList amp lt QVariant amp gt imgRange QList amp lt QVariant amp gt opacityRange changeRenderSpeed QString speed renderSpeedUpdated QAction action handleModified handleEnabledChanged update VTK forceRender resetCamera setMPRImage int 1 double offset Qlmage image int min 0 updateMIPPointers imageLoaded int 1 imageUnloaded imageUpdated int 1 update V olumeColors interactive startInteractive endInteractive transform const vtkMatrix4x4 mat VTKViewer Object Function Description setEnableGradient bool toEnable renderingProgress vtkObject obj setAzimuthAngle int ang renderUpdate resetCamera resetPosition vtkUserEventsHandler vtkObject obj VTKController Object 11 12 2015 Forces re rendering of VTK 184 VS VivoQuant Manual DicomRepository Object Function Description get const QString key set const QString amp key const QString amp val setUsername const QString amp u setPassword const QString amp p username password wasCanceled project stop DicomRepository Object 11 12 2015 185 Viewer Control The Viewer Control palette is a powerful tool for manipulating image appearance in the main window Getting There Three different methods exist for reaching the Viewer Control window The first method is to use the Viewer Control thumb
35. to the computer s IP address e Check the DICOM Server logfiles on the computer that you want to access located in C Program Files Mediso DICOM Server logs Troubleshooting 28 VS VivoQuant Manual 11 12 2015 e Enable debugging in the VQ and collect output while trying to access the DICOM Server Troubleshooting 29 Network The Network panel consists of two sections Network Settings and Auto Import Display Data DICOM Network VivoScript Registration Network settings Proxy Port 3128 Enable online check Please restart IVS after changes on this page Auto import Directory Repository y InviCRO PACS v Cancel The Network Settings section includes an option for enabling a proxy server for use with the VQ There are fields for entering a proxy and a port number associated with that proxy The Enable Online Check checkbox will automatically detect any available proxy servers If you believe a proxy server is needed please speak with your local IT representative The Auto Import settings may be used to designate a folder through which files may be automatically transferred into a Repository According to the setup in the above screenshot DICOM files placed in the VQ AutolImport directly will be automatically imported into the NSOOWS_DCMSRYV repository upon the next restart of the VivoQuant Network 30 Registration Getting There The registration panel may be reached from the Configuration Panel o
36. 1 e use Fast instead of Fine disabling the use of normalization see Settings menu below using Fast Cone Beam FBP instead of Exact Cone Beam FBP to reconstruct reconstructing only a portion of the total volume see Expert Settings in the Help menu below or re acquiring data with smaller projection data 1 e Fast instead of Ultra Fine in Nucline The exact memory requirements are as such Algorithm Bytes per Voxel 2 4 per thread When using the normalization matrix this adds two more bytes per voxel This matrix is requires to adjust the sampling for helical acquisition orbits For circular scans the normalization matrix can be disabled without side effects Typical dimensions and their memory requirements using matrix normalization Fast cone beam 6 bpv bytes per voxel bpv Exact cone beam thread 10 bpv Exact cone beam 2 threads 18 bpv Voxels 9 720 000 Fast cone beam 55 MB Exact cone beam 1 thread 93 MB Exact cone beam 2 threads 167 MB Mouse 36x36x37 mm 100um voxels Voxels 47 952 000 Mouse 36x36x60 mm 200um voxels Study Details Progress and Controls 286 Mouse 36x36x20 mm 50um voxels Rat 62x62x90 mm 400um voxels Rat 62x62x60 mm 200um voxels Rat 62x62x20 mm 100um voxels VivoQuant Manual 11 12 2015 Fast cone beam 274 MB Exact cone beam 1 thread 457 MB Exact cone beam 2 threads 823 MB Voxels 207 360 000 Fast cone beam 1187 MB Exact cone beam 1 t
37. 1 sec Viewer Control in Multi View 188 VivoQuant Manual 11 12 2015 If at any point you wish to reset all viewports to the same slice again simply click the button located next to the Link Views box It 1s important to note that Link Views only affects the slice by slice navigation between viewports Regardless of whether Link Views 1s checked zooming and panning within each viewport will remain independent File View Tools Advanced Modules Help e SY SY M oe 0000 as E T 9 O BD eve ee m Mu Multi View v Layout y Quick Scripts gt 4 D Y VC xX Display MultiView 1 igs _ Link Views S Sliders X 85 E Y 130 Z 295 Color Controls Voxel Value Intensity v Ref 61 1302 HU 100 Y Inp1 0 000962465 uCi 100 v Inp2 C Show ROIs Operator VC DM Resampling images to reference image took 0 1 sec To reset the zoom and pan in a specific viewport select the viewport you wish to reset either by selecting it from the drop down menu or by clicking on the viewport and click the button in the Viewer Control This will reset only the viewport selected To reset all viewports at once click the amp button on the toolbar Viewer Control in Multi View 189 MIP Controls The MIP Maximum Intensity Projection control can be used to automatically rotate the MIP and also allows for manipulation of active data sets in the main window See MIP Explained for a more d
38. 2015 the license key After the software has been successfully installed you will be prompted to register your computer for a license Click Yes ye DEMO MODE VivoQuant has not found a valid license and thus started in a limited DEMO MODE This allows you to check out basic functionality of VivoQuant however we recommend you file a license requests with your institution you will need the INSTITUTION CODE or use DEMO for a time limited evaluation license with all functions Would you like to proceed to the registration process now e Enter the company code provided in the email along with the email address to which the registration email was sent VW Configuration P F B 2 License Key lt 00000000 gt Customer Code P123 Use the code provided by your institution or DEMO for an evaluation license Department Imaging Contact address ExampleUser Pharma 123 com To file a registration request please fill out above form and hit Register If you already have a license key please install it with Install key Show Key Install key HW Keys Register a e After clicking Register your Internet Browser will load and navigate to the license registration confirmation page You will need to enter the password provided in your email to finalize the process IL Trail Accounts 7 VivoQuant Manual VivoQuant License Request Customer Pharma 123 Core Imaging Lab Your N
39. 3 ROI Loading Saving and Quantification Tools 1 Load an ROI from disk Save an ROI to disk Render ROIs in the MIP view Reset the camera view Reset all ROIs Show the image histogram Load an ROI from an iPACS Save an ROI to an iPACS 9 Merge ROIs from an iPACS or disk 10 Show the quantification table 11 Save the quantification table to disk 12 Perform a cut on an image using an ROI 13 Show hide the MIP data with the rendered ROI 14 Show hide the 3D ROI table 15 Perform a copy paste on an image using an ROI 4 Painting Tools 1 Sync position while painting 2 Erode dilate an ROI 5 2D Drawing Tools 1 Spline tool 2 Bully tool 3 Freehand tool 4 2D thresholding tool 5 Delete a 2D ROI 6 Submit 2D ROI 6 3D Segmentation Tools 7 Expert Settings 8 Undo Redo Functionality COND NM BB W LW Overview The 3D ROI operator provides advanced tools for drawing visualizing saving and quanitfying both 2 and 3 dimensional regions The acronym ROI stands for region of interest and 1s used to describe a particular area or volume within an image for which the user wishes to characterize some quantity or quality 3D ROls 37 VS VivoQuant Manual 11 12 2015 Getting There The 3D ROI tool can be accessed via the tool pull down menu on the VQ front panel File View Tools Advanced Modules Help SY M fone 0000 05 o gt O 1 eee ee Mc Mu Slice View Navigation Quick Scripts gt 4 D
40. 373 FUNCOM Perea etna even NOtRR A ee ear aera el erg Ee RTE Pea EDIT ACRE TORN T on Oot aT mT IC eT Re CREA TE 373 Saving SD ROIL Tares MOVIES AAN 374 Kn own Issues With Stripes ae ne te a 374 VOR A O cs oeracscets EEE saws scanuecsacsseckocanaubeteusasceasuasevecnecsuaeevaces 375 XIV VivoQuant Manual VivoQuant supports the processing and analysis of image data across multiple modalities including PET SPECT CT MR and Optical Up to 3 modalities can be displayed simultaneously and any number can be co registered DICOM NifTi and 15 native data formats Bruker Inveon Siemens etc can be imported for processing Images and quantification results can be easily exported in a variety of formats image movie spreadsheet Communicate with any DICOM client including seamless integration with inviCRO amp apos s iPACS data management platform for bi directional data transfers VivoQuant Manual 1 VivoQuant Installation e Installation Ouick Guide e Installation Details e Configuration e Memory Configuration VivoQuant Installation Installation Quick Guide This document should guide you through the first steps to get VivoQuant running on your system 1 Downloading 2 Installing 3 License Registration 4 Installing License Key 1 Downloading Please point your favorite web browser to the VivoQuant Download Page for access to the latest stable release VQ features HTm Plugins Download VQ 3011 0
41. Act Calculator DICOM SUV Calculator xr Advanced Analysis gt OHH Crosstalk removal 383 Biodist Visualization Split Projections Histogram Volume rendering F Image Magick gt A mu Min Max EKG split W Workflow Assistant Save Calibration txt Show user data Sum projections Append projections Semi Stationary Data Processing Calibration b Update Check THU si Function To use the Biodistribution Visualization function enter the total measured activity for each region of interest available in the atlas list Biodist Visualization 2 8 VivoQuant Manual 11 12 2015 IVS Biodistrubution Visualization Organ Id Yolume mm3 Activity Concentration 1 mm3 background O 66676 3 10 0 000115372 skin 1 16612 11 0 000662173 skeleton 1473 96 20 0 0135689 eye 6 516 0 293427 medulla 45 056 0 0872296 cerebellum 30 152 0 0994959 olfactory bulbs 18 312 0 273045 external cerebrum 133 376 0 0449856 striaturn 23 136 0 345781 heart 231 45 0 0604504 rest of the brain 190 528 0 03674 masseter muscles 121 744 0 lachrymal glands 35 384 0 bladder 13 201 76 25 0 12391 3 After entering the appropriate values select one of the buttons at the end of the list utton ew ad ave ancel Closes the Biodist Visualization window 8 Z E O Prepares the atlas with the entered biodistribution information Function 279 Split Projections The Split Projections tool may be used to split a si
42. Another option is to select any one or shift select more than one of the ROIs in the operator right click and select Reset ROI s ROI Creation and Deletion 41 VivoQuant Manual 11 12 2015 Operator r 01 X e A vie Oe ah EEC ROI H M background E Brain E LeftKidney E RightKidney Heart Edit ROI Liver Add ROI Toggle Hide ROls Toggle Immutables Reset ROls Delete ROIs Export ROls Hide an ROI To make an ROI invisible in the slice and MIP views without deleting the ROI click on the Nazarm Hide ROI button If the ROI is not immutable it will be possible to edit the ROI even if it is hidden This will only hide the ROI that is selected in the ROI dropdown menu Another option is to select any one or all of the desired ROIs right click and select Toggle Hide ROI s Operator a x t o Jo xs 2 A tk OO alk Ela a el 6 ROI H M background E Brain E LeftKidney E RightKidney Edit ROI Liver Add ROI Toggle Hide ROIs Toggle Immutables Reset ROIs Delete ROls Export ROls ROI Creation and Deletion 42 VS VivoQuant Manual 11 12 2015 All selected ROIs will become hidden Operator lk oO Je xi 2 4 O amp O alh BE we amp ROI H M background L a Brain MM LeftKidney MM RightKidney E Heart iv E Liver Ti ROI Loading Saving and Quantification Tools The left
43. Bounding Cylinders v Generate cylindrical ROIs encompassing each animal in a multi animal NM image Image Ref Cylinder radius mm 16 00 F Apply ROIs A XxX F RightKidney If there are any ROIs present prior to using this tool they will be deleted 3D Segmentation Tools 55 VivoQuant Manual 11 12 2015 O In order to proceed all existing ROls will be deleted Continue Yes No BEFORE Expert Settings The Expert tab denoted by Exp presents the advanced settings of the 3D ROI Operator For the typical user these settings will not need to be changed Operator Gx e olwe x e Data Rendering Y compressed 1 X Quality High Segmentation Crop range Smoothing Iterations 5 Multiplier 2 5 4 4 Time Step 0 125 Neighborhood 2 ROIs A CT RightKidney v Expert Settings 56 VivoQuant Manual 11 12 2015 Data By default VQ ROIs are written in a compressed format To extend compatibility with other tools e g ITK uncheck compressed If the ROI files will only be used within VQ leave the compressed box checked Importing and Exporting ROIs To import an ROI loaded in the Data Manager from an image file click the T button and select the corresponding dataset to import To export a 3D ROI as an image to allow manipulations outside of the 3D ROI tool click the X button Rendering If auto is checked ROIs will be re re
44. Brain Atlas Tool 259 fMRI Brain Atlas Segmentation Tool 1 Install Atlas 2 Getting There 3 Load Data into the Tool 4 Select an Output Repository 5 Customize Analysis Pipeline 6 Run the Tool Overview The fMRI Brain Atlas Segmentation Tool uses a species specific atlas to evaluate functional or structural MRI fMRI or phMRI data Several pre processing and analysis options are available to enable accurate characterization of signal change for a variety of acquisition paradigms Install Atlas Before using the fMRI tool the user should download and install the available atlases by going to Tools gt Advanced Analysis gt Install Atlas gt Mouse amp Rat To change where the atlases are automatically stored go to Tools gt Advanced Analysis gt Install Atlas gt Change Atlas directory and re install the atlases to this location File View Tools _ Advanced Modules Help a O QUA gt 2 tr cT Bed removal Whole Body Atlas Atlas NM CT analysis fMRI Tool instali Atias Change Atlas directory Split RO to DICOM Mouse amp Rat Learn more Average body calculation Specify ROI center Specify ROI center 2 Upload tumor ROI TumorPK Model Dosimetry Calc Getting There The fMRI Tool is accessed by navigating to Tools gt Advanced Analysis gt MRI Tool fMRI Brain Atlas Segmentation Tool 260 VivoQuant Manual 11 12 2015 File View Tools Advanced Modules Help
45. Bubbles Jobs Menu Batch CT Status 1 57 File te Help 4 R Pause A stoplob Pa Details Patient Parameter Status 4 gt MoveUp MoveDown 0505072353640 ct exp time St Eco CT Helical Scan Topogram CT Running EditJob prj 20070912 3 DeleteJob Mos Thread number gt q Thread priority gt Statis Move v Show bubbles 1 NA 0 AL 0 OE OO AS RR O ES NA E Total e e 0 O OL EditJob DeleteJob 2008 04 30 15 02 47 Welcome to batchCT 1 57 2008 04 30 15 02 48 BatchCT started 2008 05 05 07 23 54 Job added batch 0505072353640 ct exp time CTReco CT Helical Scan 2008 05 05 07 23 54 Job started batch 0505072353640 __ Li The BatchCT tool may be given different priority levels Lower priority means that the tool will run only when the computer is completely idle A higher priority means that the tool will continue to run even when other processes are occurring Information bubbles pop up in the task bar as jobs are added completed etc This switch controls whether or not these bubbles appear 310 Calibration This tool can be used to evaluate data from several different NanoSPECT calibration measurements including CT Geometrical Multi Pinhole SPECT and Near Field Flood It also points to a separate VO Calibration application Getting There The Calibration menu is available in the Tools Menu File View Tools Advanced Modules Hel Whole Body Atl
46. DICOM Add Comment Add Screenshot The Add Files button opens a window that can be used to manually select files Note that multiple files may be selected simultaneously for inclusion in the report How to use the VQ Reporter Tool 357 t Li DEMO Organize v New folder 351 Favorites di customers E Desktop Je Downloads S Recent places 2 Homegroup jm This PC e Desktop E Documents Je Downloads db Music E Pictures B Videos i Windows8_OS C w File name VivoQuant Manual v Search DEMO va E DEMO rmha DEMO inp mhd DEMO inp raw Ma E DEMO ref raw test inp mhd test inp raw DEMO ref mhd test ref mhd All Files 11 12 2015 The Add DICOM button opens the Data browser where files may be selected To load into the Reporter either press the Open button or right click and choose Load into Reporter Repository SECURE Qem iPACS invicro_demo vivoquant VivoQuant N A Projects 12 383 EO Filter Patients Name Patient ID Description Study Date Y Data Show data type All data types NOS Apply default shift Auto Start reconstruction Force planar C Stack 3D Append Open Transfer O Close Study Browser Patients Name StudyDate gt O A A F AA Load into Reporter gt DC M1_1_ 2010 gt DC M1_1
47. Desktop and follow the default install instructions To open the VivoQuant double click on the VQ icon the option to place the VQ icon on the Desktop is presented during installation The VQ Help Reporter can be selected from the help menu in the taskbar on the top of the VivoQuant window under Request Help SON OF ol Display Request Help eee Log out Ctrl Shift X Registration Enable Logfile Debug View Hints Manual We About Initializing the VQ Help Reporter will save a copy of the session currently in progress VQ Reporter 356 VivoQuant Manual 11 12 2015 Most reports will first request a written description of the problem to be included in a text file attached to the report Va inviCRO Service Reporter 2 50beta8 0 Components System Info Add Files OS Version Unknown Windows AMD64 8 proc 64 bit Hostname kgoettler Add DICOM QT Version 4 8 2 IP addr F ESA3 FE80 462 193C 53EF E5A3 FE80 5EFE AC 10 1A5C Add Comment App Version VivoQuant 2 50beta8 vq 2 Salpha 148 g9c2b020 User kgoettler Station UKN Report Type v Add Screenshot Content b 01 System gt 02 Session Please describe your issue gt 03 Registry Controls y INVICRO wai fe Your name Your mail address Save Send For all reports it is possible to add additional files and images using the four Add buttons arrayed across the left hand side of the tool Components Add Files Add
48. Files dialog Construct new image names by typing into the Template text box using the key beneath the text box for reference Each token represents a particular field of the DICOM header The new names of the selected files will be displayed in the Examples window as they are entered Names must be unique or else the files will not be renamed Renaming will also fail 1f illegal characters e g backwards or forwards slashes are used To execute renaming click OK oF B PatientsBirthDate D StudyDate E AcquisitionDate I SOPInstanceUID J StudyID K AcquisitionNumber M Modality O ProtocolName P PatientsName S StudyDescription T StudyTime d SeriesDate e Acquisition Time i InstanceNumber j SeriesNumber k AccessionNumber m ManufacturersModelName o Manufacturer p PatientID s SeriesDescription t SeriesTime 0 files loaded qnqxqgq f lt A 8 A Rename DICOM Files 212 Keyboard A list of the keyboard Keyboard Shortcuts Shortcuts shortcuts which are available for many basic operations Windows Linux Mac Shortcut Shorieut Shortcut Function trl 0 trl N trl D D Open DICOM Data trl 1 I Savelmage trl M Save Movie O p i N M UN p M irl S S Save Data DICOM format _ irl P P Print o fn F2 Show Reference fn F5 Slice Control UN Y ar fn F6 MIP Control oomout irl 0 0 Nor
49. Horizontal bed offset 4 Absolute distance between aperture center gt 1 5mm and detector center y or Z O A D 4 Point gt 3 0 A U Templates 321 VS VivoQuant Manual 11 12 2015 Preview The Preview panel displays calibration data for a particular calibration selected using that calibration s Preview button This panel is useful for checking head order in the 4 point calibration or determining a missing point in the Linearity Check calibration The slider bar at the bottom allows movement between heads Aluminum Grid Preview y Preview Collimated Beam Preview a Previen y Four Point Preview Templates 322 Head 1 1 Output VivoQuant Manual 11 12 2015 ee mm The Output panel provides a log of the steps being performed For example the Output section will inform the user that files have been found provide the numerical results from the analysis and help identify potential errors Found ColBeam for head O Found IntRes for head 3 Found ColBeam for head 3 Found 4 Point for heads 15 MMP Menus Output as Several useful fixes and features may be found in the MMP Menus of File Tools and Help MMP Keyboard Shortcut File Open Data Basic Configuration Templates Identical to the Open button in the Control panel this opens a browser to allow Ctrl O the loading of calibration data files The ID of the NanoSPECT and o
50. No Images No Images Show ROIs Show ROIs All Operator VC DM Resampling images to reference image took 0 1 sec The 5x5 grid in the Operator window is used to control both the datasets displayed in each Viewport and the slice type To load data into a particular Viewport click on the corresponding box in the grid and in the three menus labelled Data in the Operator window select the Reference Input 1 and Input 2 dataset s for the Viewport The dataset s will be loaded automatically Setting Up the Multi View Display 138 VS VivoQuant Manual 11 12 2015 VivoQuant 2 50rc10 64bit DEMO DEMO CT DEMO NM DEMO NM DEMO CEN File View Tools Advanced Modules Help Tal ve gt SOOM OS WiO 8 9 Pe E E E de mnver vio Ja Operator 8X Display Use the data manager to drag and drop images into your layout E Sag Sag Layout 2 rows 2 cols Data 1 CT DEMO vy 3 NMDEMO None Show ROIs Show ROIs All No Imag No Imag Operator DM Resampling images to reference image took 0 1 sec In the 5x5 grid itself the boxes will read either Cor Sag or Tra which corresponds to the type of slices displayed in the Viewports To change the type of slices in a particular Viewport simply double click on the corresponding box in the grid and select the desired slice type Setting Up the Multi View Display 139 VS VivoQuant Manual 11 12 2015 E Mw y VivoQuant 2 50rc10 64bit
51. ROI E icf l Toggle Hide ROI EE Ric Toggle Immutable E En Reset ROI MX Delete ROI Export ROI ROIs 1 xX Y Brain Delete an ROI To delete an ROI click on the red X Delete ROI button Use the interface that appears to move the pixels of the selected ROI to either the background or another selected ROI The ROI will no longer appear in the drop down menu of ROIs after being deleted This will only delete the ROI that is selected in the ROI dropdown menu ROI Creation and Deletion 40 VivoQuant Manual 11 12 2015 Move pixels to ROI background Another option is to select any one or shift select more than one of the ROIs in the operator right click and select Delete ROI s Operator y k amp all a Ak a sy me h ROI H x E i M background W Brain E LeftKidney W RightKidney Edit ROI Liver Add ROI 1 34 EI gL CERS E Le CI Toggle Hide ROIs Toggle Immutables Ye Reset ROIs Delete ROIs Export ROIs Reset an ROI To reset an ROI click on the broom Reset ROI button Use the interface that appears to move the pixels of the selected ROI to either the background or another selected ROI The ROI will still exist after it has been reset but it will no longer have any voxels associated with it This will only reset the ROI that is selected in the ROI dropdown menu Move pixels to ROI background
52. SPECT 317 sets and 1 4 point data set from the Data Browser The MMP Tool will read in the calibration data recognizing which data corresponds to which calibration The panels for the individual calibrations see VivoQuant Manual 11 12 2015 below display the completeness of the data Once all necessary data is present the Run buttons are used in succession from the top calibration Aluminum Grid to the bottom calibration Four Point Results for each calibration are presented in their respective panels a description of possible errors is listed in Calibration Failures Open Calibration Data 2 K Look in E MMP calibration a er EE Ea ud 4 My Recent Documents Desktop My Network Places E 1 3 6 1 4 1 12542 1 1 14 2 20071113 185627 296 729921615 i 1 3 6 1 4 1 12842 1 1 14 2 20080125 142515 109 3642609221 1 1 3 6 1 4 1 12842 1 1 20 2 20071113 140737 125 2602351871 Es 1 3 6 1 4 1 12542 1 1 20 2 20071113 140825 937 2948522600 E 1 3 6 1 4 1 12842 1 1 20 2 20071113 140915 343 2101409203 E 1 3 6 1 4 1 12542 1 1 20 2 20071113 141012 406 244511268 1 3 6 1 4 1 12842 1 1 20 2 20071113 141059 812 546678475 E 1 3 6 1 4 1 12842 1 1 20 2 20071113 141146 953 3006267643 E 1 3 6 1 4 1 12842 1 1 20 2 20071113 141242 375 3625115377 E 1 3 6 1 4 1 12842 1 1 20 2 20071113 141338 546 3725074632 EE 1 3 6 1 4 1 12842 1 1 20 2 20071113 141432 937 2781974288 E 1 3 6 1 4 1 12842 1 1 20 2 20071113 141525
53. VTK image Hold this button down to specify the resolution of the image m VTK Viewer 192 Data Manager The Data Manager presents information about the datasets loaded into VQ While VivoQuant only displays up to three datasets in the Display at a time post processing operations may be performed on any number of datasets in the Data Manager The system memory is the only limiting factor in the number of simultaneously loaded datasets Getting There There are three methods to open the Data Manager The first method is using the DM thumbnail in the controls palette of the Main Window m lt 3 Dieribar EL AE The Data Manager may also be reached via the Tools Menu z View control MIP contro Data Manager Min Max Histogram Ctrl Shift H Workflow Assistant Pre processing Resarnple data DICOM di pi ki m gt a Image amp Movie gt Update Check Ctrl Shift U Configuration Ctri Shift C Ex Finally the Data Manager is also available by using the keyboard shortcut F7 Using the Data Manager Data Manager 193 VivoQuant Manual 11 12 2015 DM a x Data List Loaded 4 Memory 21364MVB X Available Data Type CT CT Reconstruction Name DEMO DEMO 1 Desc DEMO Dim 176x176x452 Vox 0 200 20 mm 3 500 Type NM NM Reconstruction Name DEMO DEMO 2 Desc DEMO Dim 176x176x452 Vox 0 200 20 mm 00 Type NM NM Reconstruction Name DEMO DEMO 3 Desc
54. and Thresholding tools C C Within the Spline tool clear 11 12 2015 214 VivoQuant Manual 11 12 2015 the currently drawn contour Keyboard Shortcuts 215 Autoradiography Calibration Autoradiography data can be loaded viewed analyzed and saved using the same tools VivoQuant uses for in vivo image data Once loaded into VivoQuant data can be reoriented cropped rescaled and quantified The Autoradiography Calibration tool allows a user to calibrate autoradiography data based on known calibration standards in the image This tool is available only with a CiQuant Module license If you are unable to use the tool and would like to please contact support invicro com Getting There To access the tool go to the 3D ROI Tool then Operator gt Autoradiography Calibration File View Tools Advanced Modules Help se 99M0 BOGOF 2 2 90 E BS mu siceview 7 toate 7 R Quick Scripts LO O Y avigation A Display Quantification Reorientation Registration Time Series Distance Annotation Checker board Cropping Arithmetics Filtering les Operator Help O A Autoradiography Calibration x Display Function Getting Started Once the tool starts it will ask questions to establish how it will be used The first prompt asks for the number of calibration standards being used This will determine the number of ROIs that populate the 3D ROI Tool Ya Autoradiography Calibration BESI
55. box Can contain any alphanumeric Data Browser Repository Panel 242 VivoQuant Manual 11 12 2015 Repository Local folders are simple directories Type available on the local computer also via a shared network Such directories with many files take rather long to scan in this case the performance of a DICOM server 1s Superior Such DICOM servers are network services on the local or a remote computer They provide a database to efficiently browser study data An PACS server 1s an online PACS server a regularly used picture archiving and retrieval system for medical images Select a local directory All sub folders will be displayed as projects in the second repository drop down window Username and password are specific to the user for their site s iPACS system Hostname will be the site of the server for the PACS and Port is the communication channel through which the iPACS server communicates DICOM server A DICOM server is specified by a calling AET application entity title a called AET as well as a TCP address consisting of a host name and a port the default settings are localhost 104 The AETs have to be configured on the DICOM server too For VivoQuant use port 23104 on the remote server PACS server An PAGS server is specified by setting the appropriate Hostname and Port and by entering user specific Username and Password A DEMO iPACS server may be registered by using Hostname demo ipacs invic
56. datasets Recalculates the min max values for all data sets from Re calc the original data Min max value will be min max voxel values in dataset Resets the min max values to the values stored in the Reset cache 1 Stores min max values in cache and applies values to the PPly datasets The buttons with the icon will clip the data based on values in the tool This can be useful when trying to clip dense bone from a CT scan for instance or background noise from a PT scan 0 Min Sets all values below the minimum to 0 4 0 On Sets all values above the maximum to 0 minimum maximum Histogram The Histogram button ist opens the Histogram Tool This tool generates a histogram of voxel values in the loaded datasets For more on this visit the Histogram Tool page Percentile Tool The Percentile button _ brings up the Percentile Tool which calculates the pixel value associated with the Xt percentile from the histogram of the image MM Gx Min Max Min Max Unit Reference 0 4000 HU Re calc Input 1 0 0 00101808 uCi Reset Input 2 N A alt Hist 0 Hd 0 Tool min max Y Apply Percentile Tool Percentile 99 900 Ref v E amp ROI FieldofVi Copy To Max Function 198 Percentile Tool VivoQuant Manual 11 12 2015 Calculate the percentile value for selected image in the drop down list to the right COPY to Copy computed pecentile value to the Max value above Sho
57. different than functions for controlling the slices VTK MIP To freely rotate the VTK MIP click and drag the mouse across the MIP To zoom in and out scroll the mouse wheel forward and backward To pan around the MIP hold the Shift key and drag the mouse across the MIP To rotate the MIP about a fixed axis of rotation hold the Ctrl key and drag the mouse in a circular motion across the MIP scrolling 34 VivoQuant Manual 11 12 2015 Classic non VTK MIP The Classic MIP cannot be freely rotated panned or zoomed in out on like the VTK MIP The only navigation available is changing the View Angle i e rotation about the transverse axis This can be accomplished by scrolling with the mouse wheel or by dragging the View Angle progress bar in the MIP Control window Tooltip The tooltip feature is available by briefly holding a mouse click on any of the three slice views transverse sagittal coronal in the Navigator window The tooltip feature displays x y z coordinate locations and voxel values for each displayed data set for that x y z position VTK MIP 35 VivoQuant Manual 11 12 2015 80 114 292 CT 17 2846 NM 0 000646776 This information is also found in the Viewer Control For more on using the Viewer Control see the Viewer Control page Tooltip 36 3D ROIs 1 Getting There 2 ROI Creation and Deletion 1 Add an ROI 2 Edit an ROI 3 Delete an ROI 4 Reset an ROI 5 Hide an ROI
58. download destination for each file downloaded via iPACS sync from the global setting iPACS Sync deleted files Store Job 11 12 2015 Click Save at the bottom of the window to save any changes to the Sync configuration Click Cancel to discard all changes since the last time the configuration was saved Return to the Top Advanced 368 PACS Sync GUI The following sections describe how to run an iPACS Sync job e Run a Sync Job e Icon Descriptions e Quick Sync Run a Sync Job Sync jobs are created modified in the configuration window To run a job select the appropiate job and click Run iPACS Sync File Jobs Help Loafile Job test y A Run Y Create New Job 2014 08 04 17 44 34 pacesync o 264 Done 2014 08 13 12 07 38 Reloa 2014 08 13 12 07 38 ds iris from registry 2014 08 13 12 07 38 Found 9 job entries Starting normal operation now 2014 08 13 12 07 44 ipacssync test2 to iPACS Start Sync Status Starting Checking sending incremental file list Sample_Data_Set zip ric OS via NN Icon Descriptions E Pause a Sync Job S Run all active Sync Jobs x Stop a Sync Job A Open the configuration page 2 Open the help guide Quick Sync This feature 1s a simple way to quickly download all files from a WebDisk folder or 1t can facilitate the transfer of large amounts of data from the PAGS to a local location To download all files and folder
59. fu si gt CT Geometrical CT Reconstruction Ctrl L CT Window Presets gt Abdomen Bone Brain Cardiac Liver Lung Pelvis ST Soft Tissue Spine Whole Body 282 CT Reconstruction The CT Reconstruction tool offers a variety of algorithms and filters for generating 3D images from x ray projection data Also included is a tool for performing Batch CT jobs Getting There There are multiple ways to reach the CT Reconstruction panel First it is available in the Tools Menu VivoQuant File View 600 15 VivoQ vce Slice control FS onkFocused CT CT Reconstructed Slices M mc MIP control F6 B ew y VC MC DM MM Sice View a y W om Data Manager F7 A J Display v Link MIP Slice control v Global scale per mod v Apply default shift CT Reconstruction DICOM Bed removal Advanced Analysis Resample data Histogram CT Window Presets Volume rendering Image Magick mu Min Max W Workflow Assistant Calibration Update Check It can also be reached via the Data Browser by selecting Open when a set of CT Projection data is highlighted and the Auto Start Reconstruction box is checked Right clicking on an appropriate data set in the Data Browser will also present the CT Reconstruction and Batch CT programs CT Reconstruction 283 VivoQuant Manual Repository SECURE Q Demo Pacs invicro_demo vivoquant VivoQuant Y A Projec
60. hit L again to refresh the Study Browser Note that filtering uses a Unix like naming structure Therefore if you want to find all studies that begin with Mouse enter Mouse in the filter for Patient s Name In addition if you wanted to find any study containing 1123 enter 1123 in the filter for Patient s Name Also available in the filter options is the function used to expand or collapse the entries currently displayed in the Data Browser The first click will expand all data at the patient study level the second click will then expand at the series level the third click will collapse the series level the fourth click will collapse patients studies Repository 336 VivoQuant Manual 11 12 2015 Before expansion 4 12 50 Demos tudy aa demo Datab 2010 03 24 13 44 an 2010 03 26 12 52 DemoStudy 2010 03 08 12 51 DemoStudy 2010 03 08 12 09 DemoStudy 2010 03 26 17 40 DemoStud 2010 03 24 12 50 DemoStudy StudyDescription Patient ID Study Description Patient ID 2010 05 2215 01 176176 2010 05 26 02 46 Image Date Dimensions 2010 05 26 02 46 176x176 Topo CT SPEC Dimensions 176x176 Ima Image Date Dimensions InstanceNo Wi 2010 05 26 01 43 96 96 0001 4 STUDYIAZ2 B 2010 05 19 18 34 CT SPECE INT Filter 337 10 Expanding large numbers of datasets can take several minutes Data VivoQuant Manual 11 12 2015 The Data section provides several functions for manipu
61. iPACS If for some reason the wizard is not able to download the key it can be accessed via a web browser on the home admin page The admin page is only available to users with the admin role Once the Sync Key is installed click Next Specify the direction of the Sync Provide the complete path to the local directory to use in the Sync Select the project on the iPACS to use for the Sync 0 N ANA Configure a Sync Job 363 VivoQuant Manual 11 12 2015 The 9 button will retrieve a list of projects on the iPACS which can be selected by clicking the arrow to the right of the text field The path of the iPACS project can also be manually entered in the iPACS Project field e g project testing_wc 9 The WebDisk folder for the selected project will automatically be entered into the WebDi sk Folder field Subfolders can be selected by clicking the arrow to the right of the text field 10 After entering the required information click Next O PACS Sync Job Wizard Sync Folders Select the source and destination folders to keep in sync Sync Direction To iPACS Local Foider C fUsers User 1 Desktop New foider iPACS Project petstudy1 WebDisk Folder webdisk projects invicro_lab petstudy 1 Cancel 11 A summary page shows all the selected settings for the new Sync job 12 Enter a name for the Sync job then click Finish O iPACS Sync Job Wizard New Sync Job Host https t
62. image Creates a new ROI entry representing the Select field of view the entire volume of the image The OV quantification table will be populated with this entry and labelled as FOV Cutting and Quantification Table Control 70 Reorientation Registration Tool The Reorientation Registration Tool enables manual and automatic realignment of image data via translation rotation or flipping Reference and input data may be manipulated separately and specific translation settings may be saved loaded for future studies including the option for setting automatically applied default image shifts 1 Manual Registration Options 2 Automatic Registration Options 3 Landmark Based Registration Options Getting There The Reorientation Registration Tool can be accessed via the tool pull down menu on the VQ front panel File View Tools Advanced Modules Operator Help SY SY M ot 0000 05 OU OO YD ec S Mc i Mu Slice View v _Reorientation Registration i Navigation A Display 3D ROI Tool Quantification i Pe Quick Scripts gt 4 D O Reorientation Registration Time Series Distance Annotation Using the Tool When the Reorientation Registration tool is selected a Reorientation Registration operator window 1s displayed Reorientation Registration Tool 71 VS VivoQuant Manual 11 12 2015 19 VivoQuant 2 10 64bit DEMO DEMO CT DEMO NM DEMO EY File View Tools Advanced Modules Operator Help
63. most panel in the 3D ROI Operator presents the interface for basic input output operations quantification and viewing functionality To freely naviagate through the slices with the cursor 1t is necessary for this panel to be active Operator r le je js ja 4 vk e ND X al e ROI H M background MM Brain E LeftKidney El RightKidney _ E Heart gt Liver ROIs 1 X gt l background v The buttons at the top of the operator window perform various functions within the operator A Load or save an ROI from disk or iPACS s Render ROIs in the MIP view G amp Reset the camera view Reset all ROIs ROI Loading Saving and Quantification Tools 43 VivoQuant Manual 11 12 2015 ll Show the image histogram E Show the quantification table Bl Save the quantification table to disk bl Perform a cut on an image using an RO El Perform a copy or paste on an image using an ROI Load an ROI from disk The 3D ROI tool supports file formats of VQ 3D ROI rmha and vtkStructuredPoints vtk To load an ROI from disk click the Load ROI button and select the desired ROI Save an ROI to disk To save an ROI to disk click the Save ROI button and specify a name and location for the file The ROI will be written as an VQ 3D ROI rmha file All existing regions will be written to the same ROI file Load an ROI from an iPACS To load an ROI from an iPACS c
64. of the Layout operator and select the Navigation operator from the drop down menu The functionality of the Navigation operator in Multi View is identical to its functionality in Slice View Mouse and keyboard functions including Keyboard Shortcuts are preserved Viewer Control in Multi View The functionality of the Viewer Control is extended in Multi View to cover the new viewport layout This extended functionality includes the ability to view voxel and color information for each viewport in the Display as well as the ability to unlink the viewports enabling them to be navigated independently of one another Using the Multi View Display 141 10 Eroding Dilating took 1 6 sec VivoQuant Manual 11 12 2015 VivoQuant 2 50rc10 64bit DEMO DEMO CT DEMO NM DEMO NM DEMO DES File View Tools Advanced Modules Help So vc ak TERE Y lt W te 0000 08 T AOO Bove Mu Multi View v Navigation y 2 VC Xx Display MultiView 2 2 cn Y Link Views Sliders X 72 E Y 126 Z 295 Color Controls Voxel Value Intensity Y Ref 310 603 HU 100 Y Inp1 0 000817677 uci 100 Y Inp2 0 000817677 uCi 100 Show ROIs VC DM MM For more information on using the Viewer Control in Multi View see the Viewer Control in Multi View section of the Viewer Control page Viewer Control in Multi View 142 MPR View The MPR Multi Planar Reconstruction View simultaneously displays a s
65. sade 212 EONCU OI N 212 Keyboard SO 213 Autoradios raphy Calra On esssscccscencesceseesssecnecacenscesiacssscudssdnceseesedotesceudasesccidadssvadvasdvesseeesevecssnsecsoueceadeusswes 216 Getino Tete ns 216 EUA tdt lts caes 216 GENO SLAC ii iaa 216 AA A eee tre ere ee vaCrne ns monte Sart re ent eener ne tran ye Semon tetera rete aa 217 MTA VTA kiari E E EE OES 219 Ec e A T OA N 219 A a a NA 219 SDE Movie TMO TAME a a E NE 219 OMG Framnes tO MOV Gersei a a oda ees sendasoss 219 chanse Dean a a a aN 220 Mito POS a a a ren Te WNT Memerer myer er vert 220 Made to Caputo iio 220 Howto Make dynamic MOVIE rai a 220 Upd te COCK PUC UU un A 231 Getin Tecnos 231 UTA OMe lt losas e aaued 231 VIVOO UAT CONSUL ION a asia 232 Contisutatio Ral a a E E 232 O 232 A RO 233 E A ION 233 Maximum mtensityuPro ECON tido 234 AS A A 234 DAA AAA 235 Data COn ea ida e Tt ree 235 OU anal OM PONS poso io A iS 237 Data Mahad ie io ed eos ts esata stds vaca de aca itales 238 viii VivoQuant Manual Table of Contents DICOM SC iaa ais 239 A AN a 239 CO mit OU ATOM MD AOS osa 239 DICOM SENNO sun idas 240 PTOI GAG Suso ett lata atte he sata eased sacl shite esi eae tad tas SUN 241 CAN di e a io rer ret 241 Data Browser Repository Pal Riad 241 DICOMDMEE CIDE toscas ui outros te REE ol coi e ua sae 242 PAC SAPO CUS AA A e PEE US E O 243 How to configure the NanoSPECT s DICOM Servet S ccccccccccccceceeeeeeeeeeeeecsaeesseessssses
66. shooting categories below Trouble shooting categories e Service Reporter Gather information automatically and manually selected to send a service support report e Memory Solve memory issues on Windows 32 bit systems e Debugging View VQ debug messages and or activate log file e Saving images movies Solve issues saving images or movies e Logfile Where to find the VQ logfile e Mac OS X stability Solve stability issues especially during the upload of ROIs due to the limit on file descriptors allowed by a program Service Reporter The VivoQuant Service Reporter is the easiest and most efficient way to report issues you run into Troubleshooting File View Tools Advanced Modules Help Request Help PET v Log out Ctri Shift X f Display Registration l B Enable Logfile Debug View Hints Manual We About 371 Memory configuration Windows 32 bit Please consider using a 64 bit operating system to avoid memory problems To allow VivoQuant to access the entire Windows memory please add a 3GB switch to your local C boot ini start up file as shown below boot loader timeout 30 default multi 0 disk 0 rdisk 0 partition 1 WINDOWS operating systems multi 0 disk 0 rdisk 0 partition 1 1WINDOWS MS WinXP Prof noexecute optin fastdetect 3GB Please note the file is a Windows system file and might be hidden Please use the Windows folder settings to remove this filter or ask you
67. the H column to hide ROIs Check the boxes in the T column to make ROIs immutable ROI Loading Saving and Quantification Tools 46 VivoQuant Manual 11 12 2015 Operator F Xx ok ole e A tk AX alk Eee ROI H M background E Heart El BM Liver C AI E MM LeftKidney Y A ia Brain Y ROIs xi X gt HE background x Copy paste the 3D ROI Click the Copy or Paste ROI button to copy and or paste ROIs between instances of VivoQuant Painting Tools There are a variety of paintbrushes to choose from when creating an ROI The sphere cylinder or cube paintbrush can be selected by clicking the corresponding radiobutton on the Painting tab The radius of the paintbrush can be set by changing the number of pixels shown in the numerical spin box These 3D paintbrushes extend across multiple slices to activate 2D mode mark the 2D only checkbox In 2D mode the paintbrush will only paint on the current slice Note an ROI must be added before utilizing the painting tools Operator ax e ole als Use a sphere or circle to paint ROI over data a O Sphere _ 2D only Cylinder 12 px Cube C Sync Pos Erode Dilate to remove add layers of voxels to an ROI 5Dilate v Mapto Liver Y _ 2D only _ Current Slice only Re render ROI ytk ROIs 1 x Mio E background Painting Tools 47 VS VivoQ
68. the DICOM Editor Shows list of additional dictionaries used by the DICOM library Please set environment variable DCMDICTPATH to set this value For more on the DICOM dictionary see DICOM Dump When this box 1s checked the palette window will be loaded in accordance not checked the palette window will be set to whatever the window was set to last Checking this box enables support for PRONTA DICOMDIR files Folder Filter Allows users to dictate the type of dicom files loaded into VQ Users can configure loading extensionless dicom data by adding a space and to the end of the default settings DICOM Settings 20 VS VivoQuant Manual 11 12 2015 Folder Filter dom dc3 dicom IM_ S_ DICOM Cache DICOM Cache Current size 0 0 MB 0 Max size 1000 MB gt free 870422 3 MB Life Time 14d 5 Clear The DICOM cache allows the storage of frequently used data sets locally thus improving load time into VQ Every time the VQ is started it checks the current size of the cache against the maximum cache size If the currect cache size exceeds the maximum cache size then older files those opened least recently in the VQ are removed i Size in Mb of the data currently stored in the DICOM Cache The percentage to the right of the field indicates how close the cache is to capacity Maximum amount of memory that can be made available for the DICOM Cache ZE default 1000 0 MB Length of time ove
69. the default settings though Choose Components 5 VivoQuant 1 05 Setup Choose Components Choose which features of VivoQuant 1 05 you want to install Check the components you want to install and uncheck the components you don t want to install Click Mext to continue Select components to install VivoQuant PEST IPUN QT4 libraries ImageMagick binaries BatchCT service 4 1 21 CFR part 11 4 1 Options CT Disable options C Debugging Space required 49 6MB lt Qt4 libraries Installation Details Unless you already have Qt installed on your system it is highly recommended that you use the version coming with VQ Installs the IM programs mpeg2encode required for generation of MPEG movies and convert general tool to convert image formats After installation the manual is available by pressing lt F1 gt on the main VQ screen or using the HelplManual menu Alternatively you can also find the manual online at http www vivoquant com manual index html without further user interaction environment FDA s electronic record keeping regulations VivoQuant Manual 11 12 2015 Shortcut on desktop Install an VQ icon on Windows desktop Place a quick start icon for the CT reconstruction module on desktop CT Reconstruction shortcut on desktop DicomBrowser quickly Open DICOM data Add local DICOM Adds an example DICOM folder to the list of folder repositories CTReco shortcut on des
70. the image in the Input 1 position visible with all other images of the series The Time Series operator also enables users to set a global min max value which will apply to all loaded images To set simply check the Global box and enter a minimum and maximum into the respective boxes Use the slider or image index field to manually scroll through the datasets of the series Click Play to run the sequence in a loop Saving a Movie To save a Time Series movie open the Save Movie dialog with the Time Series operator open This can be done by clicking the Save Movie icon in the toolbar navigating to File gt Save Movie or by the keyboard shortcut Ctrl M Time Series 82 VivoQuant Manual 11 12 2015 Look in C Users kgoettler Desktop DEMO OO BESI A My Computer R kgoettler Save Files of type Movie files gif mng mpg mpeg X Cancel File name TimeSeries gif Movie type Time Series Sagittal slice Colorbar options none Storage Type Local image file The options for the output movie are similar to those in the regular Save Movie dialog box The only difference is the options in the Movie Type drop down box reflect the Time Series movie types Once the desired options are set select Save to save the movie file Saving a Movie 83 Distance Annotation Tool The Distance Annotation tool enables you to measure the distance between two points in any image For example 1
71. the model fit by clicking on it with the image viewer e BPxp R k k and mean squared error MSE of fit are shown when the cursor is hovered over the model fit plot e Parameter maps for BPyp R k k and MSE References 1 Simplified reference tissue model for PET receptor studies Lammerstma and Hume Neurolmage 1996 Link 2 The simplified reference tissue model model assumption violations and their impact on binding potential Salinas et al JCBFM 2015 Link Simplified Reference Tissue Model SRTM 107 VS VivoQuant Manual 11 12 2015 3 Kinetic modelling using basis functions derived from two tissue compartmental models with a plasma input function general principle and application to 18F fluorodeoxyglucose positron emission tomography Hong et al Neurolmage 2010 Link Additional Resources Reference region input compartmental models Vesa Oikonen Turku PET Center website Link Simplified Reference Tissue Model 2 SRTM2 SRTM2 is a two pass version of SRTM that attempts to reduce noise in parametric images by fitting all voxels with a fixed global k 1 In practice SRTM estimates k for every voxel or region but since there is only one reference region in principle there is only one true k value 1 Fixing k reduces the number of parameters estimated and thus reduces noise in parametric images 1 However this improvement in precision may come at the price of an increase in bi
72. the reconstruction of the data collected at that energy Set each Intercept 1000 Ensure that the enable calibration box Shown in the Hounsfield panel above is checked Reconstruct the CT a second time Select a region of the syringe encompassing both water and air Values in water should be near 0 while those in air should be near 1000 Hounsfield Calibration 297 VivoQuant Manual 11 12 2015 BB invivos ope 1 3 3beta3 ct_linearity_test_take4 CT CT recon for_HU2 Ele Wew Tools Heb bem E 5 o mM at Bm 30 volume Sum Mean Rddev Steer Mn Max rren HUfMBQ HUlKBq Mus MUS GNB 1906 63 511746 2 14723 46 5562 0 0959796 212 711 143 513 _inewky_test_take Patient 392 392 1 856030 07 990 036 27 9221 0 126076 1000 774 129 C_inearty_test_taket O res Isocourt tax Hounsfield Calibration 298 CT Reconstruction The CT Reconstruction tool offers a variety of algorithms and filters for generating 3D images from x ray projection data Also included is a tool for performing Batch CT jobs Getting There There are multiple ways to reach the CT Reconstruction panel First it is available in the Tools Menu VivoQuant File View 600 15 VivoQ vce Slice control FS onkFocused CT CT Reconstructed Slices M mc MIP control F6 B ew y VC MC DM MM Sice View a y W om Data Manager F7 A J Display v Link MIP Slice control v Global scale per mod v Apply default shift CT Re
73. the tool Upon selection of the Arithmetics operator the Arithmetics operator window is displayed Operator Operator Scalar Multiply Scalar Selected y Apply to i Ref inp1 7i Inp2 Scalar 1 00000000 4 x Cancel The drop down menu under Options contains a selection of the available operators e Add Subtract Multiply Divide and Average each operate on the two images loaded in the Ref and Inp1 positions These operations are performed voxel wise e Scalar Multiplication and Scalar Addition can be applied to any of the first three images loaded by checking Ref Inp1 Inp2 or to all images beyond the first three by checking Inp Set the factor or addend by increasing or decreasing the scalar value e Merge whole integer value phantoms to load into the 3D ROI tool Can be applied to any of the first three images loaded by checking Ref Inp1 Inp2 or to all datasets beyond the first three by checking Inp This is very useful for fixed volume ROI analysis Arithmetics 92 VivoQuant Manual 11 12 2015 Operator ax Operator Add Ref Inp1 Subtract Ref Inp1 Divide Ref Inp1 Average Selected Merge Selected Scalar Multiply Scalar Selected ScalarAdd Scalar Selected Scalar Exponentiate Selected Scalar Click OK to perform the chosen operation A dialog will appear to indicate successful application of the chosen addend or factor Applied Addition For scala
74. to SUV Calc The calculator will automatically import the associated data Activity os91 MBa vi Patientweight 0o00 9 vw Volume 0 2870 m v Injected dose Concentration suv File Menu The Quantification package also provides several options for saving quantification and ROI information Quantification Table Options 68 VivoQuant Manual 11 12 2015 40 File View Tools Advanced Modules a Help 00 a v e SY W ES ae 0 M Save table Ctrl S as 1c BE Append to table Ctri A Operator Clear table Mode Options ai W Load RO Ctrl Shift L a 2 a Save ROI Ctrl Shift S On Submit to iPACS Threshold Ref O amp View b OK dl eet ee Cut outside ALL Cut gt Help Global Rotate Shift Wheel Scale Alt Wheel Submit O Select FOV Points Drag Left Remove Mid Open curve Shift Mid Curve Drag Shift Left Add point Double Click Close Right Bully Add start point inside curve Remove outside curve Menu _ Saves the current Quantification table Accepted Save table formats include csv txt and xls Note For opening data in Microsoft Excel save it in xls format Append to Appends the current Quantification table to a table previously saved table oad ROI Loads a O saved ROI ave ROI Saves Saves the currentROIasa roifile current ROI as a roi file Copy Copies the data in the Quantification table to the table clipboard Sal Clears the current Q
75. to and stored Once the folder is selected click OK to run the job Download individual files from the PACS via PACS sync Downloading individual files using iPACS sync is advantageous for large data sets To do this follow the steps described here iPACS Sync 362 Configure a Sync Job This page contains information on the various steps and options available for configuring an iPACS Sync job e Create a Sync Job using the Wizard e Configuring Additional Settings e iPACS Setu e Directory Setup e Scheduler e Notifications e Advanced e Store Job Create a Sync Job using the Wizard To create a new job click Create New Job at the top of the iPACS Sync application window This will launch the iPACS Sync Job Wizard which will guide you through the process of setting up a Sync job pad Specify the iPACS URL or IP address in the iPACS Address field Previously used addresses are available by clicking the arrow at the right of the text field 2 Enter the username and password to use for the Sync Data transfers adhere to the roles associated with an iPACS user s account 3 After entering the required information click Next O PASS Sync Job Wizard Configuration This wizard will help you configure an iPacsSync job to a selected iPACS Server PACS Address training ipacs invicro com User testUser Password so 4 The wizard will attempt to download and install the sync key file for the specified
76. to be configured on the DICOM server too For VivoQuant use port 23104 on the remote server PACS server An PAGS server is specified by setting the appropriate Hostname and Port and by entering user specific Username and Password A DEMO iPACS server may be registered by using Hostname demo ipacs invicro com Port 80 and leaving Username and Password blank iPACS servers also enable the use of Projects a useful tool for organizing DICOM data Optimized local access To use the optimized local DICOM access much faster use localhost all lower case otherwise a normal DICOM connection is used as the host name Additionally you have to define the DB path see above PACS Projects The PAGS repositories permit the use of projects Projects represent a directory structure for DICOM repositories Data may be stored and accessed via different projects aiding organization of DICOM data In DICOM Editor 23 VivoQuant Manual 11 12 2015 this example an iPACS repository for bioscan demo is being configured The bioscan demo repository contains three projects on Displayed Name iPACS Documentation Repository Type Mb Local folder DICOM server Pacs Local DICOM folder lt Username Password Hostname ipacs invicro com bioscan demo Cancel If any projects are present within a configured iPACS repository a second pulldown menu will appear in the Repository panel of the D
77. transformation settings rotation translation flips as default settings for image data If the Apply Default Shift checkbox is selected these settings will be automatically applied to any image data that then gets loaded See the How To Guide for more on setting a default image shift Resets all transformation Ctrl R settings rotation translation flips back to the default values Ctrl Return Applies the current transformation settings rotation translation flips to the active 76 VivoQuant Manual 11 12 2015 Provides the option of flipping the data in any of three directions described as Head Feet Left Right and Anterior Posterior Directs the user to the Resample Data tool The Resample Data tool allows rebinning of reconstructed data into an arbitrary voxel size Transformation which applies T1 to the source and then applies T2 to that result to obtain the target Transformation which applies T2 to the source and then applies T1 to that result to obtain the target Sets reference point for transformation as center of ROI instead of center of image Toggles appearance of Scaling under 3D and 2D manual registration panels Automatic Non Linear Registration The 3D Automatic Non Linear Registration tool provides deformable registration of the data by computing a unique transformation matrix for all voxels of data represented After selecting your preference from the dropdown the number
78. two subsets 12 and 18 e The final element of the DICOM entry is the description of the data entry For DICOM defined tags this field will display relevant information regarding the content of the data entry 1 e VQ DICOM Example For private tags this field will display Unknown Tag and Data Function 208 VivoQuant Manual 11 12 2015 Anonymizer The Anonymizer anonymizes the data to the user Getting There Go to the Tools Menu in the Main Window then DICOM File View Advanced Modules Help e SY View control F5 POS PAo MIP control F6 DM Data Manager F7 as Display Data List Min Max Loaded Histogram Ctrl Shift H Workflow Assistant Pre processing Resample data _ DICOM a DICOM dump Ctri Shift D E Image amp Movie gt Anonymizer IT Rename DICOM PA Y EDak HOR Type NM Vl Update Check Ctrl Shift U Name DEI 2 per A Configuration Ctrl Shift C Relabel Study Dim 176x17 Function Upon selecting the Anonymizer a dialog box appears prompting the user to decide whether to anonymize each loaded dataset individually Yes or anonymize them all together No O Do you want to anonymize each loaded data set individually If not the same anonymization will be applied to all data sets In the Anonymizer header fields can be edited to remove sensitive information such as the imaging dates or identifying text fields The fields can be edited ma
79. vivoquant VivoQuant Y A Projects VivoQuant Manual Study Browser Patients Name ADC_M1_1 48h ADC _M1_1 48h ADC_M1_1 3h ADC_M1_1 24h ADC_M1_1_144h StudyDate 2010 07 22 11 25 2010 07 24 13 29 2010 07 20 12 18 2010 07 21 12 01 2010 07 26 11 52 StudyDescription Patient ID Topo CT SPEC Topo CT SPEC Topo CT SPEC Topo CT SPEC Topo CT SPEC 11 12 2015 o aro Show data type All data types v ge Bw C Apply default shift Y Auto Start reconstruction _ Force planar C Stack 3D gt Append Open Adjust the Zoom and Color Palettes to your liking How to make a dynamic movie 221 VS VivoQuant Manual 11 12 2015 Mw sa a es ae File View Tools Advanced Modules Help e SY M fats 0000 os o gt Sa O O Bove ee Mu Slice View Navigation y Quick Scripts 41 D VivoQuant 2 50beta8 64bit DEMO DEMO CT DEMO NM DEMO NM DEMO aS DM xX Display Data List Loaded 5 Memory 267 05MB X Available Data Type CT CT Reconstruction Name DEMO DEMO 1 Desc DEMO Dim 176x176x452 Vox 0 20x0 20 mm 3 52 03 Type NM NM Reconstruction Name DEMO DEMO 12 Desc DEMO Frame 01 Dim 176x176x452 Vox 0 20x0 20 mm ood WI REconNu uco Type NM NM Reconstruction Name DEMO DEMO lA Desc DEMO Frame 03 Dim 176x176452 Vox
80. well as important registration and set up information Configuration Panels The Configuration window consists of six panels including e Display e Data e DICOM Settings e Network e Registration e VivoScript Getting There The Configuration window is available in the Tools Menu on the PC On the Mac it is available in the VivoQuant menu under Preferences File View Advanced Modules Operator Help GQ g View control FS y 3 s MIP control F6 m A VivoQuant File View Tc perator gt es Data Manager F7 A About VivoQuant la h Min Max e a vtk at Histogram Ctrl Shift H 20 id l gt M Workflow Assistant EE iotishinatin z El Pre processing Hide VivoQuant 36H ROI Hii Resample data 1 Load Hide Others 36H Show All lt DICOM gt M backgrou ae A d T x mae Image amp Movie Quit VivoQuant Q VW Update Check Ctrl Shift U Configuration Ctrl Shift C mn Another method for reaching the Configuration window to use the keyboard shortcut Ctrl Shift C For more on keyboard shortcuts in VivoQuant please see Keyboard Shortcuts VivoQuant Configuration 232 Display Several appearance features of VivoQuant may be customized in the Display panel including General display information Maximum Intensity Projection attributes and Color Palette defaults General Display Option Font Style Font Size Cross hair style color Pal Path Preview Pa
81. will be installed on VivoQuant will then be located in the Applications folder C Linux Double click and unzip the VivoQuant zip archive then move the VivoQuant folder to the desired location To run VQ double click the VivoQuant script contained in this folder 3 License Registration Active Accounts VivoQuant License Management Site manages all licenses allocated to an account An on site license manager login credential will be provided to each account to access the VivoQuant License Management Site For detailed information on how to manage your acount s VivoQant licenses Click Here ll Trail Accounts Methods for Obtaining a Trial License If you are a current end user and have an active software account contact your account representative for a trial license of a plugin module Your account representative will pre approve the trial license and you should follow section II b below If you do not have an active account please follow the below steps a Requesting a Trial License e Download the latest stable version of VivoQuant Once you have successfully installed VivoQuant you will be prompted to register your computer Click Yes yi DEMO MODE MODE This allows you to check out basic functionality of VivoQuant however we O VivoQuant has not found a valid license and thus started in a limited DEMO recommend you file a license requests with your institution you will need the INSTITUTION CODE or use DEMO
82. 0 to estimate the gradient field present in the image and uses this filter to normalize each voxel of the image Due to the higher performance cost a preview of its filtering is not available but the filtering can be applied via the filtering operator The user may optionally adjust the field smoothness to avoid or allow high spatial frequency corrections and also append the estimated bias field as an image to the data manager Bias Field Correction 97 VivoQuant Manual 11 12 2015 Bias Field Correction 98 Modeling 1 Getting There 2 Function 3 Models 1 Two Tissue Compartment Model 2 TCM 2 One Tissue Compartment Model 1 TCM 3 Logan Graphical Method Logan Plot 4 Simplified Reference Tissue Model SRTM 5 Simplified Reference Tissue Model 2 SRTM2 6 Logan Non Invasive Graphical Method 7 Patlak Analysis The Modeling operator provides an integrated solution for representing the loaded data set with one of the following relevant mathematical models to allow for predictions and analysis Getting There The Modeling operator can be accessed via the tool pull down menu on the VQ front panel File View Tools Advanced Modules Help GQ oO M P aa 0000 os OU gt O O ove a Mu Slice View y Navigation y d Quick Scripts x O x St 3D RO Tool a Display Quantification Reorientation Registration Time Series Distance Annotation Checker board Cropping Arithmetics Filtering Modeling
83. 0 20x0 20 mm Type NM NM Reconstruction Name DEMO DEMO 15 Desc DEMO Frame 04 Dim 176x176x452 Vox 0 20x0 20 mm cnt Downloading Annotations took 0 0 sec Use the Cropping Tool to select only the region of interest How to make a dynamic movie 222 VivoQuant Manual 11 12 2015 A A A E ERA MAA PACA Alka PACAP nt 2 50beta8 64bit DEMO DEMO CT DEMO NM DEMO NM DEMO PAPEL Er de mni ner File View Tools Advanced Modules Help e Smm ES oO 0000 os O Pp Moo oOo Dove a Mu Slice View Cropping El Quick Scripts gt 1 D Operator xX Display CroppedArea xX Y Z From 27 47 173 To 108 1115 240 gt Embed 176 176 1452 Information Voxel mm Old size 176x176x452 35 2x35 2x90 4 New size 82x69x68 16 4x13 8x13 6 Auto crop Ref v Set Operator DM Downloading Annotations took 0 0 sec If desired now is a good time to employ the Filtering Operator Note that 1f the Input box is checked then smoothing will be applied to loaded data sets not displayed in the Main Window but visible in the Data Manager How to make a dynamic movie 223 VivoQuant Manual 11112 2015 6 File View Tools Advanced Modules Help e veiw 23 0000 08 DAO pogo F E qu Mu Slice View Filtering Operator VivoQuant 2 50beta8 64bit DEMO DEMO CT DEMO NM DEMO NM DEMO Quick Scripts gt 4 O Y 8X Display Data S Reference
84. 0070912 MoveUp MoveDown Current job MMM F EditJob DeleteJob 2008 04 30 15 02 47 Welcome to batchCT 1 57 2008 04 30 15 02 48 BatchCT started 2008 05 05 07 23 54 Job added batch 0505072353640 ct exp time CTReco CT Helical Scan 2008 05 05 07 23 54 Job started batch 0505072353640 Hide Hides the Batch CT window from the desktop Also reached using the Ctrl H keyboard shortcut Quit Quits the Batch CT application Also reached using the Ctrl Q keyboard shortcut Stop Stops the Batch CT application Also reached using Service the Ctrl T keyboard shortcut eae Starts the Batch CT application Service Jobs Menu The batch file can be altered using the icons to the left of the window or via the Jobs menu in the main window The job icons are located on the left side of the window Status Pause Pauses the current reconstruction job 309 VivoQuant Manual StopJob Stops the reconstruction job Moves the selected projection data up the list of MoveUp studies to be reconstructed Moves the selected projection data down the list of MoveDow P studies to be reconstructed EditJob Allows you to edit the reconstruction parameters Deletes the projection data from the reconstruction DeleteJob list 11 12 2015 These functions can also be accessed under the Jobs menu in the main window Additional functions available here include Thread Number Thread Priority and Show
85. 015 Once the X ray projection data has been sent to BatchCT the BatchCT window can be opened by clicking the small white BatchCT icon on the bottom right hand corner of the screen This window displays all the projection data previously sent for batching and contains various functions to control the process Batch CT Status OX Pause Mod Details Patient Parameter Status Sil o Pa St CT 09010900206 Stoplob HA CT Girls Stella s CT 03 01 08 C42B G Running e 20080103 272 prj gt Stella s CT 03 01 08 LNCap batch 0201091503687 boys MoveU CTReco CT 03 01 08 LNCa P ae P Stella s CT 03 01 08 LNCap Waiting v SD a d MoveDown E Current joo AAN Editlob Total ANA E y Logfile DeleteJob he The BatchCT window is divided into 3 main sections Job List Status and Log File There are icons along the left side of the window for manipulating the batching process Job List The job list provides a list of the X ray projection data to be reconstructed Information about each individual scan is divided into a number of sections Mod Provides information on the modality used 1 e CT Displays the batch number ID the number of Details projections used and the name of the reconstruction as it will appear when loaded into VQ Patient his is the name of the folder from which the X ray Patient nobus projection data was taken Provides information on the status of the reconstruction If the s
86. 11 12 2015 Geometrical Calibration 4 point The 4 point calibration provides a wealth of geometrical information for the NanoSPECT CT This geometrical information is then used by special algorithms to determine the forward model necessary for successful SPECT reconstruction Geometrical calibration 4 POint seems Headi 7 Head3 7 Head2 7 Head4 7 Quality N A Calibration failures In each calibration panel there are also fields relaying information about the completeness of the data for each head and some quality measure either Resolution Linearity or Quality The table below includes information about the limits for passing a particular calibration and how to interpret error messages In each case x designates a head number For example in the 4 point calibration a R1 as shown in the screen shot would indicate that the Radius of Rotation for Head 1 was outside the acceptable limits Geometrical Calibration 4 POInt seem Headi lt f Head3 7 Head2 7 Head4 7 Quality Ri Run Error os Message Intrinsic detector Rx gt 2 4 mm resolution mm m l lt 0 97mm or Quality of linearity gt 30 A U Detector plane to gt 130 1mm or aperture plane distance lt 134 1mm Absolute aperture offset X gt 1 transaxial or axial l Absolute detector offset X gt 1 5mm transaxial or axial 4 Point Rx Radius of rotation ARI On lt 43 9mm Overall quality of the calibration Point
87. 12 2015 e Curvature Flow e Gradient Anisotropic Diffusion e Curvature Anisotropic Diffusion e Positivity Smoothing to remove negativity from FBP reconstructions e Zero Crossing Edge Detection e Bilateral Smoothing e Bias Field Correction Each filter uses a different subset of the configurable parameters consult the table below if parameters other than the default settings are desired ja Default Full width Gauss Zero FWHM half maximum kernel Crossing Edge size l Anisotropic Diffusion Parameter governing Conductance sensitivity to edge contrast z of iterations If the fraction of voxels that are CutOffFrac negative falls below Positivity this value further iterations of the filter will not be performed Curvature Flow Gradient Stepsize effectively Anisotropic Time Step analogous to kernel Diffusion width Curvature Max Error Difference between Zero Crossing 0 5 the area under the Edge Detection discrete Gaussian Using the tool 95 VivoQuant Manual 11 12 2015 curve and the area under the continuous Gaussian The standard deviation of the gaussian Range Sigmajblurring kernel in the image range Units are intensity The standard deviation of the gaussian blurring kernel in each Bilateral dimensional direction Smoothing Units match image spacing units After a left click on OK the smoothing function is executed depending on the image size and filter selected this could tak
88. 15 study Details Patientname ct exp time ume 35 2 35 2 x32 4 mm Yoxel Pixel size 0 20 0 192 mm Memory Volume 38 3 MB Estimated time 00 01 46 2 pp o The Study Details panel provides information about the particular study and reconstruction such as patient Name Object Volume Voxel Size Pixel Size and Memory The Memory setting provides information on how much memory is needed to reconstruct the volume with the selected settings Memory values that are too large will be displayed in red Several options exist for reducing memory usage including changing reconstruction settings 1 e use Fast instead of Fine disabling the use of normalization see Settings menu below using Fast Cone Beam FBP instead of Exact Cone Beam FBP to reconstruct reconstructing only a portion of the total volume see Expert Settings in the Help menu below or re acquiring data with smaller projection data 1 e Fast instead of Ultra Fine in Nucline The exact memory requirements are as such Algorithm Bytes per Voxel 2 4 per thread When using the normalization matrix this adds two more bytes per voxel This matrix is requires to adjust the sampling for helical acquisition orbits For circular scans the normalization matrix can be disabled without side effects Typical dimensions and their memory requirements using matrix normalization Fast cone beam 6 bpv bytes per voxel bpv Exact cone beam t
89. 2015 Data Manager In the Data Manager panel there is a checkbox to enable or disable a confirmation message when moving data confirm Check to enable a confirmation message when moving rearranging data in the Data Manager Check to display the seconds in the study date column in the DICOM browser VQ has to be restarted to configure this change Check to apply a default reorientation to data being loaded into VQ The default shift can be defined in the Reorientation Registration operator For more on this please see the Reorientation Registration page Data Manager 18 DICOM Settings The DICOM configuration allows the user to add edit DICOM repositories These repositories can be local folders containing DICOM files or DICOM network servers located on the local or a remote computer The DICOM Dictionary is used by the DICOM Dump to identify information in the DICOM header A How To on configuring the NanoSPECT s DICOM Servers in the VQ is provided Getting There There are three methods available to access the DICOM Repositry First the repository index is accessible via the Repository panel in the Data Browser Repository SECURE fexampleproject therapeutic_track_1 20 13 ov N Projects 28 28 The second method is to select the Configuration option in the Tools menu and to then click on the DICOM panel File View Advanced Modules Operator Help Y g cs View control FS O E MIP co
90. 271 GUI TNC he asia ahah A o ES A T O 271 A NEEE E EE EEEE EAE AEE N OE AEEA 271 Ouantiticaton Database a a EA 272 SDECHIC A COV IDV ACU AGOR ASAS AAA AAA 273 Geine TR e re etn nr vree 273 J SAU TALE AN 273 SUVEC a Ciao iia 275 A A Tien ir eeette eNeNGT even Hem AN 275 EUC 01d ROPE etn A A A A MTF A VOR 275 Crosstalk Removals a a r aa a 277 Geins EHEren mnee war meu ne enone et Snr mn nr meaner nt ee Nery 217 A A sae eat eta ee hetets aa ee dal ated tae be cc A tei oe 217 BPiodist Vis alZA COL ai 278 Gentine A O ANN 278 PUNCE Oke aaa tn A EE OTTER VUE OO 278 DIE AE ECON SAA A 280 A A Meee ann very 280 UTI Ol OM ceca cn i at te Ae tae at cn nh eect haat delaras telat MO Ma iat A idea et ehhh he Menta 280 CET sia ida ia 282 CTReconstrucion ciai aaa 283 SP e o o a e eE RO dendosac ane dctcaes seacaneses 283 A A A A asacedeae ae 284 VivoQuant Manual Table of Contents CT Reconstruction RRECONS MUCH A tan tiers sacha dba ant nck sa as andew nonce a uot atoene 285 Study Details Progress sand Controls 285 ETS Vile W AMO olor Panes idad ose 287 A ACES 288 AA Ginn iaaaala hati Ghale hist eh tanta wins ate ucln sbi daselitisaales 289 Fee IVD A O NT 289 ri A O Oe OEP vn CPOE tn nena Praia ootre ee ay Seer Eee Peery Peete oe 291 O 292 A A A A A 293 LOS eae orisie ic neha sec ttact saade tsa odessa a tense eaouon aon eaten iavaiedconsatenoges 293 Mn 293 AS A O A O Catbaaancnccsacsseesehe 293 Hoinstield Cala aa 295 CT
91. 296 1118074281 E 1 3 6 1 4 1 12842 1 1 20 2 20071113 141610 859 1283935913 E 1 3 6 1 4 1 12842 1 1 20 2 20071113 141657 421 1173445755 lt File name MMP calibration Files of type 1 dem dicom v a 1 3 6 1 4 1 1284 Ej 1 3 6 1 4 1 1284 i 1 3 6 1 4 1 12844 E 1 3 6 1 4 1 1284 ls 1 3 6 1 4 1 1284 E 3 6 1 4 1 1284 E 1 3 6 1 4 1 1284 E 1 3 6 1 4 1 1284 E 1 3 6 1 4 1 1284 E 1 3 6 1 4 1 1284 E 1 3 6 1 4 1 1284 Es 1 3 6 1 4 1 1284 E 1 3 6 1 4 1 12844 E 1 3 6 1 4 1 1284 gt e Cancel After successfully completing the analysis the result CalibrationData_Y Y Y YMMDD txt file can be copied into C Nucline Calibrations CalibrationData txt to update the calibration information used by the NanoSPECT Function 318 VivoQuant Manual 11 12 2015 Multiplexing MultiPinhole Calibration File Tools ENS Ss COTO eS Input template Cu Empty template Output file gs Scott My Documents MMP_Calib CalibrationData 20080129 txt E Use input file A AAA CHECK ses SA ii Head1 7 Head3 s7 10 0k Head2 Y Head4 go Resolutions Linearity 7 AA seem Pinhole OF seL COlMMmated DEST see Head1 7 Head3 s7 Head2 uf Head4 us Geometrical calibration P0InE pS Headi 7 Head3 7 Head2 7 Head4 7 Quality NifA WUTC Found ColBeam for head 0 A Found IntRes for head 3 Found ColBeam for head 3 Found 4 Point for heads 15 E
92. 4 12 Mees New VveQuant webera Guncmed 2011 04 10 Mews Release condidated for VO 1 19 end BD ROL Tool aeelette 2011 044 News ViveQuert 1 19 Welcome to the Third Genenster Versions alpha beta rc stable patch Alpha version Beta version Release candidate Stable version Besides the last couple of stable releases the web page may also offer preview and test versions For a production system you should use either stable or if available patch releases These versions are divided in four classes stable release Installation Quick Guide VivoQuant Manual 11 12 2015 These versions are the officially released and fully tested versions of VivoQuant They have undergone intensive testing by our software developers service engineers as well as selected expert users Unless you require a special feature only available in a newer version or want to participate in the software testing process we recommend to only use these stable releases in productive environments Subsequent changes to stable versions are released as patched versions Such releases only contain few and significant bug fixes patch release established after the release of the original stable version and no other updates Further stable releases will unless noted otherwise also contain such patches At the end of the development cycle multiple release candidates rc are released which allow users to sneak a peek on upcoming versions These versions hav
93. 5 C Crop Range Register Inp1 to Ref All to Ref Resampling images to reference image took 0 1 sec 3D and 2D Automatic Options 75 va VivoQuant Manual 11 12 2015 NOTE WHEN SCALING DATA PLEASE USE CAUTION AS SCALING CAN LEAD TO ERRORS IN QUANTITATION FOR MORE REFER TO THE TREATMENT OF QUANTITATIVE DATA PAGE Menu Options The Reorientation Registration Operator menu can be used for storing transformations setting a default image transformation and controlling the behavior of the operator File View Tools Advanced Modules Operator Help a ee 00 Load Transformation Ctrl Shift L WC GQ SY M me 50 00 oad Transformation rl Shi Ne Operator Ref Inp1 vk eso Interpolator Linear 73D 4 2D X axis 0 00 0 000 mm Uniform Load Transformation Save Transformation Save as default Menu Options Reset Ctrl R z Quick Previe Apply Ctrl Return R30 R2 A Flips Rotation Resample Y axis a Pre compose 0 00 5 Post compose Translation Reorient ROI around Center Enable Scaling 0 000 mm ir KASSA Trine Tey Scaling Save Transformation Ctrl Shift Save as default nee mg Cc oN f e save Reg Movie Applies a pre defined Ctrl Shift L transformation to the active data Set Saves the current transformation Ctrl Shift S settings rotation translation flips into a xml file Saves the current
94. 6004608 bytes Y 0 2000 mm Z 0 2000 mm Datasize 56004608 bytes Difference y o bytes Modality NM Data Unit luci Add Info Function 347 Sessions VivoQuant i 2ialphad0 64bit STUDYLA283C ICT CTReco s bed removed NM NM Reco Co Registered ESTE al VO MC DM ran e Vie DR A x 45 Save Session Name STUDY 1A2B3C 222 STUDY1A2B3C 54 f A 3 Ar IS 2115 Operator vc J DM Confidence Connected Thresholding took 10 711 sec Sessions allow the user to save the current working environment of VivoQuant The exact location in the software is saved along with the image data that is currently loaded in the Data Manager The operator or tool and parameters being used are saved as well A session can be saved to the local cache or exported as a compressed zipacs folder structure that can be used to share with colleagues Getting There A session can be saved loaded or exported by selecting the appropriate option under Session in the File menu File View Tools Advanced Modules Help Data Browser Ctrl D 32 0 08 O O g Open Loca Data gt ee Save image Ctrl Save Movie Ctr M Save Data gt p Session gt B Load VivoScript Ctrl Shift V ga Save 4 Export 7 4 d Exit Sessions 348 VivoQuant Manual 11 12 2015 Session Manager The Session Manager allows users to load prev
95. 6362 uCi mm Heart DEMO DEMO CT red 28734 229 872024536133 307599 63092041 1338 13425770764 HU mm Heart DEMO DEMO NM red 28734 229 872024536133 0 8731347461935 i 0 00379835148689986 uCi mm Liver DEMO DEMO CT 16633 133 064010620117 277116 709106445 2082 5819679942 HU mm Liver DEMO DEMO NM 16633 133 064010620117 1 4082953747311 i 0 0105835933260093 uCi mm LeftKidney DEMO DEMO CT 48796 390 368011474609 3022752 94122314 7743 34180150863 HU mm LeftKidney DEMO DEMO NM 48796 390 368011474609 3 60530338860917 i 0 00923565272418248 uCi mm RightKidney DEMO DEMO CT 43468 387 744018554688 2177921 65826416 5616 90588131403 HU mm 10 RightKidney DEMO DEMO NM 48468 387 744018554688 3 8008735285448 i 0 00980253297707215 uCi mm S lt gt Save the quantification table to disk To save the quantification table to disk as a comma separated values csv file click the Save Table button Perform a cut on an image using an ROL To remove voxels from image data based on an ROI choose the desired ROI from the ROI selector and click the Perform Cut button All visible images will be cut the ROI remains unchanged The cut tool is useful for eliminating undesired features in images such as metal instrumentation that may appear in some CTs Show hide the 3D ROI table Click the Show hide ROI Table button to turn the ROI table on or off ROI names can be edited within the ROI table by clicking on the desired field to set the cursor Check the boxes in
96. 91 e8 The Info field includes many boxes and buttons that affect the output image Pull down menu to choose image Image selected here will be reflected in the Series Desc field Function 146 VivoQuant Manual 11 12 2015 PatientsName Patient name as stored in the DICOM header Study Desc Protocol used to collect the data Series Desc Series description including modality Name of image movie to be saved Manually entered by user Date and time at which the image movie was Content Data i loaded into the Capture Viewer Size of the original data referred to in the Series Data Size o Description pull down menu Capture Desc Image Size Size of image currently being displayed DICOM When pressed displays the DICOM Header for the data Close When pressed closes the Capture Viewer without saving image When checked maintains or returns to the original image size and Increases or decreases image size respectively orig Convert Convert Save Image Save Capture v 8 No compression Lossless JPEG Lossy JPEG The Convert field includes several options that affect the output image Save Image Opens the Save Image screen Save Movie Opens the Save Movie screen Play Movie Plays the movie Click again to stop the movie Save Saves image movie into the repository specified in Capture the pull down menu There are also several radio buttons that enable the user to select the level of
97. Activity Calculator NanoSPECT MMP SPECT Calibration Near Field Uniformity OC Reconstruction Batch Mode BatchTool Generator PSF Manager Quantification Tables 0 ECG Split Save Calibration txt Crosstalk Removal e CT Tools CT Reconstruction 0 BatchCT Hounsfield Calibration 0 CT Geometrical Calibration e Bed Removal e Plug In Modules Whole Body Atlas Tool e NM CT Brain Atlas Segmentation Tool gt 4 MRI Brain Atlas Segmentation Tool Tumor Segmentation Tool LumiQuant 3D BLI Reconstruction Tool e TumorPK Model e Dosimetry Calc AdvancedModules 252 Plug In Modules VivoQuant offers a variety of additional Plug in Modules in addition to the base license These are accessed through the Advanced Modules Menu e Whole Body Atlas Tool e 3D Brain Atlas Tool gt e MRI Tool e Tumor Segmentation Tool e LumiQuant 3D BLI Reconstruction Tool For more information on the inviCRO s Advanced Segmentation Tool Kit please contact your inviCRO representative or email supportO invicro com You can also access a helpful How To illustrating the main features of the 3D Brain Atlas Tool by going to Tools gt Workflow and selecting the 3D Brain Atlas Analysis Tool workflow Plug In Modules 253 Whole Body Atlas 1 Overview 2 Getting There 3 Adding to Reference Library 4 Segementing With The Tool 1 Settings 2 Select Images 3 Run Tool and View Log 5 Downloading Sample Library Overvie
98. Advanced Function The slice number can be seen on the bottom right hand corner of each cross sectional image sagittal transversal and coronal To display the slice number in the images go to view and highlight Slice Number a tick will appear beside it to show that it has been enabled Slice number To conceal the slice number from view unselect Slice number by left clicking on it Slice number Slice Number 150 Cross hairs This function enables you to display cross hairs on the images to assist navigation through the slices Getting There To display the cross hairs on the image go to view under the view menu and select Cross hair File View Tools Advanced Modules Help Undo Ctrl Z E gt O Yeso g Redo Ctrl Shift Z Dis E E mu its Show Reference Show Input 1 Show Input 2 Slice number Cross hair Position labels Patient name Layout Reset View Transform Ctrl R Zoom Advanced Function The cross hairs can be are displayed over each cross sectional image sagittal transversal and coronal To display the cross hairs in the images go to view and highlight Cross Hair a tick will appear beside it to show that it has been enabled Cross hair To conceal the cross hairs from view unselect Cross hair by left clicking on it Cross hair Cross hairs 151 Position Labels The position labels are displayed on each image plane and MIP They clearly indicate which si
99. DEMO Dim 176x176452 Vox 0 20 gt 0 20 mm toto Type NM NM Reconstruction Name DEMO DEMO 14 Desc DEMO Dim 176x176x452 Vox 0 20x0 20 mm loco The Data Manager displays a list of all datasets loaded into VivoQuant along with information about each The Data Manager can hold as many datasets as the system memory allows however the first second and third datasets in the Data Manager are the only three that appear in the Display These datasets are the Reference Input 1 and Input 2 respectively The information displayed by the Data Manager includes the image type name dimensions and voxel size For DICOM data the Study Date Series Date and Series Description will also be included when available Below this information is a color bar specific to each dataset The color bar defines the colors that will be used to represent the dataset in the Display The colors can be changed by right clicking the color bar and selecting the desired color palette VivoQuant selects color palettes for datasets by default based on modality CT PT MR etc Default color palette options may be changed in the Display tab of the Configuration window Featured on the colorbar are the minimum and maximum intensity values the data is subject to in the Display These can be adjusted by clicking on the black markers at either end of the colorbar and dragging them to the desired location Note that this does not affect the minimum and maximum val
100. DEMSRAY wv Databases Regi lient Archives egistered Clients Application Entity Title Host Port Clients ANY SCP 192 168 200 136 5555 HELICT LOCALHOST 4104 HISPECT LOCALHOST 3104 Equipments HISPECT_BATCH LOCALHOST 3105 INVIVOSCOPE LOCALHOST 23104 MS _AnyName NANOSPECT27W S 23104 MS _LACKAS 10 8 0 10 23104 Quit Add Client Edit Client Delete Client Click on the Clients button On the WS you should already see listed there the HiSPECT and InterviewXP entries To add the VivoQuant add the line at the bottom of the following list Application Entity Title HiSPECT LOCALHOST 3104 HiSPECT_BATCH LOCALHOST 3105 INTERVIEWXP LOCALHOST 11112 NVIVOSCOPE HOSTNAME 23104 In place of HOSTNAME in the VQ entry use LOCALHOST on the WS Computer and NANOSPECTxxWS or the workstation IP address on the ACQ computer Computer Calling AET Hostname Port INVIVOSCOPE NANOSPECTSWS 2310 I NVIVOSCOPE LOCALHOST 2310 IP Address or 2nd WS Computer Name Adding VQ as a DICOM Client 27 VivoQuant Manual 11 12 2015 What is of importance in this configuration is not the specific name INVIVOSCOPE but the fact that the same name INVIVOSCOPE was used in the DICOM Client Configuration and at the Calling AET in the VQ Repository Configuration To illustrate this point note the client in the image above with the name VQ_anyname Also separate names must be used for each configuration In other words to configure the VQ on a 2nd wor
101. EPE S mis AN JG J J i J gt Previous slice AAA Next slice AAA Previous row PageUp To switch between views 1 e coronal sagittal transversal in the Tile View right click on a tile and choose the desired view Sagittal Coronal Transversal Two operators are available in Tile View The first is the Time Series operator which enables dynamic data to be viewed as a time series For more information on this operator see the Time Series page The other available operator is the 3D ROI View operator which enables ROIs to be displayed in Tile View Note ROIs may not be edited in Tile View For information on editing ROIs see the 3D ROI Tool page Using the Tile View Display 135 VivoQuant Manual 11 12 2015 Using the Tile View Display 136 Multi View The Multi View offers users the ability to create a fully customized Display for data Users may select how many Viewports will be displayed in what orientation they will be displayed and which datasets will be rendered in them This 1s especially useful for users who work with data across multiple image modalities Getting There The Multi View 1s available via a pull down menu on the Main Window File View Tools Advanced Modules Help e GQ SY M Es ac 0000 an a AROOM eee bi Me ou Mu nat ew Ef Newigator Quick Scripts 4 D Display Tile View S Multi View MPR View Setting Up the Multi View Display Selecting Multi View
102. ICOM browser All projects within that repository are available via the second pulldown menu The three projects associated with the bioscan demo repository are shown in the screenshot below Repository PACS Documentation bioscanfdemo subproject1 bioscan demo subproject1 Ibioscanfdemo subproject2 bioscanfdemofsubproject3 Select any project to view only data associated with that project OO PACS Documentation i Patients Name StudyDate bioscan demo subproject1 esa 1YS Documentation Example 1 2007 10 05 16 27 bioscanfdemo bioscan demo subproject1 bioscanfdemo subproject2 Ibioscan demosubproject3 By default data will only be displayed when the project to which it belongs is selected from the second pulldown menu For example in this screenshot no data appears in the bioscan demo repository because all data within the larger repository belongs to individual projects Repository SECURE ES Training w fexampleproject therapeutic_ track 1 2013f Iratvart ff amp A Projects 28 28 Oo To simultaneously view all data belonging to a repository AND its projects place a at the end of the PACS Projects 24 VivoQuant Manual 11 12 2015 hostname during respository configuration The will cause all data within the repository and its projects to be displayed recursively This behvavior applies across all repository and project leve
103. M Dump 11 12 2015 Activating the DICOM Dump tool opens a new DICOM dump window Information from the DICOM headers for any active datasets is displayed in this window In the top left corner is a pull down menu where you can choose which set of DICOM header information to display Getting There 207 VivoQuant Manual 11 12 2015 Data set 00 CT DEMO Find 00 CT DEMO Dicom Dat Set Used TransferSyntax Unknown Transfer Syntax 0008 0008 CS ORIGINAL PRIMARY AXIAL NANOSPECT 32 4 ImageType 0008 0016 UI CTImageStorage 26 1 SOPClassU 0008 0018 UI 1 3 6 1 4 1 33793 1 4 862821930 5500 1439925891 13 50 0008 0020 DA 20131107 B 1 0008 0021 DA 20131107 0008 0022 DA 20131107 0008 0023 DA 20131107 0008 002a DT 20131107173938 672 0008 0030 TM 163217 0008 0031 TM 174102 0008 0032 TM 173938 0008 0033 TM 175416 0008 0050 SH 2824 0008 0060 CS CT 0008 1030 LO DEMO 0008 103e LO DEMO 0008 1090 LO NanoSPECT 0010 0010 PN DEMO 0010 0020 LO DEMO 0010 0030 DA 20000101 0010 0032 TM no value available 0010 0040 CS 0 0010 1030 DS 0 0010 4000 LT no value available 0018 0050 DS 0 2 0018 _ NARAI DS M 21 lt assulu StudyDate z T E z In the upper right portion of the DICOM dump window is a Find option A search string may be entered in the Find
104. Manual 11 12 2015 jh_nff 2008 04 07 17 28 Once the data are analyzed the x y z calculated source position will be displayed in the lower left corner of each Raw image These images are indicated by the appearance of the word raw in the upper right corner Also the raw images are displayed when the All Pre push button is selected The red plus sign on each image indicates the source position with respect to the detector E AET 17 15 Pie The corrected images may be viewed by clicking the All Post button Ctrl T may also be used to toggle between the two sets of images The FOM for each data set is displayed in the lower left corner A green checkmark in the Results section indicates that the head passed the calibration A red FOM in the Results section means that the data are questionable and should be sent to a service engineer for further analysis Finally to create a PDF containing the pre and post correction images press Report Function 327 VivoQuant Manual 11 12 2015 A EIA Function 328 Dosimetry Calc Whole body dosimetry data can be estimated using VivoQuant s Dosimetry Calc tool in conjunction with the third party application OLINDA Organ Level INternal Dose Assessment The Dosimetry Calc tool calculates the cumulative activity per unit activity administered units in uCi hr uCi which is the required input to the OLINDA application for dosimetry calculations The cumulative activity per un
105. O Ye 8X Display DICOM dump Ctrl Shift D Anonymizer Rename DICOM 11 12 2015 Upon selecting the Anonymizer a dialog box appears prompting the user to decide whether to anonymize each loaded dataset individually Yes or anonymize them all together No Do you want to anonymize each loaded data set individually If not the same anonymization will be applied to all data sets Enter the desired Data fields to change Select the desired Repository and Project to store then click OK or Open if no data are already loaded Getting There Data Patients Name DEMO Patient ID DEMO Study Description DEMO Series Description DEMO Patients Birthdate 20000101 Protocol Name Storage LC keep StudyUID _ keep SeriesUID 211 Rename DICOM Files The Rename DICOM function can be used to rename locally stored DICOM files according to information from selected fields of the headers Getting There DICOM files can be renamed by selecting Rename DICOM under the Tools menu Engg tl Tools Advanced Modules Help SY is few contro y o e a MIP contro F6 L et Data Manager F7 Min Max Histogram Ctrl Shift H Workflow Assistant Pre processing Resample data DICOM gt DICOM dump Ctri Shift D Image amp Movie d Anonymizer Rename DICOM Update Check Ctri Shift U Relabel Study Configuration Ctrl Shift C Function Choose which files to rename by using the Add Files button in the Rename DICOM
106. P picture can also be saved using this feature MIP viewer must be active Images will appear exactly as they do in the viewer Getting There Four different methods exist for saving images The first method is to go to Save Image under the File menu File View Tools Advanced Modules Help Data Browser Ctrl D a 0000 08 O Open Local Data Save Image Ctrl Save Movie Ctrl M Save Data gt Session gt VivoScript Ctrl Shift V SE IN ca Exit The second method is to use the keyboard shortcut Ctrl I For more on keyboard shortcuts in VQ please see Keyboard Shortcuts The third method to save image slices is to use the thumbnail in the Main Window The fourth method is through the MIP Control which can be opened via the thumbnail in the Main Window There is an option here to save the image Function Selection of the Save Image option opens the Save Image window Save Image Data 121 VivoQuant Manual 11 12 2015 Look in 1 C Users lkgoettler Desktop DEMO JO o0 op A My Computer R kgoettler File name test png Files of type Image files png jpa bmp gif tif v Cancel Image type Sagittal slice Colorbar options none Storage Type Local image file Magnification 1 There are several options for the output images Filename Set name of image file Set type of image file Images can be saved as png Jpeg bmp gif ti
107. Please specify how many standard values are in the image 10 OK Cancel The second prompt asks 1f there will be a background ROI used This influences the calibration curve In most cases a background ROI is recommended Autoradiography Calibration _ Would you like to specify a background ROI to eventually subtract from the image Autoradiography Calibration 216 VS VivoQuant Manual 11 12 2015 Based on the answers to the previous questions the ROIs will be populated Now they need to be manually placed in the correct locations in the image Use the 3D Paint Mode tools to perform this task Regions should appear similar to the image below Image Calibration Once the calibration standards have been segmented click Read Values from Image The table will display the mean value of each region Provide the true value of each standard as well as the correct output unit Also choose from the available Error Weight techniques Once the settings are established click Run The plot will populate with the values of the standards and provided values along with the calculated fit line Changing the settings particularly the Error Weights will change the output calibration curve To see how the curve changes with different settings change them and again click Run Once the curve fits as desired click Apply to apply the calibration to the data Getting Started 217 VivoQuant Manual 11 12 2015 W Aut
108. QC Bed removal SUV Calculator QuantiCalc 4 opos Display Whole Body Atlas Crosstalk removal Atlas NM CT analysis Split Projections fMRI Tool Install Atlas EKG split Save Calibration bdt Split ROI to DICOM Show user data Sum projections Average body calculation Specify ROI center Specify ROI center 2 Upload tumor ROI Append projections Semi Stationary Data Processing TumorPK Model Dosimetry Calc If running the VQ Calibration Application enter the tool by pressing Multiplexing Multi Pinhole SPECT Calibration IVS Calibration PB Nucline base C Mucline v Multiplexing Multi Pinhole SPECT calibration Near Field Flood Energy Calibration CT Geometrical Near Field Flood Calibration Uniformity Calibration Function Several calibrations are necessary to successfully implement multiplexed multiple pinhole methods in small animal SPECT The MMP SPECT panel may be used to analyze four different small animal SPECT calibrations including linearity collimator depth pinhole offset and geometrical The panel is split into eight sections Templates Control Preview Qutput and a section for each of the four calibrations There are also several helpful tools in the Menus To run the tool hit the Open button and select all of the relevant data should be titled Service SPECT_0 CalibName and will consist of 64 Intrinsic Reoslution data sets 4 Collimated Beam data Calibration MMP
109. Quant Manual 11 12 2015 Projections vs Reconstructions The Display window recognizes whether a loaded data set is projection data or reconstructed data The default viewing scheme known as Slice View for reconstructed data presented almost exclusively throughout this manual includes a MIP and three separate viewing directions sagittal coronal and transversal When viewing projection data or sinograms sets of CT projection data the VQ displays the data accordingly For example transverse slices of projection data are displayed with a P in the top left corner Display py w lt 120 104 35 NM 34 For CT data selecting the correct layout will display the relevant sinogram data For the corresponding windows the data are labeled as sinogr denoting sinogram NOTE It is not possible to view projection non volumetric and reconstruction volumetric data simultaneously Attempting to append reconstruction data to projection data or vice versa will result in an error message Projections vs Reconstructions 119 VivoQuant Manual 11 12 2015 Cannot append data of a type that does not fit to already loaded data Cur Projection Data New Volume Data Projections vs Reconstructions 120 Save Image Data This function enables the images to be saved as picture files The slices can be saved individually sagittal coronal or transversal or all in one image A Maximum intensity Projection MI
110. RE Date Dior Desc NM Reco Co Registered DEMO Dim 192x192x380 Vox 0 200 20 mm The second method for reaching the DICOM Dump is to use the keyboard shortcut Ctrl Shift D For more on keyboard shortcuts in VQ please see Keyboard Shortcuts The third method is via the Data Browser Right click on a dataset and click Dump Header DICOM 206 Repository SECURE VivoQuant Manual Study Browser Q Demo pacs invicro_demo vivoquant T StudyDate VivoQuant Y A Projects o Filter gt DC M1_1_48h gt DC M1_1_3h gt E gt DC M1_1_144h Open data Append data k Export to Openin Patients Name Patient ID X Delete Data Description Study Date FileType dem Data Show data type All data types De Q C Apply default shift Auto Start reconstruction Force planar Stack 3D Append Open Transfer Cose st The fourth method is via the Data Manager Right click on a dataset and click DICOM Dump op DM Dump header Topo CT SPEC Topo CT SPEC Topo CT SPEC Topo CT SPEC E a x Data List Loaded 2 Memory 106 82MB x Ol 2 Function Use as Input 1 Annotate Copy Details Type NM NM Reconstruction Name DEMO DEMO Desc DEMO Dim 176x176x452 Vox 0 20 0 20 mm Save Data as X Unload Data DICO
111. ReconstruciOMaiiiaaids 299 E A ner ene 299 O O O NETO 300 Reconstiucion ParamelS alusitiiiaitd 301 Study Details Pro oress and CONTEOLS saraaa ii 301 PONTO WAIN Color Panel e UE ta do ISO TO e eS TR DE 303 A A A r 304 SAA A aa ahen cate pecae aries suede deanna iscated a comeshcinbeaeeeitasstandaastencaw acts 305 PS E TU A eo A o acetate tartaantaenceais 305 A A A REI OO ERIE ORTON II SAE SI A UE ITT RA 307 O fue ene ams Vc Pea SU RVD E A VIBE Peers E AO A OTE 308 OLE eee ee a ee eee ee eee ee slds diodes 309 A O 309 A AO 309 A a del Gude cath te gl hell acta eit Decl aie estat itl hc ane 309 Calbr atomic a 311 Geine A A O ANN 311 O O UTE 311 CTGeometrical Calbra k lt nidaii 312 A A ect mT ann vere 312 PU CU OM cinch Sater a Accel aul set ade UA taht ah ied ahaa ies Mar tenia e 312 Calibration lt MMP SPEC Doscssesccdeccscsdeesssevcsteccsstwsnswossessiecevesstevessapetensasdssensesosateabececselesssssndswoseveseeasedsesascetese 317 A A ser scan rr eee Te 317 NI A oo Te er 317 A e o O o sersecaceusaas se aomasoneecnaees seteencte 319 XI VivoQuant Manual Table of Contents ING ANSE TONG Uniformi in aid 325 E A O A eae ner ree 325 NS N O E O UT 325 Dosimetry CAES N ETE 329 A a a nem ner nent yr renty e men in nce ann vere 329 ECU Oien sect sh settee coe ete teckel E ah haat ah ie ak dela i seh ae eal 329 EI Ai A o gp a erst rime at eer erat tye ree eery tet n eet 329 Usmo the AWC Cale AO Mis scetsct tees eacdause
112. Results and Control The Projections panel displays the projections collected in the calibration measurement as they are being analyzed Each of the three metal fiducials is marked by a red green or blue circle The progress of the measurement is also noted in this panel Function 313 VivoQuant Manual 11 12 2015 Projections i The Orbits panel displays the trajectory of the three metal fiducials as the projections are analyzed The trajectories appear flat in the primary view however by drawing a box around a given trajectory it may be expanded to fill the entire panel providing a more illustrative view Orbits trans pxl PJ MI uy i b D CI O mm un o un DO G a o gn o co oO Oo 0 Ai Orcas De tment De 0 50 100 150 200 250 axial pxl To zoom in on a particular orbit draw a box by holding down the left mouse button and dragging Function 314 VivoQuant Manual 11 12 2015 N N Ww Y A AA O 4 CDC O O COIE trans pxl pu on o m o o 58 5317 108 2915 on Oo 0 50 100 150 200 axial pxl Upon release of the button the display will show only the selected orbit To return to the full view just right click trans pxl axial pxl The 2nd Order Corrections panel displays an important result of the calibration This panel plots the axial and transaxial wobble of the gantry as it rotates It is critical that these value
113. S fm ecT y u e gt CT gt Js Display Bed removal Whole Body Atlas Atlas NM CT analysis fMRI Tool instali Atlas Split RO to DICOM Average body caiculation Specify ROI center Specify ROI center 2 Upload tumor ROI TumorPK Model Dosimetry Calc Load Data into the Tool The Load Data section in the upper left corner of the GUI window allows the user to load in a data set from a local folder or import a data set that is already loaded into the software For Bruker MR data the user can select the 2dseq file from the appropriate folder or use the Bruker Loader to load the data into VQ prior to running the tool Load Data Input Data Ho Data Loaded TR 100s Number of Time Points 0 Import from DM Reset Settings The folder location and file name will be displayed Input Data in this window when a data set is loaded in from a local folder Click on the ellipsis button to open a window from which the user can locate and load in a locally stored data set The repetition time in seconds should be entered TR here The user should either type the correct value or use the up and down arrows to adjust the TR Time Points update upon loading a data set DM Tool that has already been loaded into VQ Click on this button to unload data from the tool and reset the pipeline settings back to the default settings Reset Settings Getting There 261 VS VivoQuant Manual 11 12 2015 Selec
114. Templates The Templates section controls the input and output files used generated by the calibration analysis lemplate s Input template Mu Empty template Output file gs Scott My Documents MMP_Calib CalibrationData 20080129 txt E Use input file e Input Template A previously generated CalibrationData txt file may be used as an input template for the data This feature is particularly useful if partial calibrations 1 e only a 4 point measurement have been performed e Empty Template As a default an empty template designed for use with the Nucline software is used to generate the CalibrationData txt file e Output File Any name may be specified for the Output file of the calibration analysis The default name is CalibrationData Y Y Y YMMDD txt e Use Input File This feature is not yet implemented in the VivoQuant Please check back soon Control The Control panel has four buttons for manipulating the MMP Calibration window Templates 319 VivoQuant Manual 11 12 2015 e Show Calib Opens the current CalibrationData_Y Y Y YMMDD txt file for viewing e Open Opens a browser that is to be used for loading MMP Calibration data DICOM format e Clear Clears the Output panel of the MMP Calibration window e Close Closes the MMP Calibration window The Calibrations Four different MMP calibrations may be analyzed with this tool For each calibration Preview Details and Run buttons are provided Preview al
115. The above table described configuring VQ to access the Workstation DICOM Server VQ may also be configured to access the Acquisition computer s DICOM Server The procedure is similar but there is no WS in the naming convention General Information Displayed Name AcQ_NSxx_DCMSRV Repository Type O W Local folder 8 DICOM server Y Pacs Local DICOM folder DICOM Server Calling AET INVIVOSCOPE Called AET NSxx_DCMSRV Hostname manoospectxx Port 104 Use localhost lower case for optimized local access Test OK Cancel Name preference Port where xx is replaced with the NanoSPECT number typically no leading O for numbers lt 10 In place of hostname i e nanospectxx it is also possible to use IP addresses 1 e 192 168 1 1 for local WS ACQ computer connections Please verify that the hostname resolves by using ping hostname in a Command window Also in order to access the ACQ computer from the WS computer you must configure the DICOM Server on the ACQ computer How to configure the NanoSPECT s DICOM Servers 26 VS VivoQuant Manual 11 12 2015 Adding VQ as a DICOM Client Start C Program Files Mediso DICOM Server DICOMServerMegr exe On the main panel you see the name of the database NSxx WS _DCMSRV where xx is the NS number and WS is present on the workstation which should be used as the Called AET DICOM Server Manager v1 00 077 0000 2JE3 Database dicom N517W 5_
116. There The QuantiCalc tool is available via the Tools Menu VivoQuant File View Help LO ve Slice control f5 bit RenamedPatient CT CTReco s bed ri D cs i is VC MC DM MM Sice View DE a ata Manager A CIC play Y Link MIP Slice control v Global scale per mod v Apply default shift gt QuantiCalc CT b Spec Act Calculator DICOM gt SUV Calculator Advanced Analysis gt Histogram OHH Crosstalk removal Volume rendering 983 Biodist Visualization Split Projections Image Magick gt mu Min Max EKG split W Workflow Assistant Save Calibration txt Show user data Calibration gt S 2 ti Update Check OU um projections Append projections Semi Stationary Data Processing Function The Quantification Calculator is used to calculate a Quantification Factor To perform absolute quantification Quantification Factors must be calculated for each isotope and aperture combination used in the NanoSPECT CT The Quantification Factors are stored in the Quantification Database For information on collecting the data necessary to calculate Quantification Factors please see the NanoSPECT CT documentation 60 90 QuantiCalc Dose meter p 000 m MBq 1 1 00 12 00 AM 7 NanoSPECT 0 000 kCounts 1 1 00 12 00 AM gt Isotope Tc 99m Half life 6 01 h Decay factor 1 00 Aperture APTO z Quantification factor nan EWin E EA The procedure for collecting Quantification Factor data involves performing a highly spe
117. VivoQuant Manual 11 12 2015 pa A EE A Jo a EE AA Color Panel Resolution CAPO Algorithm Exact Cone Beam FBP FBP filter typefcut off Frequency SheppLogan v fio lt Study Details seem walt rani gt A Pee a Patientname N A MS Hounsfield se up AA volume 0x0x0 mm Voxel Pixel size 0 0 mm Energy Slope Intercept 4Sk p 1 000 0 0000 A v A sskwp 1 000 0 0000 A v 65kvp 1 000 0 0000 Filter SheppLogan 100 i enable calibration 0 frequency Estimated time 00 00 00 0 A sas autostart Fill a large gt 2 5cm diameter syringe with water and collect CT data at 45 kVp with standard settings It is not necessary to image the entire syringe just the section that is full of water Repeat the acquisition at 55 kVp and 65 kVp Reconstruct each CT Using the Quantification Tool select a region of the reconstruction consisting entirely of water inside the syringe Hounsfield Calibration 296 VivoQuant Manual 11 12 2015 br TA a Oy g2 Ww 28 a VC MC Quantfication mi R volume Sua Mean StdDev amp Patiert S fm umea URSA HAABA r akiert se Mn Max HBa HND 39920 94 43 591056 1 45527 0 125021 0 000197848 1 07071 2 09337 HU Test CT recor Set the Slope 1000 Mean In the screenshot above Slope 1000 1 4527 687 15 Typical slopes are near 650 Be sure to set the Slope for each energy to correspond to the value from
118. VivoQuant User Manual VivoQuant 2 5 Version Thu Nov 12 17 36 12 EST 2015 VivoQuant Manual Table of Contents VivoQuant Mani all cun is 1 VivoQ ant Installation iaa 2 Installation Oc Giideon DAA AAA AA AAA AAA aada 3 PA A A tes sen At eats 3 NAST AU E PP RN 4 PASS NN ANNO WS acct steeds sacatccuisscin sashsataautancaa ie secau a aed aecaaussmemb ta oedae noes oak ut aan Maacsaut sac aataenetes 4 O O 4 Sl A O A AN A A SIE NEA 5 SECAS REIS AON sc 5 EACE ACOS etc canedctad 5 YN BH O OMS sa RR GE RE A O Saaeae te S 5 AOS CE e 8 Installation PC UANIS sards cass seek iaccecttacs a sdaaccucsadceceaudsnereet eases vtacosusssuabassedsecaees 9 CHOOSE COMPONEN ados 9 CHOOSE stall Lac roto ios 10 VIVO QUAN CONACULA OA A A A Ae 12 Contisuration Panels ta EE A 12 CA A i en nre eras nem neon Were wr eae Smee Na mre e Tne Tre tne 12 DISPARO ac aio seas RTE 13 E A E 13 Maximum Intensity Pro ECON ela 14 COOL A A Nt a SOR O ATR AN 14 Dita ds NAAA ete 15 DA II rere eee nee NTE rng eee 15 Oui TEAC ALOT LOTS A A A AA eet Mea Reena 17 DD eit chs dC nee Cn RN 18 DICOM SOUS ses ixecscssswccseascuccucssvcusesewacsvaavadsduchncassusceutaussvaivaseccesdusieleacuswncasbusceaseasavciussduaxseeseenssauwasdssseeigeds NS 19 Gen Ne free sas ant co A aeons 19 CO mite SUA ONT Id iria idlida 19 DIC OMS CUS cant aii add ida 20 ICON o e lo ere o ld o A eo o eL 21 CAPI N 21 Dati Browser Repository Panel ica 2l DIECON CO enoa E T E A R 22
119. XY XZ YZ Toggles the display of the coronal sagittal Checkboxes and transveral slices Using the MPR View Display 144 Capture Viewer The Capture Viewer enables editing of image and movie files prior to saving Getting There When saving an image or movie the second option in the DICOM Repository drop down menu is DICOM Secondary Capture Selecting this option and clicking Save will load the image movie into the Capture Viewer Look in L C Users lkgoettler Desktop DEMO O00090 i E W My Computer R kgoettler File name Save Files of type Image files png jpa bmp gif tif v Cancel Image type Sagittal slice Colorbar options none Storage Type DICOM Secondary Capture v l Local image file Magnification DICOM Secondary Capture Function The Capture Viewer panel is split into four fields Info Convert Edit and Image Capture Viewer 145 VivoQuant Manual 11 12 2015 Capture DEMO DEMO Image View DEMO DEMO DEMO Capture Desc test Content Date 2015 08 3109 40 25 v Data size 65535x65535x1 Image size 337x865x1 _ orig 191 A O Convert Save Image Save Capture 8 No compression O Lossy JPEG Info Info 01 CT DEMO b PatientsName DEMO Study Desc DEMO Series Desc DEMO Capture Desc test Content Date 2015 08 31 09 43 07 Y Data size 65535x65535x1 Image size 33 x865x1 DICOM Close L orig 1
120. Y Navigation A Display Quantification Reorientation Registration Time Series Distance Annotation Checker board Cropping Arithmetics Filtering When the 3D ROI Tool is selected a 3D ROI Tool operator window is displayed 1 VivoQuant 2 10 64bit DEMO DEMO CT DEMO NM DEMO OEM File View Tools Advanced Modules Operator Help SY SY M T sa 0000 os O y 9 ove Hi ve Mi Slice View 3D ROI Tool y El Quick Scripts gt 1 OD 0 Y Operator 8 xX Display Palette ce JoJe x z AMAR cal WB background BB Brain E LeftKidney RightKidney Heart E Liver ROIs xXx e e H background y Reorienting Images took 0 3 sec Each panel of the 3D ROI Operator window provides a grouped set of functionalities Use the tabs to move between panels ROI Loading Saving and Quantification Tools e Painting Tools e 2D Drawing Tools 3D Segmentation Tools Getting There 38 VivoQuant Manual 11 12 2015 Expert Settings ROI Creation and Deletion ROIs can be created and deleted from the strip of icons at the bottom of the 3D ROI Operator ROIs AA RO v Add an ROI gt EditamROI Delete an ROI D Reset an ROI HideanROT O Add an ROI To add an ROI click on the plus sign Add ROI button Use the interface that appears to specify a name and color for the ROI To alter the transparency of the ROI in the slice and MIP views respectively in
121. Y1A2B3C STUDY1A2B3C STUDY1A2B3C STUDY1A2B3C FDG_IT_Dynamic DICOM MR demoData2 demoDatat CT PET Data Set CT unreg SPECT CT rat bed 4107369 4107369 4107369 012610 saline 2011 06 09 14 54 2010 05 19 22 32 2010 05 19 18 34 2010 05 19 22 32 2010 05 19 21 41 2010 05 19 19 24 SqMonkFocused 2012 01 25 18 36 slo Speer CT Aron 201006 18 222 gt SPECT_CT_Anon 2010 05 19 23 32 Filter gt RenamedPatient 2010 05 19 23 32 x 7 RAT_PET_IT 2011 12 02 14 41 Patients Name RAT_CT_IT 2011 12 02 14 05 PET Mouse Hotel x3 2012 02 20 14 10 Patient ID Mouse_SPECT_Brain 2011 12 03 19 35 Se Mouse_CTbed_SPECT 2011 09 28 12 57 Description m17709_v1 img 2006 09 26 09 37 2011 12 02 14 41 2012 01 25 11 21 2010 03 26 13 40 2010 03 24 12 50 2012 03 26 18 10 2010 01 26 11 12 2010 10 25 10 09 2012 12 11 15 30 2012 12 11 16 03 2012 12 03 15 41 2010 01 26 16 12 Oo es Repository The repository displays the Data Browser or local folder from which data files are currently being displayed in the Study Browser See DICOM Configuration for more information on configuring your Data Browser including the use of projects in an iPACS repository There is a projects filter within the repository that allows the user to reduce the projects list in order to more easily search for a desired project There are three ways to filter the project list as described in the following table Filter Option Description Exampl
122. _ 2010 gt DC _M1_1 Open in Dump header Export to Delete Data b StudyDescription Patient ID The Add Comment button opens a text dialogue that may be used to add additional written comments to the report How to use the VQ Reporter Tool 358 VivoQuant Manual 11 12 2015 I m having a problem with my VivoQuant software The Add Screenshot button opens a screenshot acquisition dialogue The dialogue has a capture delay to allow files to be opened or procedures begun prior to acquisition of the screenshot vo inviCRO Service Reporter 2 50beta8 i Components System Info Add Files OS Version Unknown Windows AMD64 8 proc 64 bit Hostname kgoettler Add DICOM QT Version 4 8 2 IP addr F ESA3 FE80 462 193C 53EF ESA3 FE80 5EFE AC10 1A5C Add Comment App Version VivoQuant 2 50beta8 vq 2 Salpha 148 g9c2b020 User kgoettler Station UKN Report Type v Add Screenshot Content 01 Sy 02 Se gt 03 Re Preview Options Description Delay Ss S Hide this window Controls Hs ae Your name Your mail address Save Send In addition to the manual Add button options the pre defined report options will automatically gather certain files If we again look at CT Image Quality as an example we can see that certain X Ray configuration and calibration files were automatically added to the report In this example report we can see these files as well as the description txt file system reg
123. aded image is less than the given threshold 1 e MaxVoxSizeRatio gt LD X the data set will be loaded as an interpolated volume image with isotropic voxels Below is an example MR image loaded as an interpolated volume file Other modalities besides MR can be loaded into VQ as planar or interpolated volume files based on the Max voxsize ratio for volume setting specified in the configuration window Note As described on the Open DICOM Data help page e If the amp apos Force Planar amp apos check box is checked in the Data Browser then the image will load in planar mode regardless of the value set for Max VoxSizeRatio e If the amp apos Force Planar amp apos check box is unchecked in the Data Browser then the image will load in the appropriate mode according to the value set for Max VoxSizeRatio Quantification Options Use the amp apos Quantification Options amp apos panel to set options used by the Quantification Operator and the 3D ROI Operator Select the unit to be used for quantifying SPECT data Options include MBq kBq mCi and uCi Note Concentration units e g nCi cc will not be converted to the unit of activity specified The Tumor Segmentation and NM CT Brain analysis plugin modules do support converting from concentration units to units of uCi Choose the CSV file delimiter of their choice applied Separator when saving Quantification data Quantification Options 17 VS VivoQuant Manual 11 12
124. age to Capture The Image to Capture feature allows an image or movie to be loaded from a file on the local machine edited and then re saved The Capture Viewer also supports importation of the image movie into a DICOMAPACS repository by using the Save Capture button How to make a dynamic movie NOTE See the BatchTool Generator to learn how to quickly generate reconstructions for use in dynamic movies Dynamic and cardiac gated images and movies are a useful tool for illustrating the changing distribution of radioactivity governed by a dynamic physiological process This guide provides step by step instructions on the proper generation of such files Use the links to visit the VQ Manual for more details on any particular feature Before using this guide it is important to understand how to process images so that they are color comparable across multiple frames Matching color scales between two images is not enough to ensure that they are directly color comparable Instead it is necessary to ensure that the colors in each image correspond to the same physical voxel values It is possible to achieve this relationship using the Min Max tool to define the range of voxel values spanned across the color bar Load all relevant data sets These data sets may be only SPECT images as in this example or a reference CT image in addition to multiple SPECT images Change Delay 220 Repository SECURE Q Demo Pacs _finvicro_demo
125. agittal coronal and transversal slice of the reconstruction The Viewer Control 1s used to change the active planes while the sliders and checkboxes across the top of the window may be used to rotate the view display the bounding box reset the view and turn on off individual planes Getting There The MPR View is available via a pull down menu on the Main Window File View Tools Advanced Modules Help SY SY M on 0000 08 E oa O e o ee m Mu Slice View v Navigation y 2 Quick Scripts x O Slice View Display Tile View Multi View Click here to initialize MPR View z BB YZ XZ XY The image in MPR View may be rotated by using a left click and dragging the mouse Similarly panning may be controlled by holding the Shift key using a left click and dragging the mouse The zoom may be changed by using the mouse s scroll wheel To change the active planes in the MPR View use the X Y Z sliders in the Viewer Control MPR View 143 VS VivoQuant Manual 11 12 2015 X 89 5 Y 88 Z 225 Several other options for manipulating the MPR View are available in the top of the display window These checkboxes and sliders may be used to rotate the view display the bounding box reset the view or turn on off individual planes Pedet Resets the MPR View display to the default settings X Y Z Sliders Rotates the MPR y around the X Y Z BB Checkbox Toggles the display of the MPR View Bounding Box
126. ails about the study It is important to label the Study Description box in the Study Details section because this will be the name assigned to the reconstructed data The repository location is also displayed To continue with the batching function press OK invivoscope Resolution C Algorithm Exact Cone Beam FBP vi FBP filter type cut off frequency SheppLogan v Patientname IVS manual exa mple Patient ID Study date 20071219 Study desc IYS manual example Description CTReco CT Helical Scan NanoSPECT2WS iv BatchCT Tool 307 VivoQuant Manual 11 12 2015 Once the X ray projection data has been sent to BatchCT the BatchCT window can be opened by clicking the small white BatchCT icon on the bottom right hand corner of the screen This window displays all the projection data previously sent for batching and contains various functions to control the process Batch CT Status OX Pause Mod Details Patient Parameter Status Sil o Pa St CT 09010900206 Stoplob HA CT Girls Stella s CT 03 01 08 C42B G Running e 20080103 272 prj gt Stella s CT 03 01 08 LNCap batch 0201091503687 boys MoveU CTReco CT 03 01 08 LNCa P ae P Stella s CT 03 01 08 LNCap Waiting v SD a d MoveDown E Current joo AAN Editlob Total ANA E y Logfile DeleteJob he The BatchCT window is divided into 3 main sections Job List Status and Log File The
127. ain Setting the Input and Output ROI The Input ROI must be selected from the Input drop down menu before applying thresholding If an ROI other than the background is selected only image pixels within the chosen ROI will be considered when thresholding is performed The Output ROI is the ROI specified in the ROI drop down menu located at the bottom of the 3D ROI Operator window If the Output ROI is not empty prior to thresholding the result of the thresholding will be added to the existing voxels of the Output ROI Keep in mind that other ROIs may be overwritten if the result of a thresholding technique intersects them To prevent other ROIs from being altered set them to immutable See Editing an ROI to learn how to make an ROI immutable Operator ax e e XX s Classify input voxels to output ROI Global Thresholding v Global thresholding classifying all voxels of the input to the output class that fall in the Input v Image Ref v Min Max Apply ROIs 1 x y l Brain X Choosing the Image Data The segmentation algorithm will work on the data from the image specified in the Image drop down where Ref is the first image loaded according to the data manager Inp1 is the second image etc Setting the Seed Point For methods that require a seed the cursor location at the time the thresholding is performed will be used 3D Segmentation Tools 51 VS VivoQuant Manual 11 12 2015 Setting the T
128. ame Example User Email ExampleUsen Phamma123 com Department Imaging HW Key 54 d4 da Se de 17 40 25 02 59 5d 54 04 da 5e dc 1 40 25 02 59 30 0 Pre Approved Licenses 11 12 2015 e After you click Submit the system will validate the request If successful the below page will appear License approved Your license request has been pre approved and your HWKey has been added License de7 d7 6 cupelo Imaging Features VivoQuant segAtlasNMCT segAtlasfMRI segWholeBody Expiry 2028 12 31 HWKey 64 d4 da 5e dc 17 40 25 c2 59 5d 70 Please restart VivoQuant for it to fetch and install the new license or download the license here 4 Installing License Key If the end user s computer has internet access VivoQuant will automaticaly detect and install a pre approved license key If the end user s computer does not have internet access he or she will need to download the license provided in the link and install manually To install a license key file manually go to Help gt Registration within VivoQuant and click on Install key Your VQ 1s now registered and fully operational If you experience any problems please contact support vivoquant com 4 Installing License Key Installation Details After accepting the VivoQuant license you have the option to choose components which allows you to tailor the installation to your specific needs Please note that 1t is typically safe to accepts
129. and CT data are perfectly aligned Typically only shifts are needed for this operation If rotations are needed they should be only plus minus 1 degree Before clicking Apply go to File Save As Default and save the transformation Load Transformation 2 Save Transformation S x Operator Ret Y inp 1 y RO A ae ie Olly Return to the Data Browser or go to the Tools Menu and re check the Apply Default Shift box Display Data DICOM Data Loading _ Disable MIP viewer _ Ask Disable MIP MinVoxSize 0 00mm Quantification Options Unit of Activity Data Manager Y confirm moving _ Apply default shift How to Set a Default Image Shift VivoScript Registration Grow reference to input volume yes Max voxsize ratio for vol 2 50 Anchor input data at center w CSV Separator Comma _ Show seconds in Browser default I Save Reg Movie a Quick Preview Reset R TEST TT 3D a 2D EE SD HS 2D poty YE e i Close sar Rotation X axis Y axis Z exis o li 0 Translation E 3 Y E 0 0 mm e 0 0 mm m 0 0 mm E 80 VivoQuant Manual 11 12 2015 Data Show data type All data types Apply default shift Auto Start reconstruction LI El e Force planar Force 3D gt Append Open Transfer Close Stop Reload the image CT phantom data that were just acquired They and all other data sets will now b
130. another spreadsheet software Tip It is likely easier to make changes in batch in a spreadsheet software Please fill in Patient ID Group and Time Point fields i Patient ID Group Time Point Injected Dose Organ Uptake Unit 11 STUDYLA2B3C Heart 1 88724 MBq 2 STUDY1A2B3C Liver 2 74427 MBq 13 STUDYLA2B3C Left Kidney 1 34748 MBg 4 STUDYLA2ZB3C Right Kidney 1 7184 MBq 5 STUDYLA2B3C Brain 1 09018 MBq 6 STUDY1A2B3C Remainder Body 21 8757 MBq Time unit haar The column labeled Group asks for the group number This allows for multiple groups to be used at once The column labeled Time Point asks for the time point of the study for each frame The time units can be manipulated using the drop down menu on the bottom left of the window or manually in another spreadsheet software The column labeled Injected Dose asks for the initial injected dose Once the spreadsheet is complete save the information as an easily accessible CSV file In VivoQuant you may append an existing CSV file or start a new one Using the AUC Calculation Go to the Advanced Modules tab then select Dosimetry Calc gt AUC Calculation Advanced Modules Bid SPECT gt co CT gt Bed removal Whole Body Atlas gt Atlas NM CT analysis fMRI Tool Install Atlas gt Split ROI to DICOM Average body calculation Specify ROI center Specify ROI center 2 Upload tumor ROI TumorPK Model Dosimetry Calc gt Gettin
131. anual Preview 9 Resolution CE 65 C Algorithm Fast Cone Beam FBP v FBP filter typefcut off Frequency SheppLogan v A 100 Reconstruction Parameters g Color Panel 11 12 2015 Reconstruction parameters consist of resolution algorithm and filter if filtered back projection FBP is selected Resolution choices include Fast Standard and Fine with typical reconstructed voxel sizes ranging from 50 200 um depending on the pixel size of the projection data Algorithm choices include Exact or Fast Cone Beam FBP and available filters include RamLak SheppLogan Hamming Hanning Cosine and Blackman The slider bar below the filter choice allows selection of a filter cutoff frequency Study Details Progress and Controls Function 285 VivoQuant Manual 11 12 2015 study Details Patientname ct exp time ume 35 2 35 2 x32 4 mm Yoxel Pixel size 0 20 0 192 mm Memory Volume 38 3 MB Estimated time 00 01 46 2 pp o The Study Details panel provides information about the particular study and reconstruction such as patient Name Object Volume Voxel Size Pixel Size and Memory The Memory setting provides information on how much memory is needed to reconstruct the volume with the selected settings Memory values that are too large will be displayed in red Several options exist for reducing memory usage including changing reconstruction settings
132. ards the L and R in the transversal slice respectively L and R have a physical representation as the left side and right side of the object Moving through the object to the left or right is equivalent to stepping through the sagittal plane of the object and thus the sagittal slice changes Continuing with this example the and will move the crosshair towards P and A respectivly P and A represent the posterior and anterior of the object and are also visible in the sagittal slice of the object rotated 90 degrees Therefore using the in the transversal plane will shift the vertical crosshair in the sagittal plane identically to using the when the sagittal plane is the active view and correspond to stepping through the coronal views of the object Using the Slice View Display 131 R update disabled DEMO Scrolling Shortcuts Table VivoQuant Manual 11 12 2015 This table illustrates the points made in the above example with a table displaying the function of the arrow and paging keys for each active view al al Scrolling Example Active El Tr Previous Next Previous Next transversal coronal coronal slice slice slice Next Previous transversal sagittal slice slice Next Previous Next coronal transversal transversal slice slice slice 132 VS VivoQuant Manual 11 12 2015 Other Slice View Tools Scrolling through slices is also possible through the Viewer Control panel using the sliders and the
133. are enabled the analysis workflow will go in order of the display tabs Motion Correction Check the Enable box to perform a motion correction of the input data Y Enable Skice by Slice D 2 Reg to Mean Reg tolmage fol ne The user can choose to have the tool perform either a slice by slice or 3D motion correction The user must also choose to register each time point to a single time point or to the mean of all the time points If Keep Data Steps is checked in the Output section of the tool then the motion corrected data will be stored to the output directory with suffix mc Similarly if the Save QC box is checked then before and after motion correction QC movies will be stored to the output directory Smoothing Check the Enable box to smooth the input data Y Enable FWHM 11 00 mm gt Skice by Slice Before After The user can choose to have the tool perform either a slice by slice or 3D spatial smoothing The user can also edit the full width at half maximum FWHM setting to adjust the level of smoothing If Keep Data Steps is checked in the Output section of the tool then the smoothed data will be stored to the output directory with suffix sm Similarly if the Save QC box is checked then before and after smoothing Customize Analysis Pipeline 263 VivoQuant Manual 11 12 2015 QC images will be stored to the output directory as well as displayed under the smooth
134. as 1 Note SRTM2 can be used on both the region and voxel level but generally shows greatest advantage over SRTM when used at the voxel level Model Assumptions This model makes the following assumptions e The tracer binds reversibly e Tracer concentration in all regions or voxels of interest as well as the reference region see below can be represented by a 1 tissue compartment model e A region tissue exists which is devoid of the target site receptor We call this region the reference region It represents the concentration of the tracer which is free in tissue and or bound to off target sites non specific binding An ideal reference region is a devoid of the target site receptor and b has the same concentration of tracer free in tissue and nonspecifically bound as the ROI e There is only one true k value k is the rate of tracer efflux from the reference region to the plasma Note Violation of any of these assumptions will invalidate the model and may produce biased parameter estimates While the model will still run in VivoQuant the estimated parameters may not accurately reflect the true tracer kinetics SRTM2 is currently implemented in VivoQuant using a basis function method approach and unweighted fitting 2 Required Inputs This model requires the following inputs e Reference tissue curve e ROI s or voxels e A fixed k e Selection of a fixed k The value to which to fix k should be selected based on the
135. as Atlas NM CT analysis fMRI Tool Install Atlas Split ROI to DICOM Average body calculation Specify ROI center Specify ROI center 2 Upload tumor ROI TumorPK Model Dosimetry Calc Function Several calibration measurements are required to calibrate and maintain the NanoSPECT CT imaging system The Calibration menu provides options for analyzing e CT Geometrical Calibrations e Multi Pinhole SPECT Calibrations e Near Field Flood OC Measurements e Access to the VO Calibration Application Calibration 311 CT Geometrical Calibration This tool can be used to evaluate CT Geometrical Calibration data Getting There The CT Geometrical Calibration menu is available in the Tools Menu File View Tools Advanced Modules Help NM SPECT som Display NA C lece P CT Geometrical F Bed removal CT Reconstruction Ctrl L Whole Body Atlas CT Window Presets Atlas NM CT analysis fMRI Tool Install Atlas Split ROI to DICOM Average body calculation Specify ROI center Specify ROI center 2 Upload tumor ROI TumorPK Model Dosimetry Calc If running the VQ Calibration Application enter the tool by pressing CT Geometrical Calibration IVS Calibration PE Nucline base v Multiplexing Multi Pinhole Near Field Flood SPECT calibration Energy Calibration CT Geometrical Near Field Flood Calibration Uniformity Calibration Function The gantry of the NanoSPECT has a reproducible w
136. as to be restarted to configure this change Check to apply a default reorientation to data being loaded into VQ The default shift can be defined in the Reorientation Registration operator For more on this please see the Reorientation Registration page Data Manager 238 DICOM Settings The DICOM configuration allows the user to add edit DICOM repositories These repositories can be local folders containing DICOM files or DICOM network servers located on the local or a remote computer The DICOM Dictionary is used by the DICOM Dump to identify information in the DICOM header A How To on configuring the NanoSPECT s DICOM Servers in the VQ is provided Getting There There are three methods available to access the DICOM Repositry First the repository index is accessible via the Repository panel in the Data Browser Repository SECURE fexampleproject therapeutic_track_1 20 13 ov N Projects 28 28 The second method is to select the Configuration option in the Tools menu and to then click on the DICOM panel File View Advanced Modules Operator Help Y g cs View control FS O E MIP control F6 Operator 4 Data Manager F7 f R Min Max lan A vt at Histogram Ctrl Shift H l Workflow Assistant E a E Pre processing ROI E Resample data pa lt gt DICOM E backgro 3 123 Image amp Movie W Update Check Ctrl Shift U 4 Configuration Ctrl Shift C The third method is to r
137. atasets this can improve the loading speed Choose amp apos yes amp apos to allow the addition of zero padding to a reference image to match the volume of an input image or amp apos no amp apos to keep the reference image size static and potentially crop the input image if it is larger than the reference Choose amp apos ask amp apos to allow a window to appear upon loading in an input data set that is larger than the image in the reference position Specify the maximum pixel ratio largest pixel dimension smallest pixel dimension by which a 15 VivoQuant Manual 11 12 2015 data set is interpolated as a volume image file Specify the minumum allowed voxel width Data will be resampled upon loading if their voxel width is less than the specified minimum The voxel width will be doubled until it exceeds the minimum Specify where to anchor the input data Data can be anchored at the following options center head or foot mb X A _O E Longest Dimension LD In the above image LD represents the out of plane resolution and the X and Y represent the in plane resolution If the pixel ratio of the loaded image exceeds the given threshold 1 e MaxVoxSizeRatio lt LD X the data set will be loaded as a planar 2D by n file Below is an example MR image loaded as a planar 2D by n file Data Loading 16 VivoQuant Manual 11 12 2015 If the pixel ratio of the lo
138. atchCT tool is reached via the Data Browser by right clicking on the CT scan of interest and selecting send to BatchCT sda yatta PINES Patients Name StudyDate StudyDescription Patient ID E Series Description Series Date Modality Model name Topograrn oil BF doh Pete Ba Me WS e NanoSPECT IVS manual exa 2007 12 19 11 43 NM NanoSPECT Helical SPECT 2007 12 19 11 27 NM NanoSPECT 2007 12 19 11 23 NanoSPECT 2007 12 19 11 23 CT recon IVS CT Helical Scan Open as Reference Send to CTReco Send to BatchCT h Export data Dump header The BatchCT reconstruction panel is then displayed This panel provides options for Reconstruction Parameters Study Details and Repository The user can define which reconstruction parameters to use see CT reconstruction above and can enter details about the study It is important to label the Study Description box in the Study Details section because this will be the name assigned to the reconstructed data The repository location is also displayed To continue with the batching function press OK invivoscope Resolution C Algorithm Exact Cone Beam FBP vi FBP filter type cut off frequency SheppLogan v Patientname IVS manual exa mple Patient ID Study date 20071219 Study desc IYS manual example Description CTReco CT Helical Scan NanoSPECT2WS iv BatchCT Tool 291 VivoQuant Manual 11 12 2
139. ate Ki Vesa Oikonen Turku PET Center website Link Additional Resources Patlak Analysis Patlak Plot 113 VS VivoQuant Manual 11 12 2015 Multiple Time Graphical Analysis MTGA Vesa Oikonen Turku PET Center website Link Patlak Analysis Patlak Plot 114 Main Window Upon starting the VivoQuant the VQ Main Window appears The Main Window contains the primary VQ display and also serves as the focal point for reaching all other VQ functions w E AAA VivoQuant 2 50alpha9 64bit DEMO DEMO CT DEMO NM DEMO 0 ES File View Tools Advanced Modules Help SY W A tay 0000 08 O y fon O Pp ee Hi ne Me Slice View v Navigation y El Quick Scripts gt amp D Y Display Palette Resampling images to reference image took 0 1 sec Menus Five Menus are arrayed across the top of the Main Window These include Menu Function Used for file manipulation and includes options for opening saving printing and publishing files Used to control the display of data already loaded into the VQ Entire data sets may be toggled as may a variety of display options including layout and ZOOM Provides access to several VQ image processing tools including data control reconstruction calibration and configuration features Advanced Provides access to more advanced VQ image Modules processing tools including data control Main Window 115 VS VivoQuant Manual 11 12 2015 recons
140. ate SPECT projection data set A pulldown menu of split options is presented After splitting a confirmation message is presented to verify successful saving of the new data sets Split Projections 280 Function VivoQuant Manual Select Split Vector Please select the DICOM vector you veould like to split on Image Type ORIGINAL PRIMARYIGATED TOMO EMISSION 0054 0070 TimeSlotWector 0054 0010 EnerayWindowWector 0054 0020 Detectorvector 0054 0050 RotationVector 0054 0060 RRIntervalVector 0054 0070 TimeStotvector v Split data on 0054 0070 producing 8 files of 16 Frames Storing data to TempFolder Result OK 11 12 2015 281 CT Tools The CT Tools Submenu contains features to aid in the preparation of CT data for analysis and display e CT Reconstruction e Bed Removal e Resample Data CT Window Presets can also be selected from within this window CT Tools File View Tools Advanced Modules Help SY SY M NM SPECT S C DM r Bed removal Data List Whole Body Atlas Loaded 2 Atlas NM CT analysis fMRI Tool Install Atlas Type CT CT Rec Name Segmentat Split ROI to DICOM 1 CT Date 2010 05 19 1 Desc CTReco s E s Average body calculation Dim 192x192x380 Specify ROI center Type NM NM Re Specify ROI center 2 Name Segmentat 2 WM Date 2010 05 19 1 Upload tumor ROI Desc NM Reco Ca Dim 192x192x380 TumorPK Model Dosimetry Calc 1 O DB cco E qa
141. ation Displayed Name NS13WS_DCMSRV Repository Type i Local folder DICOM server Pacs Local DICOM folder DICOM Server Calling AET IvS WS2 Called AET NS13WS_DCMSRV Hostname nanospecti3ws Port 104 Use localhost lower case for optimized local access Test OK Cancel Displayed NS13WS_DCMSRV or customer s Name e a o Type DICOM Server 1 Server Calling AET VQ WS2 Called AET NSI3Z3WS_DCMSRV Hostname _ nanospect13ws or IP Port 104 Troubleshooting e Double check the settings in VQ and the DICOM Server Manager Remember that they may be running on the same computer VQ on the WS computer talking to the WS DICOM Server or different computers VQ on the WS computer talking to the ACQ DICOM Server e Check the network connection between the two computers Can you ping the hostname configured in VQ from the computer running VQ Can you ping the hostname configured in the DICOM Server Manager from the computer running the DICOM Server If not try switching the hostname from the computer s name 1 e nanospect13ws to the computer s IP address e Check the DICOM Server logfiles on the computer that you want to access located in C Program Files Mediso DICOM Server logs Troubleshooting 248 VS VivoQuant Manual 11 12 2015 e Enable debugging in the VQ and collect output while trying to access the DICOM Server Troubleshooting 249 Network The Network panel consists of tw
142. ation X axis Y axis Z axis 0 00 0 00 0 00 Translation 0 000 mm 0 000 mm 0 000 mm _ Uniform Scaling 100 100 100 lt 1 Rotation is completed by either using the up and down buttons next to the box or by typing in the number of degrees you wish to rotate the image Once the desired positioning has been achieved click OK to apply the transformation 2 Translation is achieved by scrolling the bar to the left or the right or typing in the number of mm to be moved in the box below Translation can also be achieved by holding the Ctl button on the keyboard and dragging images in the Viewports 3D and 2D Manual Options 73 VS VivoQuant Manual 11 12 2015 3 Scaling can be enabled in the Operator menu When enabled images and ROIs can be scaled during reorientation by scrolling the bar to the left or right or typing in the by which to scale To scale uniformly in all three dimensions check the Uniform box NOTE WHEN SCALING DATA PLEASE USE CAUTION AS SCALING CAN LEAD TO ERRORS IN QUANTITATION FOR MORE REFER TO THE TREATMENT OF QUANTITATIVE DATA PAGE 3D and 2D Automatic Options 3D and 2D automatic registration options can be found in the third and fourth tabs of the operator There are Basic Settings default and Expert Settings available in each Operator qx Ref v Inp 1 Inp 2 ini JRO vy tk 8 O Interpolator Linear Quick Preview
143. based on the Patlak method for irreversibly bound tracers 2 The Logan method proposes that after some time t the plot of h Crdt f C tat Cr VS Cr where C 1s the concentration of the tracer in the tissue and C is the concentration of the tracer in the metabolite corrected arterial plasma becomes linear with slope equal to the total volume of distribution Vy 70 y 2 028x 14 79 60 gt 50 A Coat 40 Cl 38 ee 20 10 0 0 5 1 15 20 25 30 35 40 A CAD amp plt ix One Tissue Compartment Model 1 TCM 104 VS VivoQuant Manual 11 12 2015 When the Logan Plot is applied to image data with a reference region the distribution volume ratio DVR can be calculated DVR V Vyp where Vyp is the estimated disctribution volume in the reference region BPnp is related to DVR by BPyp DVR 1 The Logan plot is a rearrangement of tracer kinetic equations to yield a useful linear equation However the mapping of transformed variables is nonlinear in C t and this results in an underestimation of V which becomes more pronounced with larger true Vy and increased noise 1 3 Therefore the Logan graphical method may not be the best method to use when data are noisy and other methods should be considered Model Assumptions This model makes the following assumptions e The tracer binds reversibly jo Critidi After some time t the slope of the plot of approaches linearity Note Violati
144. ber m ManufacturersModelName o Manufacturer p PatientID s SeriesDescription t SeriesTime 0 files loaded Add Files Examples Choose which files to rename by using the Add Files button in the Rename DICOM Files dialog Construct new image names by typing into the Template text box using the key beneath the text box for reference Each token represents a particular field of the DICOM header The new names of the selected files will be displayed in the Examples window as they are entered Names must be unique or else the files will not be renamed Renaming will also fail 1f illegal characters e g backwards or forwards slashes are used To execute renaming click OK Relabel Study The Relabel Study tool allows the following fields to be edited or renamed Patient Name Patient ID Study Description Series Description Patients Birthday Protocol Name Getting There 210 Getting There VivoQuant Manual Go to the Tools Menu in the Main Window then DICOM Function File View Qs DM Data List Loaded Type NM Name DEI 2 Desc DEM View control F5 E MIP control F6 w Data Manager F7 M Min Max d Histogram Ctrl Shift H Workflow Assistant G Pre processing H Resample data Dim 176x17 Advanced Modules Help Image amp Movie W Update Check Ctrl Shift U Ctrl Shift C A Configuration Relabel Study G
145. brary is the basis of the efficacy of the Whole Body Tool The Reference Library is stored Locally and is built one data set at a time The first step in adding a data set to the Reference Library is to open the data and ROI In order to add to the Library there must be an active ROI in the 3D ROI tool There can be multiple ROIs but it is important when building the Reference Library to keep the naming of ROIs consistent that is 1f the organ of interest is the Left Kidney always call it Left Kidney do not vary between L Kidney Left Kid and Left Kidney as that will not be recognized as all the same organ however capitalization does not have an affect With the data and ROI loaded simply navigate to and click Add to Library as described above And the GUI will appear RS W Submit Ali Images to Library b image to Submit Reference y Species Mouse Repository A Loca The GUI offers four editable fields The Patient ID can be anything that is unique and will help you identify this data set when selecting which scans to use from your Reference Library The Protocol should include information as to how the image was acquired the field of view modality etc This will be used as a filter to determine which scans from the Reference Library will be used by the tool Getting There 255 VivoQuant Manual 11 12 2015 The Species dropdown list contains frequently imaged species If you w
146. brings up the Multi View display and activates the Multi View specific Layout operator Mw VivoQuant 2 50rc10 64bit DEMO DEMO CT DEMO NM DEMO CES File View Tools Advanced Modules Help ra vc a e GQ lt M te 0000 05 B ea O Doo Mu Multi View v Layout y R Operator amp XxX Display Use the data manager to drag and drop images into your layout Sag No Images Layout 1 rows 1 cols Data 1 CT DEMO 2NM DEMO None C Show ROIs Show ROIs All Operator VC DM Resampling images to reference image took 0 1 sec Multi View 137 VS VivoQuant Manual 11 12 2015 The Layout operator is where users may customize the Multi View display Users first select the number of rows and columns of Viewports Then for each Viewport users select the datasets and slices that will be displayed in them To set the number of Viewports set the rows and cols scrollboxes to the desired amounts The 5x5 grid in the Operator window in addition to the Display will populate with the number of rows and columns of Viewports ry VivoQuant 2 50rc10 64bit DEMO DEMO CT DEMO NM DEMO CES File View Tools Advanced Modules Help gt AA vc r F SOOM OS BM GOOFS Pee E E G He nve a JiR Operator 8X Display Use the data manager to drag and drop images into your layout H sl a No Images No Images o Layout 2 rows gt 2 cols gt Data None None None e
147. cal Data Save Image Ctrl Save Movie Ctrl M Save Data Session gt VivoScript Ctrl Shift V oer EEO cu Exit The second method is to use the keyboard shortcut Ctrl M For more on keyboard shortcuts in VQ please see Keyboard Shortcuts The third method to save image slices is to use the amp thumbnail in the Main Window The fourth method is through the MIP Control which can be opened via the Y thumbnail in the Main Window There is an option here to save the movie Function Selection of the Save Movie option opens the Save Movie window Save Movie 124 VivoQuant Manual Look in C Users kgoettler Desktop DEMO t O m EJ A My Computer R kgoettler File name Files of type Movie files gif mng mpg mpeg Movie type Maximum intensity projection Colorbar options smart labels Storage Type Local image file There are several options for the output movies File name Set name of movie file Set type of movie file Movies can be saved as nes of i pif a ee a 4 Set type of movie Movie types can be 1 Maximum intensity projection Movie MIP type 2 Sagittal slice 3 Coronal slice 4 Transversal slice 5 All movies separately Colorbar Set colorbar and label options for the options limage Options include None no colorbars or labels No labels colorbars with no labels 3 Simple labels colorbars with one set
148. ccess How to configure the NanoSPECT s DICOM Servers First open the Data Browser Find the Repository panel and either select the pre existing repository from the pulldown menu or select new to create a new repository For the standard access on the NS Workstation WS use General Information Displayed Name NSxx WS_DCMSRV Repository Type a Local folder 8 DICOM server Pacs Local DICOM folder DICOM Server Calling AET INVIVOSCOPE Called AET NSxxWS_DCMSRV Hostname localhost Port Use localhost lower case for optimized local access Test OK Name preference NSxxWS_DCMSRV _ _ Called AET INSxxWS_DCMSRV How to configure the NanoSPECT s DICOM Servers 245 VivoQuant Manual 11 12 2015 where xx is replaced with the NanoSPECT number typically no leading 0 for numbers lt 10 The local access VQ is able to access the DICOM Server directly so there is no need to add the VQ as a client on the DICOM Server However it does not hurt and is necessary when configuring an VQ for which access is not locally on the workstation See Adding VO as a DICOM Client for more information The above table described configuring VQ to access the Workstation DICOM Server VQ may also be configured to access the Acquisition computer s DICOM Server The procedure is similar but there is no WS in the naming convention General Information Displayed Name AcQ_NSxx_DCMSRV Repository Type O W
149. ce Tissue Model 2 SR TM i 108 Logan Non Invasive Graphical Method Logan reference plot oooooooooonnncccnccnncnnnnnnonnnnnnnnnos 110 Patak Analysis A Patak PIO cdi pias 112 Main WV MIN IOWA AA AAA 115 MEDUS athe hm abies Oia ee uate eS wacom sneisset cea as Saati bsenGau Ne sec ta sootetaanatenasabateca ab T 115 TOG A T 116 A A EE E A A ET AE OA E A N 116 MEW Mode Sanana a a A A A 117 ODO a E E a s eses 117 A A sau rautsasassatuaneescnanteinascsdeaiian 118 Projections vs REcCoNstU HONS sussie tain nace ado 119 Save Ima ce Dd E E E E N E E 121 E E O 0 OA eae 121 A A IN 121 Save VIO VNC iia AAA A ave scatasescoseaees 124 A a A staat dadtaks 124 O 124 DOCS A A A oca aRdSa 127 OESTE O A o UE O aansetatacactasncpenred se 127 BIE SL E EEEE EET PE E E E AE NE E EE E E E A AE A AOE E E T E E 129 SUCE VIEW eonan Ai 130 A A nin ee vane 130 USime the slice View DISPARES 130 SC CO HNO EaD 20h A neatyeseecemieconines 131 SCONE SAGE Cuts TaDlS nario da lia 132 AAA A A 133 Tie View SN AAA 134 Geine Thread ti ai iii 134 Wsime the Mile View DISPO 134 Malti O 137 E PE UE O O aorsematasgsinancaeneaact 137 settimo Up the Mult View Displa ci aid 137 Using the Muli View Display A oa 141 A A 141 Viewer CONTO LI MUEVA cia 141 VivoQuant Manual Table of Contents MER VIEW cis 143 A ANN 143 Usine the MER VEW DiS DN n 143 Capture VIE WEE ASA AAA 145 CI in rere a Thr event 145 FUNCION a e ae ead 145 A A O esamac E teen sensean
150. ch CT application Service Jobs Menu The batch file can be altered using the icons to the left of the window or via the Jobs menu in the main window The job icons are located on the left side of the window Status Pause Pauses the current reconstruction job 293 VivoQuant Manual StopJob Stops the reconstruction job Moves the selected projection data up the list of MoveUp studies to be reconstructed Moves the selected projection data down the list of MoveDow P studies to be reconstructed EditJob Allows you to edit the reconstruction parameters Deletes the projection data from the reconstruction DeleteJob list 11 12 2015 These functions can also be accessed under the Jobs menu in the main window Additional functions available here include Thread Number Thread Priority and Show Bubbles Jobs Menu Batch CT Status 1 57 File te Help 4 R Pause A stoplob Pa Details Patient Parameter Status 4 gt MoveUp MoveDown 0505072353640 ct exp time St Eco CT Helical Scan Topogram CT Running EditJob prj 20070912 3 DeleteJob Mos Thread number gt q Thread priority gt Statis Move v Show bubbles 1 NA 0 AL 0 OE OO AS RR O ES NA E Total e e 0 O OL EditJob DeleteJob 2008 04 30 15 02 47 Welcome to batchCT 1 57 2008 04 30 15 02 48 BatchCT started 2008 05 05 07 23 54 Job added batch 0505072353640 ct exp time CTReco CT Helical Scan
151. cified SPECT measurement on a syringe filled with isotope The fields of the QuantiCalc window may then be filled in according to QuantiCalc 271 VivoQuant Manual 11 12 2015 e Dose meter Record the amount of activity in the syringe in MBq kBq mCi or uCi as measured by a dose calibrator Include the time of the measurement e NanoSPECT Record the activity value measured by the NanoSPECT from reconstructed data Include the time of data collection e Isotope Select the isotope present in the syringe Isotopes offered include Ga 67 I 123 I 125 Lu 177 Tc 99 T1 201 In 111 and Xe 133 The half life of the selected isotope will be entered automatically in units of hours e Decay factor The information from the Dose Meter NanoSPECT and Isotope fields will be used to calculate a decay factor between the time of Dose Meter measurement and data collection e Quantification Factor The information from the above fields is all combined to determine a Quantification Factor for that particular isotope and aperture This Quantification Factor can then be entered in the Quantification Database Quantification Database The Quantification Database stores all of the Quantification Factors calculated for any isotope and aperture combination measured with the NanoSPECT CT These factors are then used by the HiSPECT reconstruction software to produce SPECT reconstructions with physically meaningful voxel values For more on setting Quantification Fa
152. compression of the output images If selecting Lossy JPEG the quality spin box becomes active and the user can specify how much quality to preserve in the output image Edit Info 147 VivoQuant Manual 11 12 2015 The Edit field includes several buttons Annotate Creates a text box in the image space Circle Creates a circle in the image space that can be moved and resized to highlight an ROI Arrow Creates a movable arrow in the image space Image View The Image field displays the image movie that is currently being edited Image View Edit 148 View Menu The View Menu is useful for modifying the information about a data set that appears in the Main Window e Show Reference Input 1 Input 2 e Slice Number e Crosshairs e Position Labels e Patient Name e Active Indicator e Layout e oom View Menu 149 Slice Number Highlighting the slice number function displays the slice number of the image being viewed This is useful if you are want to compare the same slice of a subject at different time points Getting There To view the slice number on the image go to view under the view menu and select Slice number File View Tools Advanced Modules Help Undo Ctrl Z O gt O Dove g Redo Ctrl Shift Z E E mu its Show Reference Show Input 1 Show Input 2 Slice number Cross hair Position labels Patient name Layout Reset View Transform Ctrl R Zoom
153. construction DICOM Bed removal Advanced Analysis Resample data Histogram CT Window Presets Volume rendering Image Magick mu Min Max W Workflow Assistant Calibration Update Check It can also be reached via the Data Browser by selecting Open when a set of CT Projection data is highlighted and the Auto Start Reconstruction box is checked Right clicking on an appropriate data set in the Data Browser will also present the CT Reconstruction and Batch CT programs CT Reconstruction 299 VivoQuant Manual Repository SECURE Q Demo Pacs invicro_demo vivoquant VivoQuant Y A Projects 12 380 o Filter Study Browser Patients Name A 4 ADC_M1_1_48h ADC_M1_1_48h gt _M1_1 3h ADC_M1_1_24h ADC_M1_1_144h Patients Name Patient ID Description Study Date 7 Data Show data type All data types 7 eae eB _ Apply default shift Auto Start reconstruction Force planar Stack 3D gt Append Open Transfer O Close StudyDate 2010 07 22 11 25 Open data Append data Export to Open in Delete Data FileType dem StudyDescription Patient ID Topo CT SPEC Topo CT SPEC Topo CT SPEC Topo CT SPEC Topo CT SPEC 11 12 2015 Finally using the keyboard shortcut Ctrl L will open the Reconstruction panel For more on keyboard short
154. crease or decrease the alpha values a lower percentage will increase the transparency of an ROD Check Hidden to turn the ROI off in all views Check Immutable to prevent edits to an ROI ROIs 2 gt e E background Y Another option is to select any one or shift select more than one of the ROIs in the operator right click and select Add ROI This will append a new ROI to the end of the list regardless of which ROI is selected Operator ax amp be Xx gt A vk CS sa BE ew 6 ROI H M background Brain LeftKidney RightKidney Heart M Liver Edit ROI Liver Add ROI e Toggle Hide ROls Toggle Immutables Reset ROls X Delete ROIs Export ROIs ROI Creation and Deletion 39 VivoQuant Manual 11 12 2015 Edit an ROL To edit an ROI click on the pencil Edit ROI button Use the interface that appears to change the name color transparency visibility or state of immutability Edit ROI ited Name Color OK Cancel This will edit whichever ROI is selected in the ROI dropdown menu Lefikidney E RightKidney Brain ROIs E Heart Liver A XxX BB background y Another option is to right click on any ROI in the operator and select Edit ROI Operator ax eo xX 2 A vk AX alk EEE ROI H MN background O N Edit ROI Heat m iM Add
155. csv file Opens dialog box that allows user to append percentiles to existing csv file Updates MIP Updates Main Display Updates MIP Main Display etc Opens Histogram Tool Updates ROI List 181 VS VivoQuant Manual 11 12 2015 IPACSWebDisk Object Function Description IsDir path Returns a list of files directories Saves a file from the local path specified by src and stores it on the WebDisk put src dest oe at the path specified by dest Saves a file from the local path specified by src and stores it on the WebDisk at the path specified by dest mkdir path Creates a WebDisk directory rm path recursive false Deletes a WebDisk directory put src dest sel de Retrieves the file specified by the path in src and places it locally in the path specified by dest getPublicLink const QString amp file setExtraTimeout int t getStoreFile printProgress int done int total ZipArchive Object Function Description createZip fileName srcdir Zips the contents of the directory srcdir into a zip file named fileName unzip zipfile outdir Unzips the zip file specified by zipfile to the directory outdir cancel DataList Object Function Description annotate int idx annotate int idx updateData int 1 showForm toggleForm mipViewer Object Function Description loadedSlice int 1 updateDisplay scaleImage float factor IPACSWebDisk Object 182 VS VivoQuant Manual 11 12 2015 updateCac
156. ction of t The Patlak plot as implemented in VivoQuant requires that the user inputs the t which defines the time at which the plotted data become linear In VivoQuant the default t value is 0 This is likely not be the appropriate value for your experiment t values are tracer dependent For characterized tracers we suggest reviewing the literature to see which t values have been used in Patlak analysis The simplest way to select a reasonable t value for your data is to run the model once with the default t value review the Patlak plots to find the point at which they become linear t then re run the model with the appropriate t in scan time value Outputs Region level analysis e Patlak plot with line fit for each ROI e K fitted line intercept V and mean squared error MSE of fit are shown when the cursor is hovered over the Patlak plot e K and transformed Patlak space data for each ROI can be saved out to csv Voxel level analysis e Patlak plot with line fit for each voxel Select the voxel for which you d like to see the Patlak plot by clicking on 1t within the image viewer e K fitted line intercept V and mean squared error MSE of fit are shown when the cursor is hovered over the Patlak plot e Parameter maps for K fitted line intercept V and MSE References 1 Graphical evaluation of blood to brain transfer constants from multiple time uptake data Patlak et al JCBFM 1983 Link 2 Net Influx R
157. ctors for the NanoSPECT CT please see this guide Function 272 Specific Activity Calculator The Specific Activity Calculator accepts an input volume activity specific activity for a given isotope and calculates the amount of isotope present in the sample both in moles and moles volume Getting There The Specific Activity Calculator is available in the Tools Menu File View Tools Advanced Modules Heip som eh cr ct Spec Act Calculator Display Bed removal SUV Calculator Whole Body Atlas Atlas NM CT analysis fMRI Tool instali Atlas Split RO to DICOM Average body caiculation Specify ROI center Specify ROI center 2 Upload tumor ROI TumorPK Model Dosimetry Calc Function The Specific Activity Calculator requires several values to make its calculations An activity volume isotope and specific activity are used to calculate the number of excited molecules and molarity of a given sample 8090 Specific Activity Calculator Activity lvl 3 7 14 12 00 AM Volume Isotope Half life Specific Activity i MBa pmol 3 7 14 12 00 AM Calculated values Amount pmol Amount of substance concentration a Molarity pmol mi Activity MBq kBq mCi Amount of isotope as measured in a or uCi and dosimeter or with the NanoSPECT measurement Specific Activity Calculator 273 VivoQuant Manual 11 12 2015 time Volume cm3 mm3 ml ul The volume containing the activity T
158. cuts in VQ please see Keyboard Shortcuts Function The CT Reconstruction panel controls the parameters available for generating tailored CT reconstructions Getting There 300 CT Reconstruction File Help po RECONSUMUCLCION Parameters i Resolution CE 6 CET Algorithm Fast Cone Beam FBP v FBP filter typejcut off Frequency SheppLogan v 8 100 E ss Study Details Patientname Na volume 0x0x0 mm Yoxel Pixel size 0 0 mm Filter SheppLogan 100 0 frequency Estimated time 00 00 00 0 0 KOntrols O autostart autosave Reconstruction Parameters VivoQuant Manual Preview 9 Resolution CE 65 C Algorithm Fast Cone Beam FBP v FBP filter typefcut off Frequency SheppLogan v A 100 Reconstruction Parameters g Color Panel 11 12 2015 Reconstruction parameters consist of resolution algorithm and filter if filtered back projection FBP is selected Resolution choices include Fast Standard and Fine with typical reconstructed voxel sizes ranging from 50 200 um depending on the pixel size of the projection data Algorithm choices include Exact or Fast Cone Beam FBP and available filters include RamLak SheppLogan Hamming Hanning Cosine and Blackman The slider bar below the filter choice allows selection of a filter cutoff frequency Study Details Progress and Controls Function 301 VivoQuant Manual 11 12 20
159. d clica 195 OPUS loa si 195 More WIN FIN A Ul OM eenei e e S 196 IV MMR A A TA 197 E A PFP mere ae hes reais ei su elt Site US aa ee Maa a haere ee meme 197 PIA IO Wigs A saa seh sacead nt cant sous rlaue a meget eaneosenoa al aiosaeuaaecs casita 197 PUSO OF Ali oit 552 5sceoh hag tute A A T 198 A O erm meer mene ese a OO ORE UE EO EINE ee teen 198 BRIS CO FAMA A A 200 RP e A dada 200 A a tesa tea tee Na al th ED oe ee ha dd a et aaah 200 Data Control dias 201 LECON o ieee a mala se secs shadernancaame bee ouantoeiabaae cian sheng soetenatateons 201 PFE DFOCESSING TOON ssscssncecsseseccsdsssvccescancesvessesscosncuaseusceutaxsdecuvesdnceseeresedoscuucassusecicausevcivasdness0esvessceensccsoueceateussves 202 A raced teasaad vaadverao a ean aeessea euaaueeetatietegee 202 UTA ONS lt los tease 202 Resample DAA ARA AAA AAA 205 Gelina PREIE ot laa 205 UMTS serial iciiSccso lio a alias 205 DICOM riot ns i tE SOLES IA EEEE E EEE EA EEEO TELELA E EEEE 206 DICOM DND ene E alias 206 Gedin IO o no PIE 5 5 cera atte sectes pets cence 206 ES 207 NS sia A A A 209 Geim Bl aed te e COPE O CEL E O O er tere eee er reat 209 TO GO APA PP O A O O A ttena santana tone 209 A E 209 Getme A A 210 L016 810 Were er alt nr SP EP PDE A ET er eT 210 A a ni sence Seecece seu sesouiab doinctod settee soncuaeees 210 Ge Ce TG he aid di ii n 211 vii VivoQuant Manual Table of Contents DICOM L161 611061 O O 211 Rename DICOM Files 20 A A as 212 A A E
160. d data acquisitions These tools allow the user to combine data sets in meaningful ways to reflect the dynamic nature of the physiological processes taking place Five options are provided in the Image Magick suite Split Movie into Frames Join Frames to Movie Change Movie Delay Image to Poster and Image to Capture A short How To for generating dynamic movies is provided below Split Movie Into Frames This option takes a movie options include gif mpg mng and mpeg and splits it into individual frames options include png bmp jpeg jpg and tif Join Frames to Movie This tool provides the opposite function of the previous tool allowing the user to take individual images options include png bmp jpeg jpg and tif and combine them into a movie options include gif mng mpg and mpeg Image Magick 219 VS VivoQuant Manual 11 12 2015 Change Delay Depending upon the size and style of movie made the default frame time may be too fast or too slow This tools allows the user to select a pre existing movie and change the frame time given in milliseconds Image to Poster The ImageMagick suite enables the creation of high quality images the kind of images often used at conferences and in presentations To help facilitate the ease of use of such images this option automatically allows the user to place an image into a poster This function is not yet implemented Please check back soon Im
161. d in the VQ If the reconstruction is allowed to finish this transfer occurs automatically Transfer to VQ Settings Menu CT Reconstruction r1 140 File ete Help Save Settings Re Hounsfield Threads Thread priority gt Alt Advanced El Auto Bed Removal FBP filter Eypefcut off Frequency SheppLogan vy flio lt Save Settings Saves the current CT Reconstruction Settings The Hounsfield Calibration uses the linear response of the detector at each of the x ray operating voltage to calculate dose to an object in terms of Hounsfield units For more information please see Hounsfield Calibration Allows user to enable multiple threads 1 2 3 4 6 or 8 for performing the CT Reconstruction Note that it only makes sense to enable as many threads as there are cores available in the computer amp zapos s processor Defines the priority given to the CT Reconstruction with respect to other tasks being performed by the CPU Allows the user to disable the use of normalization in the reconstruction Disabling normalization prevents the use of Hounsfield Calibration but reduces the memory usage required for the reconstruction For users imaging with the Minerve bed system this option will automatically remove the Minerve bed from the CT during reconstruction Help Menu Settings Menu 305 VivoQuant Manual 11 12 2015 CT Reconstruction r1 140 File Settings Mi
162. data transfer iteration Click the configuration button to automatically obtain the sync key file from the PACS if necessary Watch Job Yi Active Jobname New folde PACS Folders ds Schedule Messaging Advanced 4 Configuration Loaded Click to reload Directory Setup Specify the direction of the Sync Provide the complete path to the local directory to use in the Sync Select the project on the PACS to use for the Sync the o button will retrieve a list of projects on the iPACS which can be selected by clicking the arrow to the right of the text field The WebDisk folder for the selected project will automatically be entered into the WebDi sk field Subfolders can be selected by clicking the arrow to the right of the text field Configuring Additional Settings 365 VivoQuant Manual Watch Job Active Jobname New folde H Pacs Folders Schedule Messaging Advanced Sync Direction To PACS v Local Folder C Users User 1 Desktop New folder tee iPACS Project J WebDisk webdisk projects invicro_lab petstudy i v Delete local fies after transfer Delete after 14 days enan Delete i kb Save Setting Files that have been successfully transferred to the server are deleted locally This feature is potential y Delete local files after transfer dangerous and could lead to LOSS OF DATA if not used properly Schedule when files are removed from source location Scheduler
163. de of the mouse 1s being viewed Getting There To display the position labels on the image go to view under the view menu and select position Labels File View Tools Advanced Modules Help sam uz BODROS ppe 20am g Redo Ctrl Shift Z e Show Reference F2 NM e Show Input 1 F3 Show Input 2 Slice number Cross hair Position labels Patient name Layout Ctri R Reset View Transform Zoom Advanced Function The labels indicate the plane of view 1 e sagittal coronal and transversal and also the left right and anterior posterior side of the mouse There is a S on the top left corner of the Sagittal image to indicate that it is the Sagittal plane There is also a P to indicate the posterior side of the mouse and an A to indicate the anterior side of the mouse There is a C on the top left corner of the Coronal image to indicate that it is the Coronal plane There is also a H to indicate the head of the mouse and a F to indicate the feet of the mouse There is a T on the top left corner of the Transversal image to indicate that is it the Transversal Transversal plane There is also a L to indicate the left side of the mouse and a R to indicate the right side of the mouse Position Labels 152 Patient Name This feature enables you to include the patient labels in the image Getting There To display the patient labels on the image go to view under the Vi
164. dicator Layout Reset View Transform Ctrl R Zoom Advanced The Active Indicators appear in the upper right corner of the viewports The top middle and bottom indicators correspond to the Reference Input 1 and Input 2 respectively If the indicator is a solid circle the corresponding input is on If the indicator is a hollow circle the corresponding input is off Active Indicator Reference and Input 1 ON Input 2 OFF 155 VivoQuant Manual 11 12 2015 Reference and Input 2 ON Input 1 OFF Function 156 Layout This feature offers a variety of layouts for viewing your studies You can view all the slices and the MIP together simultaneously or you can view them individually Getting There To view the various layout options for the images go to view under the view menu and select layout File View Tools Advanced Modules Help A und Ctrl Z loas L h O sp sse i E g Redo Ctrl Shitt Z Show Reference Show input 1 Show Input 2 RGB data Slice number Cross hair Position labels Patient name 109 Layout Grid 2x2 Zoom Grid 1x4 o a Advanced MIP only er oe Slices only Transversal only Grid 2x2 MO Gridix4 amp MPony o8 Slices only O Transversal only Layout Options oo Grid 2x2 In the Grid 2x2 layout the MIP and the coronal slice are located on the upper half of the screen and the sagittal and transversal slices are located on the bottom half of the scree
165. do redo filling a contour in the Spline Tool the user must navigate away from the spine tool window Undo Redo Functionality VivoQuant Manual 11 12 2015 99 Quantification The Quantification Tool provides a means to quantify density and activity parameters in CT and NM MR PET or SPECT images respectively The tool provides several options for generating quantification data There are multiple methods for setting the region of interest flexibility in selection of the quantification view direction easy to read presentation of data found in the Quantification Table and options for saving and loading ROIs or plotting data Getting There Quantification can be accessed via the tool pull down menu on the VQ front panel File View Tools Advanced Modules Help SOW SE Wgt 22 Deve E BW thy sice vow gt niga Eva Navigation Pr Display 3D ROI Tool Quantficalion Reorientation Registration Time Series Distance Annotation Filtering Using the tool Upon selection of the Quantification Tool the Quantification Panel appears The first step in using the quantification tool is the definition of a Region of interest ROD Quantification 60 VivoQuant Manual 11 12 2015 File View Tools Advanced Modules Operator Help 4 SY wv eee tote 00 o5 E O BD ove ve e Slice View v Quantification v B Quick Scripts a gt Operator X Display Palette Mode Options O Thresh
166. dr txt png Filter is applied recursively through the subfolders of the top level folder The user can also provide files containing which file names file extensions and or folders to include or exclude Example text files would include the following Include 2009 CSV Exclude K In this example all folders beginning with 2009 and all csv files within those folders would be included in the transfer All other files would be excluded Notifications 367 VivoQuant Manual Watch Job Yi Active Jobname New folde _ PACS Folders Schedule Messaging Advanced Verbose Ji Compression Charset v Keep newer files CVS Exdude 4 Always Prompt for download destination global setting SSH Port 22 HTTP S Port 443 Filters Indude dcm img hdr ppt Include File LA Exdude File LA Delete ig Save Verbose Print more detailed log messages Compression Data is compressed before sending E Specify as US ACII ISO 8859 1 UTF 8 or Filename charset disable this feature Remove remote files that are no longer available locally This feature is potential dangerous and could lead to LOSS OF DATA if not used properly Keep newer files Modifie files at destination end will not be Keep newer files l overwritten Ignore all version control hidden files svn folder erence when resotring files viaiPACS sync Always Prompt for User will be asked to specify download destination
167. e Reduces project Type exampledata in the projects filter to reduce the projects list to all projects with the word exampledata in their path word Function 335 VivoQuant Manual 11 12 2015 Reduces project Type lexampledata in the projects An example of a commonly used regular expression 1s the choice expression before or the expression after the operator For example 1f the projects filter the projects list will expression reduce to all projects that have the word exampledata and all projects with the word test in their path Press enter on keyboard to apply the filter The filtered number of projects over the total number of projects is displayed For example the image below displays 2 out of 198 projects with the word exampledata in their path For more examples of regular expressions supported by the projects filter click here Repository SECURE Training fexampleprojeciftherapeutic_track_1 2013 Y projecte A Projects 2 28 w Filter As the database grows the Filter tool becomes useful for sifting through studies to find just the right one Options for filtering include Patient s Name Patient ID Study Description and Study Date After entering values in these available fields simply hit the refresh filter settings button L to refresh the Study Browser Want to view all of the data again Simply hit the clear filter button le to empty the fields and
168. e perfectly fused NOTE This same formalism may be used to generate other Transformation files Instead of choosing Save as Default in the Reorientation File Menu choose Save Transformation Then it is possible to later load that transformation using the Load Transformation option in the Reorientation File menu These saved transformations are useful when fusing data from other modalities with NanoSPECT CT data for example How to Set a Default Image Shift 81 Time Series The Time Series operator provides an easy way to visualize sets of dynamic data as a time series This operator can be used to play slice views of each image of a collection in sequence Getting There The Time Series operator can be accessed via the tool pull down menu on the VQ front panel File View Tools Advanced Modules Help SOOM OF BMW 2 2 Put LD B ie sive Ju saw OO VI A Display 3D ROI Tool Quantification Reorientation Registration Time Series Distance Annotation Checker board Cropping Arithmetics Filtering Using the Tool Data should be loaded into VQ in correct time order with the reference image if any loaded first Use the Data Manager to sort the datasets as necessary Operator Gx Sliders T 0 E Ref 8 Inp1 _ Global Min 1000 Max 9360 56 O Play If there is a reference image loaded check Lock Ref to keep the reference image visible with all other images of the series check Lock Inp1 to keep
169. e Checkerboard Tool can be accessed via the tool pull down menu on the VQ front panel File View Tools Advanced Modules Help se Qem oS ooWMsg t 2 Bow Display vC Cr _ _ ou Mu Slice View v Navigation Navigation 3D ROI Tool Quantification Reorientation Registration Time Series Distance Annotation Quick Scripts gt 4 D Y Using the tool Upon selection of the Checkerboard Tool the display of the coronal sagittal and transverse windows is automatically updated In these windows the reference and input data set s are displayed in an alternating grid pattern resembling a checkerboard Both the Input 1 and Input 2 data sets if present are displayed in the same squares of the checkerboard To return to normal viewing select Navigation in the Tools menu To adjust the size of the tiles hold Shift and use the mouse wheel All other keyboard shortcuts should work the same as in Navigation operator Checkerboard 88 G VivoQuant Manual 11 12 2015 VivoQuant 2 10 64bit DEMO DEMO CT DEMO NM DEMO O File View Tools Advanced Modules Help SY SY M A ate 0000 08 O y O BD ee La me Mu Slice View Checker board 7 ll Quick Scripts gt 4 DO O Y Display _Palette _ Use SHIFT modifier and mouse wheel to adjust tile size Using the tool 89 Cropping tool The Cropping Tool allows images to be made smaller by removing any unwanted areas For example 1f an image has been cu
170. e Getting There e Getting There e Getting There 11 12 2015 3 7 VivoQuant Manual 11 12 2015 H e Help Menu e Hide an ROI e HiSPECT e HiSPECT e HiSPECT Reconstruction e HiSPECT BATCH e How to configure the NanoSPECT s DICOM Servers e How to make a dynamic movie e How to Set a Default Image Shift e Image to Capture e Image to Poster e Image View e Info e Install Atlas e INTERVIEWXP e INVIVOSCOPE e iPACS Projects e iPACS server e iPACS server e iPACS Servers e IPACS WebDisk Object e JavaScript e Join Frames to Movie e Known issues with graphics card e Landmark based Co Registration e Load Data into the Tool e Local DICOM folder e Logan Graphical Method Logan Plot e Logan Non Invasive Graphical Method Logan reference plot H 378 VivoQuant Manual e MacOS X e MainWin Object e Memory configuration e MinMaxTool Object e MIP Rotation Speed e MIPController Object e MIPViewer Object e MMP Menus e MMP Menus e Models e MPR View e MPR View e Multi View e Multi View e Multi Pinhole SPECT e Multi Planar Reconstruction e Network e nih fire color ma e Noise Suppression e NSxxWS DCMSRV e One Tissue Compartment Model 1 TCM e Open e Optimized local access e Output e Output e Overview e Painting Tools e Placeholders e Playing a MIP Movie e Plot data e Preprocessing Tool e Preview e Preview e prism color ma e Profile 11 12 2015 3 9
171. e Troubleshoot e Troubleshooting e Troubleshooting e Two Tissue Compartment Model 2TCM e Undo Redo Functionality e Using the Tool e Versions alpha beta rc stable patch e Via ITK 11 12 2015 381 VivoQuant Manual 11 12 2015 e ViewControl Object e Volume Rendered Image e Volume Rendering Controls e Volume Rendering Parameters e VO Object e VOScript e VOScript Example Scripts e VTK Viewer e VTKController Object e VIKViewer Object e Windows 32 bit e Windows 64 bit e Windows XP e ZipArchive Object Last updated Thu Nov 12 17 17 28 2015 V 382
172. e a voxel size in either the X Y transverse or Z axial directions that differs Voxel Size from the 3 options Fast Standard Fine offered in the main CT Reconstruction panel NOTE Changing y the voxel size may slightly alter the voxel volume Allows the user to modify the reconstructed volume oxel either in terms of voxel number or total reconstructed Volume size in mm Modifications may be made in either the X Y transverse or Z axial directions Allows the user to shift and restrict the reconstructed volume to better center features of interest enabling disabled more reasonable resolution times for high resolution images Sampin Sets the number of rays used by the Exact Cone pang Beam Algorithm during the reconstruction Sets the number of threads used during reconstruction The optimal value is determined by Threads the number of cores or processors in that particular machine s CPU Up scaling may be used to reduce an image size by a Up scaling factor 2 N Smaller image sizes are often more manageable Help Menu 290 VivoQuant Manual 11 12 2015 BatchCT Tool The BatchCT tool is a useful application which enables the user to select a number of X ray projection data studies and order them for reconstruction at a later stage The CT scans are saved in an appropriate batch file and can be left to reconstruct automatically The parameter settings and file names can be predefined The B
173. e eee at it etal ae 168 A O N 168 TO 168 CAS A te re erest ner ener 168 Adding Script Shortcuts to tne PODA aos 168 MOS Ts eA Se Fo ata aise cst das 170 VOScript Objects and Object Method sscsccsssccssssssssssccsssccccccccsssscscsssscccsccsccsssccssscscccsscsesccsssssssccsss 171 OC Ci cee Ya ia eatery awe ca a aeieess sto 171 AN A e A OA 175 dataM ana Cl ODJECE psico doi aio inn ia iAn 178 Slice VIEWER ODJECE mienen aiii 179 Connor OD E iea a N eatonieenseateasaas east eiednegee 180 AA nu abel detest etetidese soecenenss 181 IPACSWebDISK OD Seba A A died 182 ADA OD ino 182 Data tOdO as 182 A sn E i esencesnceartaet 182 mpControler O Decana theta E 183 NTRKC onto ler ODE dd liada 183 VTA OD Soi aos 184 DicomkRepostory ODE a 185 NICE CONTO ai cad dro 186 Getun TNT A setae Aa aaa od aad eens ede ass 186 UE CO O y O Ne secaa temeea ae taamaeseboaabnteas nibanes yak Io um eomncaan ie iGaaetengsaeteanee tame 186 talco T A T 187 COO CONTO O N N BCE STUN A NANT OS ARS INE UCI RN 187 Viewer Controla Multi View iS a 187 yi VivoQuant Manual Table of Contents MIP Controle aria aii 190 E AAN 190 A O vO fo rant av O UTE 190 dia Te TIN ON Ale sca seas PC E 19 A esate Aaa aise eases aaah sc aacimnc E E T 19 Data MINAS Ada 193 Geri EHE fowmemeerere eer cen ee ate eee st enone mere er evereeee tere entre eee ner eee tert eee ren etn tee meri tnran tr errr tate rt Teese 193 sine the Data Manoel eir e T AT 193 Oda Di
174. e is determined by Threads the number of cores or processors in that particular machine s CPU Up scaling may be used to reduce an image size by a Up scaling factor 2 N Smaller image sizes are often more manageable Help Menu 306 VivoQuant Manual 11 12 2015 BatchCT Tool The BatchCT tool is a useful application which enables the user to select a number of X ray projection data studies and order them for reconstruction at a later stage The CT scans are saved in an appropriate batch file and can be left to reconstruct automatically The parameter settings and file names can be predefined The BatchCT tool is reached via the Data Browser by right clicking on the CT scan of interest and selecting send to BatchCT sda yatta PINES Patients Name StudyDate StudyDescription Patient ID E Series Description Series Date Modality Model name Topograrn oil BF doh Pete Ba Me WS e NanoSPECT IVS manual exa 2007 12 19 11 43 NM NanoSPECT Helical SPECT 2007 12 19 11 27 NM NanoSPECT 2007 12 19 11 23 NanoSPECT 2007 12 19 11 23 CT recon IVS CT Helical Scan Open as Reference Send to CTReco Send to BatchCT h Export data Dump header The BatchCT reconstruction panel is then displayed This panel provides options for Reconstruction Parameters Study Details and Repository The user can define which reconstruction parameters to use see CT reconstruction above and can enter det
175. e original orientation and size click the Reset Camera button Reset all ROIs To clear only the contents of all existing ROIs click the X then the Reset All button Empty ROIs will still exist under the same naming and coloring scheme To delete all ROIs completely click the X then the Delete All button The background will be the only thing left in the ROI menu Show the image histogram To view a histogram of the image or any subset of the image determined by an ROI click the Histogram button Choose the Image used to generate the histogram by selecting from the Data set drop down menu The portion of the image contributing to the histogram can be set under the ROI Controls by selecting an ROI from the drop down menu ROI Loading Saving and Quantification Tools 45 VivoQuant Manual 11 12 2015 Data Controls Histogram Plot Data set 01 CT DEMO Histogram 01 CT DEMO No bins 100 2 5e 06 Min 1000 Max 9360 56 File Controls a b Data O Close 1 5e 06 ROI Controls ROI 500 000 2 000 4 000 6 000 8 000 HU Show the quantification table To display the quantification table including all existing ROIs click the Show Table button ROI Patient Series Modality Color Voxels mm Sum i Conc Conc Unit background DEMO DEMO CT transparent 13838597 110708 7890625 9040123984 38013 81656 7867911244 HU mm background DEMO DEMO NM transparent 13838597 110708 7890625 115 696593780752 i 0 0010450533761
176. e several seconds or more Once the smoothing function is applied any subsequent operations will be based on the smoothed images Each filter will have different edge preserving and noise reduction properties choose the one that suits your application best Gradient Curvature Anisotropic Anisotropic Diffusion Diffusion The bilateral smoothing filter could take several minutes for large images in 3D especially for greater values of domain sigma Check the Force 2D option to speed up this filter No Filtering Applied Various Bilateral Smoothing Using the tool 96 6 VivoQuant Manual 11 12 2015 Inge sigma 1 ange sigma domain sigma 20 domain sigma E SU domain sigma 90 The positivity smoothing filter will also typically take longer to run than the other smoothing filters up to several minutes for larger images This filter was specially designed to redistribute the activity across neighboring voxels such that the total sum of the image is preserved but the number of voxels with negative values is reduced It is intended to be used to correct images reconstructed with FBP Bias Field Correction Intensity gradient artifacts in magnetic resonance imaging can often cause difficulties with automated segmentation and analysis tools that rely on intensity contrasts not to mention the detriment to qualtitative appearance The Bias Field Correction filter implements the N3 bias correction algorithm Tustison 201
177. e undergone testing by inviCRO and are send to our partnering expert users for evaluation Depending on the feedback of actual users release candidates are modified to fix last bugs and finally reissued as a stable release Consequently rc versions are often already stable with only minor problems to be fixed thus allow you to use new features early However rc versions are not officially supported Release candidates have a limited life time of 90 days These test versions are mainly intended for software testers They have not undergone the testing cycle required for a release candidate You can use these versions are your own risk Beta versions have a limited life time of 30 days beta versions These versions are mainly used for testing within inviCRO and alpha versions associated partners Alpha versions have a limited life time of 15 days 2 Installing A Windows Double click the VivoQuant install icon to start the installer Follow the sequence of set up steps carried out by the Installer Please accept the default settings or change the options according to your needs A detailed description of the install options can be found in Installation Details B Mac OS X Double click and unzip the VivoQuant zip archive 1 Downloading 4 VivoQuant Manual 11 12 2015 Double click the VivoQuant installer package to start the installer The only step necessary to complete the installation 1s to select the disk VQ
178. each the Configuration panel using the Ctrl Shift C shortcut For more on keyboard shortcuts in VQ please see Keyboard Shortcuts Configuration Dialog The DICOM panel in the Configuration Tool provides the most in depth DICOM information available in VQ The DICOM panel consists of three sections DICOM Settings DICOM Cache and Capture DICOM Settings 239 VS VivoQuant Manual 11 12 2015 DICOM Settings DICOM Settings DB path D DicomDB Dicom ImageFiles ne Repositories Demo iPACS Y Y e 98 A aS XA Dictionary Rev Port 23104 V load palette DICOMDIR Folder Filter dem dc3 dicom IM_ S_ Override FOR No v Location of local DICOM database Allows optimized internal access to the Mediso DICOM database See Optimized local access for details List of available repositories The bank of buttons immediately beneath the pulldown menu operate on the selected repository in this field Y Check connection to DICOM repository Local folders are verified to exist and a C ECHO is sent to DICOM servers Add a new repository x Delete selected repository A Open the DICOM Editor Shows list of additional dictionaries used by the DICOM library Please set environment variable DCMDICTPATH to set this value For more on the DICOM dictionary see DICOM Dump When this box 1s checked the palette window will be loaded in accordance not checked the palette window will be
179. ension Z When Resample data is selected a small dialog box will appear displaying the current voxel size and dimensions of the image Uncheck the box next to Isotropic Voxels to adjust the slice spacing Similarly uncheck the box next to Auto compute Dimensions to adjust the dimensions of the image Enter a new voxel size next to In plane Voxel Size and hit OK to resample the data to have voxels at the new typically larger size Resample Data 205 DICOM The DICOM Tools Submenu contains features to aid in the management of DICOM data e DICOM Dump e Anonymizer e Rename DICOM e Relabel Study DICOM Dump The DICOM Dump tool provides the information contained in the DICOM headers for DICOM files currently loaded in the Main Window The DICOM Dump is now also compatible with img and hdr files Getting There There are three ways to access the DICOM Dump The first method is via the Tools Menu in the Main Window File View Tools Advanced Modules Help s i pau View control FS O g 2 ose Hi MIP contro F6 M is Data Manager F7 X Data List E Min Max Loaded t Histogram Ctrl Shift H 106 88MB ah CB Workflow Assistant ia Pre processing Type CT Name S Ha Resample data i 1 nn Al si es x DICOM dump Ctri Shift D Dim 19 e Image amp Movie r Anonymizer Type NA W Update Check Ctrl Shift U Rename DICOM y Name S A Configuration Ctrl Shift C Relabe a wT poor 2
180. eprocessing protocol settings to be used at a later time Modifications can be made directly within the Protocol window Store Store Image data to the specified location The final section is the Information section which features information about the current state of datasets loaded in VQ Included in this information is the image dimensions and voxel size for the datasets as a whole as well as basic header metadata about each dataset specifically To execute the pre processing protocol click OK Function 204 Resample Data The Resample Data tool allows rebinning of reconstructed data into an arbitrary voxel size This tool may be useful when attempting to fuse multiple large data sets especially when dealing with high resolution modalities like MRI and CT Getting There The Resample Data option is available within the Reorientation Registration Tool via Operations gt Resample or by navigating to Tools gt Resample data File View Advanced Modules Help SY g View control FS E MIP control F6 i i Data Manager F7 CJ Min Max at Histogram Ctrl Shift H M Workflow Assistant Ll Pre processing iE Resample data DICOM gt E Image amp Movie W Update Check Ctrl Shift U Configuration Ctrl Shift C Using the tool Resample Images Isotropic Voxels In plane Voxel Size 0 20000 mm Slice Spacina Auto compute Dimensions Sagittal Dimension X Coronal Dimension Y Transverse Dim
181. erator displayed in a dock may be popped out into its own window via a drag and drop procedure with the mouse Similary any controller or operator can be re docked by dragging it back into a docking area the left right or bottom of the main window Docks 127 VivoQuant Manual DM Data List Loaded Memory 106 82MB Available Data Type CT CT Reconstruction Name DEMO DEMO Desc DEMO Dim 176x176x452 Vox 0 20x0 20 mm Type NM NM Reconstruction Name DEMO DEMO Desc DEMO Dim 176x176x452 Vox 0 20x0 20 mm 2 WM 11 12 2015 Docks may even be placed on either side of the main window allowing immediate access to many VQ tools without changing windows And if more main window space is needed for image viewing simply close or re arrange the docks to your liking File View Tools Advanced Modules Operator Help feoown os wg t eA 2 2 9 o Operator ax Ref inp1 np 2 nt Y ROI v vk 4 Ov Interpolator Linear v Quick Preview 03D 02 A3 A2 Bsn 2 Rotation X axis Y axis Z axis 0 00 0 00 0 00 Translation 0 000 mm 0 000 mm 0 000 mm L Uniform Scaling 100 100 100 DM ax Data List Loaded 2 Memory 10682MB Available Data Type CT CT Reconstruction Name DEMO DEMO Desc DEMO Dim 176x176x452 Vox 0 20x0 20 mm her Type NM NM Reconstruction Name DEMO DEMO Desc DEMO Dim 176x176x452 Vox 0 20x0 20 mm 12 NM
182. es 1 Kinetic modeling in positron emission tomography Morris et al In Emission Tomography The Fundamentals of PET and SPECT Eds wermick MN Aarsvold JN 2004 2 Comparison of methods for analysis of Icinical 11C raclopride studies Lammerstsma et al JCBFM 1996 Link 3 Effects of Statistical Noise on Graphic Analysis of PET Neuroreceptor Studies Slifstein and Laruelle JNM 2000 Link Additional Resources Multiple Time Graphical Analysis MTGA Vesa Oikonen Turku PET Center website Link Simplified Reference Tissue Model SRTM The simplified reference tissue model SRTM 1 allows for quanitification of tracer kinetics without requiring an arterial input function SRTM is a numerically robust model which assumes that the tracer can be represented by 1 tissue compartment models in both the ROIs and the reference region ROI C t Concentration in F NS S compartment Co Concentration in F NS compartment AD nondisplaceable tracer CO Concentration in plasma P compartment Transfer of ligand from arterial plasma to K mL cm min 8 P tissue Apparent transfer of ligand from tissue to arterial plasma a Transfer of ligand from arterial plasma to K mL cm min as P reference tissue Transfer of ligand from reference tissue to k gt min 2a C arterial plasma Logan Graphical Method Logan Plot 106 VS VivoQuant Manual 11 12 2015 Model Assumptions This m
183. et Using the mouse it can be manually rotated in the main window Hitting Play in the MIP Control enables automatic rotation of the MIP movie The slider bar marks the rotation progress of the MIP movie For large data sets it can sometimes take several moments for the MIP movie to be generated The progress bar in the MIP Control indicates how much of the MIP movie has been successfully calculated MIP Rotation Speed The Rotation slider in the MIP Control allows fine control of the MIP rotation speed View Controls View Angle O Play Speed Su 100 VTK Viewer Each operator will have default VT K viewer settings and will be refreshed upon opening an operator window The VTK viewer can be enabled or disabled by checking or unchecking the box in the top left corner of the VTK viewer section in the MIP Control operater window VTK Viewer stk es mw o o T The following options are availabe for adjusting the VTK viewer Function 191 VivoQuant Manual 11 12 2015 button down to toggle MIP auto rendering Reset the camera of the VTK viewer to its initial position Replace black background with VTK background Toggle Multi planar reconstruction MPR view in VTK viewer Hold down to toggle background transparency c Toggle the classic MIP in the VTK viewer 8 Toggle orientation cube in the VTK viewer T Toggle visible annotations in the VTK viewer Change performance of VTK viewer by optionally downsampling the
184. etailed description of how the MIP is generated Getting There Three different methods exist for reaching the MIP Control window The first method is to use the MIP Control thumbnail in the Main Window de The second method is to go to MIP Control under the Tools menu File View Tools Advanced Modules Help gt g View control FS E p Es MEP contro F6 i gt Data Manager F7 Min Max Histogram Ctrl Shift H Workflow Assistant Pre processing Resample data DICOM Image amp Movie Update Check Ctrl Shift U Configuration Ctrl Shift C alt M E se ES is a The third method is to use the keyboard shortcut F6 For more on keyboard shortcuts in VQ please see Keyboard Shortcuts Function The MIP Control window provides a variety of options for manipulating the MIP and the appearance of open data sets in the main window of the VQ Options include Playing a MIP Movie MIP Rotation Speed Color Maps Color Scaling Color Intensity and VTK Viewer MIP Controls 190 VivoQuant Manual 11 12 2015 MC Gx Color Controls Palette Inv Scale Intensity Ref gray 7 LJ 0 0 i 100 0 100 7 Inp1 nih_fire2 0 0 100 0 100 5 Inp2 1000 gt 100 gt View Controls View Angle O Play Speed MA 100 Y VTK Viewer stk es m o TE Reference Input 1 Input 2 Gradient Opacity Ramp ka Playing a MIP Movie The MIP movie is automatically generated upon the loading of a data s
185. ew menu and select patient Labels W VivoQuant 2 50rc3 64bit File Tools Advanced Modules Help Undo Ctrl Z T Redo Ctrl Shift Z e Show Reference F2 e Show Input1 F3 e Show Input 2 F4 eee RGB data gt 2 Slice number Cross hair Position labels Patient name F Active indicator ete Layout M4 Reset View Transform Ctrl R O Zoom gt Advanced Function Once this option is selected the patient labels are displayed on the bottom of all the images sagittal coronal and transversal and also on the MIP Patient Name 153 VS VivoQuant Manual 11 12 2015 VivoQuant File View Tools Help 600 W VivoQuant 1 23rc9 64bit SPECT_CT_Anon CT NM Reco Co Registered CTReco test NM NM Reco Co Registered CTReco test Y Y cu fy YD a8 a A VC MC DM MM Sice View s Navigation i QA Display Palette 9 SPECT_CT_Anon SPECT_CT_Anon f Function 154 Active Indicator The Active Indicator option places icons in the viewports that indicate which datasets are active in the Display Getting There To turn on the Active Indicator go to the View menu and select the Active Indicator option Function File View Tools Advanced Modules Help e Undo Ctrl Z g Redo Ctrl Shift Z lt SOFA OD Pre E MA de amp e Show Reference F2 e e Show Input 1 F3 Show Input 2 F4 Slice number Cross hair Position labels Patient name Active in
186. f Set type of image Image types can be 1 Maximum intensity projection MIP 2 Sagittal slice 3 Coronal slice 4 Transversal slice 5 All views in one image 6 All images separately Colorbar Set colorbar and label options for the options image Options include 1 None no colorbars or labels 2 No labels colorbars with no labels 3 Simple labels colorbars with one set of evenly distributed gradations placed across all Function 122 VivoQuant Manual 11 12 2015 color bars 4 Smart labels colorbars with separate sets of gradations for each color bar incremented with respect to the units of each color bar Set whether the image file will be stored as a local image file or as a DICOM via Secondary Capture Set a scalar magnification factor will be applied to the resulting image Note this does not affect the magnification of the viewports only the magnification of the image file being generated Magnification Function 123 Save Movie This function enables the images to be saved as movie files The slices can be saved individually sagittal coronal or transversal or all in one image A Maximum intensity Projection MIP picture can also be saved using this feature Getting There Four different methods exist for saving movies The first method is to go to Save Movie under the File menu File View Tools Advanced Modules Help Data Browser Ctrl D l 0000 03 O q Open Lo
187. f Inp 1 Inp 2 1p Y ROI v vk a 1 Ov Interpolator Linear vw Quick Preview 93D 02D Az A2 M 20 _ Basic Settings Transform Translation Rigid Affine Fast Fine Expert Settings Transform Versor 3D y Optimizer Regular Step Gradie v Interpolation Linear Metric Mattes Mutual Inform Sampling 20 bins 16 samp Step length 0 100 min 5 000 5 max Iterations 100 Relax 0 75 Crop Range Register Inp1 to Ref All to Ref To begin the registration select either Inp1 to Ref or All to Ref Inpl to Ref will register Input 1 to the Reference and require the user to click the Accept button to apply the registration All to Ref will register each image to the Reference individually and automatically apply the registration A window will appear that shows information about the progress of the optimization including a live plot of the Metric Value vs Iteration e M 88 0000 08 O oop Dow Hi 0 Slice View Reorientation Registration y dl Quick Scripts gt 41 DO Y Operator Xx Display Palette f O inpa np 2 nt MIRO oy Hisz vk e Ov Interpolator Linear gt Quick Preview 030 920 M30 A2 B30 2 C Basic Settings Y Expert Settings Transform Versor 3D Y Optimizer Regular Step Gradie Interpolation Linear y Metric Mattes Mutual Inform y Sampling 20 bins 16 gt samp Step length 0 100 min 5 000 gt max Iterations 200 Relax 0 7
188. f heads typically 2 or Ctrl B 4 are set in this panel pictured below By default the collimator depth phantom is not used in the MMP Calibration 323 VivoQuant Manual 11 12 2015 analysis However 1t may be enabled with this checkbox By default the collimator depth phantom is not used in the MMP Calibration analysis However 1t may be enabled with this checkbox In the presence of only one single pinhole aperture Merge 4 point 4 point data are collected one head at a time This tool merges those data into a single file On some Nucline versions a slightly modified version of Convert Calib the calibration data is needed This tool converts the calibration file accordingly Basic Configur 2 fx Basic System Configuration System ID so pe No Heads 4 heads v Templates 324 Near Field Uniformity The Near Field Flood Uniformity NFF QC is a quality control procedure for monitoring the stability of the PMT gains for each head in the NanoSPECT CT To collect NFF QC data please run the QC SPECT Near Field Flood NFF protocol in the Configuration QC Protocols panel of the Nucline software Getting There The Near Field Uniformity analysis panel may be reached via Tools Calibration File View Tools Advanced Modules Help Wess Se gt Multi Pinhole SPECT lr Cr CT gt Spec Act Calculator A NFF Uniformity QC Bed removal SUV Calculator QuantiCalc Display
189. f target sites non specific binding An ideal reference region is a devoid of the target site receptor and b has the same concentration of tracer free in tissue and nonspecifically bound as the ROI Logan Non Invasive Graphical Method Logan reference plot 110 VS VivoQuant Manual 11 12 2015 p Cyitjdt jy Critidt mana After some time t the slope of the plot of approaches linearity Note Violation of any of these assumptions may produce biased parameter estimates While the model will still run in VivoQuant the estimated parameters may not accurately reflect the true tracer kinetics Required Inputs This model requires the following inputs e Reference tissue curve e ROI s or voxels e t in scan time Selection of t The Logan reference plot as implemented in VivoQuant requires that the user inputs the t which defines the time at which the plotted data become linear In VivoQuant the default t value is 0 This is likely not be the appropriate value for your experiment t values are tracer dependent For characterized tracers we suggest reviewing the literature to see which t values have been used in Logan reference method The simplest way to select a reasonable t value for your data is to run the model once with the default t value review the Logan reference plots to find the point at which they become linear t then re run the model with the appropriate t in scan time value Output
190. field The DICOM dump tool uses the DICOM dictionary listed in Configuration DICOM to read the DICOM header Each row in the DICOM dump represents a DICOM header data entry The list below uses a dummy DICOM entry to illustrate the meaning of each field in the DICOM Dump Consider the following dummy entry 0000 FFFF AZ 12118 4 2 VQ DICOM Example e 0000 FFFF is a hexadecimal DICOM address where 0000 represents the group number for that data entry Even group numbers correspond to DICOM defined groups while odd numbers are reserved for private groups The FFFF half of the address specifies the element number for that particular entry in the group indicated by the first half of the address e A two character item of the form AZ identifies the Value Representation VR for that data entry Several VR types are specified in the DICOM standard For example a Value Representation of US indicates that the data entry will be in the form Unsigned Short e The actual data values for the data entry 12 18 are displayed next in the Value Field VE The values are shown inside square brackets e After the hash mark the Value Length VL for the data entry is displayed The VL depends on the VR type and the number of values in the data entry e Some data entries contain multiple subsets as indicated by the Value Multiplicity VM Subsets are indicated by the backslash character in the data value field In the example shown above there are
191. fit Select the voxel for which you d like to see the model fit by clicking on it with the image viewer e BPup R k gt and mean squared error MSE of fit are shown when the cursor is hovered over the model fit plot e Parameter maps for BPyp R k and MSE References 1 Noise reduction in the simplified reference tissue model for neuroreceptor functional imaging Wu and Carson JCBFM 2002 Link 2 Kinetic modelling using basis functions derived from two tissue compartmental models with a plasma input function general principle and application to 18F fluorodeoxyglucose positron emission tomography Hong et al Neurolmage 2010 Link 3 Tracer kinetic modeling of 11 C AFM a new PET imaging agent for the serotonin transporter Naganawa et al JCBFM 2013 Link 4 Parametric Imaging and Test Retest Variability of 11C PHNO Binding to D2 D3 Dopamine Receptors in Humans on the High Resolution Research Tomograph PET Scanner Gallezot et al JNM 2014 Link 5 Kinetic modeling of the serotonin 5 HT1B receptor radioligand 11C P943 in humans Gallezot et al JCBFM 2010 Link Simplified Reference Tissue Model 2 SRTM2 109 VS VivoQuant Manual 11 12 2015 6 Assessment of striatal dopamine D2 D3 receptor availability with PET and 18F desmethoxyfallypride comparison of imaging protocols suited for clinical routine Amtage et al JNM 2012 Link Additional Resources reference region in
192. for a time limited evaluation license with all functions Would you like to proceed to the registration process now e Make sure the company code is DEMO Use the email address you wish to have the license key file sent to B Mac OS X 5 VivoQuant Manual 11 12 2015 yi Configuration eats eee Display Data DICOM Network vivoSaipt Registration License Key lt 00000000 gt Customer Code DEMO Use the code provided by your institution or DEMO for an evaluation license Department imaging Contact address user organization com To file a registration request please fill out above form and hit Register i Ifyou already have a license key please install it with Install key Install key HW Keys Register A A ahha ai asi ss ai Aaa i A e After clicking Register your Internet Browser will load and navigate to the license registration confirmation page VE Key Generator Customer Demo Licenses Imaging Your Name user organization com Department imaging HW Key 64 d4 da 5e dc 17 40 25 Click Submit and a trial license will be sent to you shortly b Pre approved Licenses e An account manager can issue a license to an end user Upon issuing a license an email notification will be sent to your email with instructions for downloading the VivoQuant software and installing ll Trail Accounts VivoQuant Manual 11 12
193. function general principle and application to 18F fluorodeoxyglucose positron emission tomography Hong et al Neurolmage 2010 Link Additional Resources Compartmental Models Vesa Oikonen Turku PET Center website Link One Tissue Compartment Model 1TCM The 1TCM is a two compartment model that includes one compartment representing tracer within the tissue free and nonspecifically bound tracer which together are referred to as nondisplaceable tracer and one compartment representing tracer within the arterial plasma 1 arameter Description Concentration in F NS compartment np nondisplaceable tracer Cut Concentration in plasma P compartment Transfer of ligand from arterial plasma to K mL cm3 min sue 8 P Transfer of ligand from tissue to arterial Total volume of distribution For tracers for which a compartmental model is appropriate estimation of the rate constants provides valuable information about tracer uptake 1 The 1TCM is generally easier and less computationally intensive to solve than the 2TCM because it is a simpler model and has fewer parameters Additionally 1TCM model parameters can generally be estimated with better identifiability than 2TCM model parameters Two Tissue Compartment Model 2TCM 102 VS VivoQuant Manual 11 12 2015 In some cases the exchange of tracer between the nondisplaceable and bound tissue is sufficiently fast that the two cannot be distinguished kine
194. g amp date const QString amp event 0 getWidget name Access widget with given name of current operator s dialog currentOp Allows access to current operator currentView Allows access to current view mode stripCredentials const QString Surl_string stringMatch const QString ret const QString amp text stringMatchList const QString amp ret const QString amp text setConfig const QString amp entry const QVariant amp val getConfig const QString amp entry const QString amp defaultValue getHome Returns VQ home directory getCache Returns cache directory deleteFile const QString amp filepath Delets file at filepath rmDir const QString amp dirpath Deletes directory at dirpath Calls VQ menu use as separator triggerAction name OA VO triggerAction Tools CT Bed removal preProcess protocol Performs preprocessing given a specified protocol storeAsRaw fileName idx Store data at index idx as a raw mhd file locally with filename fileName storeAsDICOM const QString amp fileName int i int format 1 saveDataVialTK4D const QString amp fileName Store data as DICOM file locally with filename fileName VQ Object 173 10 writeFile fileName text appendFile appendFile const QString amp fileName const QString amp text brukerImporter imgInfImporter gellmporter rawImporter img HdrImporter centerCursor webDisk rep hexColorToList hex saveScreenshot fileName unl
195. g saving and quantifying both 2 and 3 dimensional regions Provides a mean to quantify density Quantification and activity parameters in CT and NM scans respectively Enables realignment of image data via translation rotation or flipping In registration mode a variety of registration algorithms are available to automatically register data from a wide variety of modalities Reorientation Registration Allows sagittal coronal and transverse slices of datasets from a Time Series time series to be played sequentially in a loop or easily scrolled through manually l l Allows you to measure the distance Distance Annotation SE E between two points in any image In checkerboard mode the reference and input data set s are arrayed in a pattern of alternating squares resembling a checkerboard removing any unwanted areas Allows voxel wise arimethic Operations on two input images or scalar operations on any number of input images filters with configurable parameters Provides an integrated solution for representing the loaded data set with one of several mathematical models to allow for predictions and analysis Modeling Display The Display field comprises the principal component of the Main Window The first three images loaded in the Data Manager are visible in the Display field Many tools and image processing steps are visible in the display of the data sets in the Display field Operators 118 Vivo
196. g Started 330 VivoQuant Manual 11 12 2015 AUC Calculation Export Quantification Click Load Spreadsheet in the top left corner of the dialog box and call the spreadsheet you created in the last section In the Dosimetry Isotope drop down menu select the isotope that was used in the experiment If the isotope used is not listed open the file 1sotopes txt located in the VivoQuant install directory default is C Program Files inviCRO VivoQuant and add the isotope information It is important to ensure you select the correct isotope because the Dosimetry Calc tool uses a curve fit algorithm and extrapolates using only isotope specific radioactive decay information Click OK te Compute and Save Area Under Curve for Each ROI Save Soreadsheet Update Plot Patient ID Group Time Point Unit Injecti 800 The Plot should now appear next to the table in the window Heart Liver LeftKidney Right Kidney Brain Remainder Body 35 Decayed Percent ID un o uw o wi oO o 0 10 20 30 40 50 60 70 Time h Using the AUC Calculation 331 VS VivoQuant Manual 11 12 2015 Click OK button at the bottom of the window and save as another CSV file This data is now ready to be used in the OLINDA software Using the AUC Calculation 332 File Management The Data Browser contains a variety of options for loading saving publishing and printing data Options include e Data Manager e Ope
197. h each MIP projection image is displayed in a saved movie Sets the delay time between MIP frames in a saved movie Sets the number of projection angles computed to construct the MIP With sync mode enabled only completed MIP frames will be displayed With sync mode disabled the MIP will freely rotate at all times but will display a message in place of the MIP for uncompleted frames The default Color Palettes for the Reference and Input data sets can be changed using the drop down menus Maximum Intensity Projection 14 Data The Data panel contains options for data handling including data loading and quantification Display Data DICOM Network vivoScript Registration MinVoxSize Data Loading Disable MIP viewer Grow reference to input volume no V Ask Disable MIP Max voxsize ratio for vol 20 00 0 00mm Anchor input data at center Quantification Options Unit of Activity uCi w CSV Separator Comma Data Manager Y confirm moving T Show seconds in Browser V Apply default shift Data Loading Cancel Use the amp apos Data Loading amp apos panel to set loading options Max voxsize ratio for vol Data Check the box to disable the MIP viewer upon loading For large datasets this can improve the loading speed Check the box to enable VivoQuant to ask for your permission to initialize the MIP viewer upon loading For large d
198. he Enable Logfile option under the Help Menu File View Tools Advanced Modules Help y 22 DO py Request Hel e 98M GO ool err 00 Log out Ctrl Shift X DM Wa Registration Data List B Enable Logfile Loaded 2 Memory 106 8 Debug View Available Data Hints Type CT CT Reconstruction 2 Manual Fl Name SegmentationExample 1007 W About 1 CT Date 2010 05 19 18 34 03 series 2010 05 19 Function After selecting Enable Logfile a dialog box will appear prompting you to restart VQ and providing the location of a new vivoquant log file la y Thanks for enabling the logfile C Users KGOETT 1 AppData Local Temp VivoQuant log Please restart VivoQuant now to enable logging Upon the next restart of the VQ this logfile will record all of the operations performed This record is useful when attempting to troubleshoot or debug problems that arise in the software Debug 352 Manual A VivoQuant manual has been created to guide the user through all the post processing functions in a clear and step by step manner Getting There To open the manual go to Manual under the Help menu File View Tools Advanced Modules Help ma SE EE SOOM 0 Bano mero a 3 Logout Ctrl Shift X i a a Registration B Enable Logfile Debug View Hints Manual wW About lie Ree te EE The keyboard shortcut of Fl can also be used to open the manual Function Once the Manual is open the user can brow
199. he Quick Scripts menu Evaluates the VivoScript file selected in the Quick Scripts menu Aborts the VivoScript in execution Activates the Peek tool used to reveal names of operator widgets for use in VivoScripts See the VivoScript page for more View Modes Four viewing modes are available via a pull down menu located next to the thumbnail icons File View Tools Advanced Modules Help e SY SY M ea on 0000 os o AOO Dove bi ou JOTA y Quick Scripts 4 D Display Tile View Multi View MPR View The Slice View default simultaneously displays images of single slices for the MIP sagittal coronal and transversal views of the loaded data sets The Tile View displays an array of slices for either sagittal coronal or transversal view of the loaded data sets The Multi View displays sagittal coronal or transversal slices of each data set adjacent to one another simultaneously The Multi Planar Reconstruction View simultaneously displays sagittal coronal and transversal slices in a single window Operators The operators are available in a pull down menu located next to the thumbnail icons Navigation Quantification Reorientation Registration Time Series Distance Annotation Thumbnails 117 VivoQuant Manual 11 12 2015 Enables manually scrolling through the image slices and rotation of the Maximum intensity Projection MIP Provides advanced tools for drawing visualizin
200. he isotope of interest and its Isotope Hours associated half life Several pre defined options are available The specific activity of the isotope being used as measured by a specific MBq pmol activity calibration Specific activity kBq pmol and describes the number of excited measurement atoms out of the total atoms present time in a given sample 1 e the amount of the activity that has not yet decayed to a ground state The calculated amount or number of Amount pmol nmol or excited molecules in the sample The calculated molarity or concentration of excited molecules in a sample of activity Function 274 SUV Calculator The SUV Calculator may be used to calculate a specific uptake value SUV given the appropriate entries of injected dose subject weight and activity concentration Getting There The SUV Calculator is available in the Tools Menu File View Tools Advanced Modules Help S py fe SPECT d NanoSPECT gt pe of CT y Spec Act Calculator Bed removal SUV Calculator Whole Body Atlas Atlas NM CT analysis fMRI Tool instali Atias Split RO to DICOM Average body calculation Specify ROI center Specify ROI center 2 Upload tumor ROI TumorPK Model Dosimetry Calc Function The SUV Calculator requires several values to make its calculations An activity and volume are used to calculate an activity concentration The subject weight and injected dose are used in conjunction wi
201. heStat setActive QList amp lt int amp gt a setSync bool s isSync parameterChanged invalidateImageCache mipControler Object Function Description setNumber int val Sets number of frames in MIP default 60 sliderPos 1nt 1 Sets View Angle slider to value i cet Alpha Returns the intensity of the image at Input 1 Better to use getAlpha setAlpha nVQ controler object Returns the intensity of the image at Reference Better to use getDim getDim setDim inVO controler object Returns the intensity of the image at Input 2 Better to use getBalance getBalance l i setBalance inVQ controler object getIntensity int 1 Returns Intensity of image at ndex i a Sets color palette of index i to name name changeParam rado Md Plays MIP movie saveMovie savelmage Use savelmage in VO mainWin object speedChanged int val Changes speed of MIP movie setEnabled bool VIKController Object Function Description getMIPEnabled getMPREnabled getAnnotationEnabled setAnnotationEnabled bool toEnable getOrientEnabled setOrientEnabled bool toEnable getRenderSpeed setInteractiveDelay int msec setUseRenderDelay bool toEnable getUseRenderDelay orce VolumeMapperMode int mode mipViewer Object 183 VS VivoQuant Manual setStillUpdateRate double factor getAutoUpdate tSmoothingIterations int iter setFeatureAngle double angle setPassBand double passBand disableAxes bool b true
202. hoose amp apos ask amp apos to allow a window to appear upon loading in an input data set that is larger than the image in the reference position Specify the maximum pixel ratio largest pixel dimension smallest pixel dimension by which a 239 VivoQuant Manual 11 12 2015 data set is interpolated as a volume image file Specify the minumum allowed voxel width Data will be resampled upon loading if their voxel width is less than the specified minimum The voxel width will be doubled until it exceeds the minimum Specify where to anchor the input data Data can be anchored at the following options center head or foot mb X A _O E Longest Dimension LD In the above image LD represents the out of plane resolution and the X and Y represent the in plane resolution If the pixel ratio of the loaded image exceeds the given threshold 1 e MaxVoxSizeRatio lt LD X the data set will be loaded as a planar 2D by n file Below is an example MR image loaded as a planar 2D by n file Data Loading 236 VivoQuant Manual 11 12 2015 If the pixel ratio of the loaded image is less than the given threshold 1 e MaxVoxSizeRatio gt LD X the data set will be loaded as an interpolated volume image with isotropic voxels Below is an example MR image loaded as an interpolated volume file Other modalities besides MR can be loaded into VQ as planar or interpolated volume f
203. hread 10 bpv Exact cone beam 2 threads 18 bpv Voxels 9 720 000 Fast cone beam 55 MB Exact cone beam 1 thread 93 MB Exact cone beam 2 threads 167 MB Mouse 36x36x37 mm 100um voxels Voxels 47 952 000 Mouse 36x36x60 mm 200um voxels Study Details Progress and Controls 302 Mouse 36x36x20 mm 50um voxels Rat 62x62x90 mm 400um voxels Rat 62x62x60 mm 200um voxels Rat 62x62x20 mm 100um voxels VivoQuant Manual 11 12 2015 Fast cone beam 274 MB Exact cone beam 1 thread 457 MB Exact cone beam 2 threads 823 MB Voxels 207 360 000 Fast cone beam 1187 MB Exact cone beam 1 thread 1977 MB Exact cone beam 2 threads 3560 MB Voxels 5 405 625 Fast cone beam 31 MB Exact cone beam 1 thread 52 MB Exact cone beam 2 threads 92 MB Voxels 28 830 000 Fast cone beam 164 MB Exact cone beam 1 thread 275 MB Exact cone beam 2 threads 495 MB Voxels 76 880 000 Fast cone beam 440 MB Exact cone beam 1 thread 733 MB Exact cone beam 2 threads 1320 MB The Progress panel gives feedback on the progress of a reconstruction Before beginning the reconstruction a plot of the selected filter including cutoff frequency is displayed Once the reconstruction has begun projection data are displayed as they are used by the reconstruction algorithm A progress bar indicates the estimated time remaining in the reconstruction The Controls panel contains two checkboxes and the Start button The Start butt
204. hread 1977 MB Exact cone beam 2 threads 3560 MB Voxels 5 405 625 Fast cone beam 31 MB Exact cone beam 1 thread 52 MB Exact cone beam 2 threads 92 MB Voxels 28 830 000 Fast cone beam 164 MB Exact cone beam 1 thread 275 MB Exact cone beam 2 threads 495 MB Voxels 76 880 000 Fast cone beam 440 MB Exact cone beam 1 thread 733 MB Exact cone beam 2 threads 1320 MB The Progress panel gives feedback on the progress of a reconstruction Before beginning the reconstruction a plot of the selected filter including cutoff frequency is displayed Once the reconstruction has begun projection data are displayed as they are used by the reconstruction algorithm A progress bar indicates the estimated time remaining in the reconstruction The Controls panel contains two checkboxes and the Start button The Start button begins the reconstruction As the reconstruction is running it can also be used to stop the reconstruction The first checkbox autostart will automatically begin a reconstruction when the CT panel is called from the Data Browser The second checkbox autosave will automatically save a reconstruction once completed Preview and Color Panel Preview and Color Panel 28 VivoQuant Manual 11 12 2015 Preview Color Panel 36 6 The Preview panel displays the CT reconstruction as it is being calculated The Color Panel provides several color map options File Menu CT Reconstruction r1 140
205. hresholds For methods that require thresholds use the number fields beneath the Image Selection drop down Click the Min and Max buttons to the left of each threshold field to fill in the minimum and maximum values respectively from the selected image The unit is assumed to match that specified in the header Available Thresholding Methods The thresholding methods available are in the Segmentation Algorithm drop down menu After selecting a seed and thresholds as necessary click Apply to perform the segmentation It may be necessary to wait approximately a minute for the thresholding to complete Seed Thresholds Global Thresholding No Yes Connected Thresholding Yes Yes Nei AT Thresholding e ROI Max Size The ROI Max Size filter can be used to fill holes in existing ROIs Any connected components in the Input ROI that are comprised of fewer voxels than the Max size specified will be mapped to the output ROI Operator a x x e S amp Classify input voxels to output ROI ROI Max Size v Re classify all voxel clusters of input ROI with less than max size voxels Input Ml background Max size voxels 1000 Apply ROIs amp amp mM HLung v 3D Segmentation Tools 52 VivoQuant Manual 11 12 2015 Low pass Smoothing Use the Low pass Smoothing filter to remove jagged surfaces from manually created ROIs The amount of smoothing can be controlled with the Low pass rad
206. ication Tools 44 VivoQuant Manual 11 12 2015 Click the 3D ROI options button and select either Merge from iPACS or Merge from disk depending on where the additional ROIs are stored The additional ROIs associated with that particular image will be appended to the currently open ROI set in the 3D ROI viewer Note Previously saved ROIs will not be overwritten If there is any overlap of existing and merged ROIs a new ROI will be created and named a combination of the two ROIs listed names For example if a portion of a Heart and Liver ROI overlap after a merge the new combined ROI created would be named Heart Liver and consist of only the specific volume of Heart and Liver that overlap Operator ax Pr Tole i A vk e D X cal e wm l le ROI H M background E E LeftKidney Bl Heart E Liver sn Ml RightKidney Brain Move pixels to ROI MB LeftKidney RightKidney background ROIs xi X e E LeftKidney RightKidney v To associate the combined ROI with the proper ROI right click the combined ROI and select delete ROI The option to move pixels to either background or other ROIs will be presented for your selection Selecting background will delete the ROI all together Render ROIs in the MIP view To trigger a new rendering of the current viewed ROIs in the MIP view click the VTK button Reset the camera view To reset the MIP view to th
207. ients button On the WS you should already see listed there the HiSPECT and InterviewXP entries To add the VivoQuant add the line at the bottom of the following list Application Entity Title HiSPECT LOCALHOST 3104 HiSPECT_BATCH LOCALHOST 3105 INTERVIEWXP LOCALHOST 11112 NVIVOSCOPE HOSTNAME 23104 In place of HOSTNAME in the VQ entry use LOCALHOST on the WS Computer and NANOSPECTxxWS or the workstation IP address on the ACQ computer Computer Calling AET Hostname Port INVIVOSCOPE NANOSPECTSWS 2310 I NVIVOSCOPE LOCALHOST 2310 IP Address or 2nd WS Computer Name Adding VQ as a DICOM Client 247 VivoQuant Manual 11 12 2015 What is of importance in this configuration is not the specific name INVIVOSCOPE but the fact that the same name INVIVOSCOPE was used in the DICOM Client Configuration and at the Calling AET in the VQ Repository Configuration To illustrate this point note the client in the image above with the name VQ_anyname Also separate names must be used for each configuration In other words to configure the VQ on a 2nd workstation would require changing INVIVOSCOPE to something different like VQ WS2 For example let s say a 2nd workstation was being set up for the NS13 In the Client Panel of the DICOM Server Manager a client would be added as in Example 3 in the above table In the VQ on the 2nd workstation a new repository would be created with the following settings General Inform
208. ight either the CT or NM data and right click A box with a number of functions is then displayed The options vary depending on the type of projection data selected Within Database or iPACS Server Right click on the Helical CT or Helical SPECT scan of interest Helical SPECT Ve HE Open data E Export to p Open in Dump header There are various options depending on the data type available with this tool Option Description Opens the selected data set in VQ and loads it as the Open data reference see Open Reference Export Allows data to be copied to a local folder or to to another data browser or iPACS repository Study Browser 340 VivoQuant Manual 11 12 2015 Allows the data to be opened in an external Application Sends the file to the DICOM dump tool which displays the information contained in the DICOM Within a Local Repository When working in a local repository 1 e a local folder as opposed to data from a database or PACS server the right click button may also be used to delete data Patients Name y Series Description y CT recon Image Type Open data B Export to gt Open in Dump header Within Database or iPACS Server 341 Open Data The first data set loaded into VQ is termed the Reference and is so named because it is often a CT image used for anatomical reference When loading multiple data sets into VQ e from the Data browser VQ recogn
209. ile Debug View Hints Manual Ma About Function The About feature provides information about VQ It informs the user what version of VQ is installed and it provides the contact information for the creator of VQ It also displays who the VQ program is registered to It also supplies the web links to the DICOM toolkit and the Qwt project used to help make this program About 355 VQ Reporter The VQ Reporter Tool is available to users and was designed to assist the user in submitting service and applications reports for review by the inviCRO service team The tool offers a variety of pre defined report sequences as well as an option for a manual report Reports are bundled into zip files and automatically submitted to the appropriate personnel NOTE Only information visible in the VQ Reporter window is uploaded when a report is submitted No personal confidential or otherwise hidden information is collected How to use the VQ Reporter Tool The VivoQuant may be downloaded at VivoQuant com Downloads stable release VivoQuant 2 1 2 ipatchi Linux MacOS Win32 VivoQuant 2 0 2 00stable Linux MacOS VivoQuant 1 23 1 23patch3 Linux MacOS W release candidate 2 5rc4 Linux MacOS Win3 2 5rc3 Linux MacOS Win3 2 5rc2 MacOS Win32 Win64 Win32 Win64 Win64 in32 Win64 2 Win64 2 Win64 To install the software double click on the installer icon on the
210. iles based on the Max voxsize ratio for volume setting specified in the configuration window Note As described on the Open DICOM Data help page e If the amp apos Force Planar amp apos check box is checked in the Data Browser then the image will load in planar mode regardless of the value set for Max VoxSizeRatio e If the amp apos Force Planar amp apos check box is unchecked in the Data Browser then the image will load in the appropriate mode according to the value set for Max VoxSizeRatio Quantification Options Use the amp apos Quantification Options amp apos panel to set options used by the Quantification Operator and the 3D ROI Operator Select the unit to be used for quantifying SPECT data Options include MBq kBq mCi and uCi Note Concentration units e g nCi cc will not be converted to the unit of activity specified The Tumor Segmentation and NM CT Brain analysis plugin modules do support converting from concentration units to units of uCi Choose the CSV file delimiter of their choice applied Separator when saving Quantification data Quantification Options 237 VS VivoQuant Manual 11 12 2015 Data Manager In the Data Manager panel there is a checkbox to enable or disable a confirmation message when moving data confirm Check to enable a confirmation message when moving rearranging data in the Data Manager Check to display the seconds in the study date column in the DICOM browser VQ h
211. iltering Tool can be accessed via the tool pull down menu on the VQ front panel File View Tools Advanced Modules Help GQ GO M oa 0000 05 OU Y Op ec 22 Mu Slice View 7 beaten E Quick Scripts gt 41 D Y Display Quantification Reorientation Registration Time Series Distance Annotation Using the tool Upon selection of the Filtering Tool the Filtering Operator window is displayed Operator Gx Data v Reference vV Input 1 v Input 2 v Input _ Append data _ Force 2D Smoothing None gt Gauss AAA Curvature Flow OK Cancel GradientAnisotropic Diff Curvature Anisotropic Diff Positivity Smoothing Zero Crossing Edge Detection Bilateral Smoothing Using this tool any loaded data can be selected for smoothing by checking the appropriate Data boxes Reference Input and Input 2 select the first three datasets loaded and Input selects the remaining datasets beyond those see Data Manager for more information on manipulating more than three data sets simultaneously Select the desired smoothing algorithm from the available options in the Smoothing drop down menu Use the parameter fields to set appropriate values The effect of the chosen smoothing filter will be previewed in 2D in the slice views to remove the 2D preview go back to None in the drop down menu of smoothing filters Currently available filters include e Gaussian Smoothing Filtering Tool 94 VivoQuant Manual 11
212. ing all desired images generate the dynamic movie using the Image Magick Join Frames to Movie option File View fools Advanced Modules Help gt g View control F5 BA mu m f HH mitra FE e rs Dt fae 10 i Display Data Manager F7 Min Max Histogram Ctrl Shift H Workflow Assistant Pre processing Resample data DICOM gt Eo apab HOR Split movie into frames Image amp Movie gt Update Check Ctrl Shift U Join frames to movie es Change movie delay Configuration Ctrl Shift C g A a Image to Capture 15 Select the images that you wish to be included in the movie In this example we use the all in one images to generate the movie How to make a dynamic movie 228 VivoQuant Manual ImageMagick Select Frames Look in O MovieFrames X Frame4 all png My Recent Documents Desktop Ly My Documents My Computer z My Network Places Framel all png Framel cor pna Framel mip pna Framel sag png Framel tra png Frame2 cor png Frame2 mip png Frame2 sag pna Frame2 tra pna Frame3 cor png Frame3 mip png Frame3 sag pnq Frame3 tra png File name Frame4 cor png Frame4 mip png Frame4 sag png Frame4 tra png 9 FrameS cor png FrameS mip png Frame5 sag png Frame5 tra pna Frame6 cor png Frame6 mip png Frame6 sag pna Frame6 tra png m Frame cor png Frame mip png F
213. ing tab as seen in image above The mean of the functional data set will be used for the QC images Anatomical Registration Check the Enabled box to co register the input data to an anatomical reference data set Motion Correction Smoothing WM Brain Mask Atlas Registration GLM V Enabled Anatomica Registration Select a Reference Anatomical re Testing fMRITool 100funcAnat mhd al Use Full Use BBox FT Manual VQ Transform Fle fal d Sice by siice Mean Functional Time Point b 2 Before After The user can choose from the following references e Anatomical Register to a reference anatomical data set Click on the ellipsis button to open a window from which the locally stored anatomical file can be located The user can either provide a manual transformation or have the tool perform an automatic registration For the automated registration the user can choose to use the entire field of view Use Full or only the brain Use BBox The Use BBox setting will use a bounding box around the brain to limit what 1s used for registration If the manual box is checked the user needs to provide a locally stored XML transformation for the registration of the functional to the reference anatomical e Mean Functional Register to the mean of the functional time series e Time Point Register to a single time point Either type a specific time point in the box or use the up and dow
214. ints Drag Left Remove Mid Open curve Shift Mid Curve Drag Shift Left Add point Double Click Close Right Bully Add start point inside curve Remove outside curve er Spline Tool Thickness 1 e Y Next empty slice MK ROIs A xl lll Ml Brain 2D Drawing Tools 49 VS VivoQuant Manual 11 12 2015 Choose the desired tool from the drop down menu to begin drawing Use the red X button to delete a contour this will not delete the ROI Use the green checkmark button to add the voxels within a drawn contour to the currently selected ROI Splimetool OOO A Ballad S Fs sat Spine Fath o RO Laietana __ Y Apply SplinePahtoRQl o x l ClearSplinePath O oo Spline tool Use the spline tool to define points between which smooth curves will be filled in The base points can be moved by using the left mouse button to drag them Additionally points can be deleted middle click point or added double click position on curve Once a shape has been closed right mouse button 1t can be re opened by using Shift middle click on a point Bully tool Use the bully tool to nudge the drawn boundary inward or outward with a circle shaped cursor The cursor size can be changed using the paintbrush size selector in the Painting Tools panel This mode provides an efficient way to fine tune an ROI made in Spline or Freehand mode You may select which image data you want to use as the input Ref is the first image l
215. iously saved sessions save new open sessions and export sessions to save locally and or on any iPACS available When saving a session users can specify the desired repository and session name for easy sorting later AS O Save Session Sessions A Name Repository Boca T 2013 01 25T16 29 12 sata ame 2 MIP 2012 12 14T16 29 13 3 100166 2012 12 12T20 44 12 Store Public Link i 4 100366 2012 12 10T17 32 42 5 100163 2012 12 10T14 24 17 6 070366 2012 12 10T11 32 05 7 070264 2012 12 10T09 18 53 a v AAA _ In addition to saving sessions locally or to a desired repository users may also associate that saved session with a specific project from within their desired iPACS repository This allows for more efficient access and organization of various sessions across multiple projects 606 W Save Session Sessions Repository Training iPACS a Project exampleproject therapeutic_track_1 201 Filter New Name Save session to iPACS repository Store Public Link Cancel OK If exporting the session specify a location on the local where the compressed zipacs folder will be saved Session Manager 349 VivoQuant Manual 11 12 2015 LB Export to G do Test gt gt 9 Organize New folder 2 g Ar Favorites te Name Date modified Type Size Recent Places de Customer ABYZ 3 12 20121 50PM_ File folder de Downloads me Desktop pa
216. ir associated spin boxes The Layout and Zoom options are also intended for manipulating the appearance of the Slice View Other Slice View Tools 133 Tile View The Tile View displays an array of slices for either sagittal coronal or transversal view of the loaded data sets The number of slices displayed depends on the size of the VivoQuant window Getting There The Tile View is available via a pull down menu on the Main Window File View Tools Advanced Modules Help Goo c g 23 0000 08 L gt A O ooo NC HE au mu slice view v Navigation y e Slice View y Quick Scripts 4 D Display a Multi View UN MPR View R update disabled Scrolling through slices in the Tile View may be achieved using the scroll wheel on a mouse or by using the arrows and PageUp PageDn keys on your keyboard The keys control the rate at which you scroll through the Tile View 134 VivoQuant Manual 11 12 2015 tiles To learn how these keys control scrolling in the Slice View click here PS gt a y ifs W jf fa VW HR RAS F cr gt A EXA A A J A Q 4 Vo I Net AS J gt 4 Ey Gay Ga i PP Ce a an gt D FSA GA GS Tab T Y i y f i 1 V 4S A wet No J Ye i gt wot on ul I oe JA J No a Soe J a i ial aaa CEE _ v IF Jfsha gt T 4 4 4 e ANS 5 d Jo ds ds do A gt Sn A gt o y gt gt rt 5 gt S a EKE C
217. is field with the minimum value in the object Sets the maximum value for which data will be displayed The Set button automatically loads this field with the maximum value in the object File Controls Saves the existing plot into a PDF file Writes the data into a text file The format is in two columns with the first column representing bin center points x axis values and the second column representing the number of voxels in each bin y axis values Refreshes the histogram plot Use this button after changing the No bins Min or Max values o Exits the Histogram Tool Data Controls 201 Preprocessing Tool The Preprocessing Tool lets you specify a unique pre processing protocol and execute it in one step There are many preprocessing operations included in the Preprocessing tool that may be added to the protocol Getting There The Preprocessing Tool is available via Tools gt Pre processing File View Tools Advanced Modules Help vc VIEW i Display be S la control MIP control Data Manager Min Max Histogram Workflow Assistant Ctrl Shift H Pre processing Teen Function Preprocessing Options CT Bed removal _ Co egister Fast Full 3D _ Autocrop a a _ NM PT Convert unit Calibration factor Resample Weight O kg InjDose Series Desc focused _ Quality Control Image
218. is folder will be plots e Add Regressor Click on this button to add a regressor to the design matrix A window will appear from which the user can select an available regressor from the drop down menu as seen in image below Atlas Registration 266 VivoQuant Manual 11 12 2015 W Add Regressor ena Drift Ramp Bolus Boxcar Region Each ideal function can be customized for the specific study paradigm For example the Bolus option allows the user to set the shape and center both in units of TR Mi Add Regressor i 4 e Remove Last Click on this button to remove the last regressor column of the design matrix e Import Design Click on this button to load in a custom design matrix that is stored locally in CSV format Run the Tool Finished in 126 32s HEBREREEEEEEEEEEGE 100 Click on the Run button at the bottom of the window to run the tool If the tool pauses due to a missing settings field the user can click on the Cont inue button to resume processing To close the tool window click on the Close button The progress bar in the bottom left corner of the GUI window will display the progress for each step of the pipeline including loading the data set The total processing time will be displayed next to the progress bar once the analysis is complete A description of what process the tool is working on will also be displayed General Linear Modeling 267 Tumor Segmentation T
219. ish to have additions made to the options provided please contact your Account Manager or support invicro com Segmenting With The Tool With the image on which the new ROI is to be drawn loaded in the Data Manager navigate to and click on Whole Body Segmentation Tool This will open the Whole Body Atlas Tool GUI from which the user can apply the segmentation settings and run the tool Select Images Basic Advanced Number of Subjects 0 Using less than 3 subjects could lead to poor Repository Mb Local v performance Project Use Patient ID Proj Filter Image Reference v Species Mouse Sensitivity Threshold 0 50 Vox Low 0 00mm gt Vox High 0 21mm gt Libraries Include Protocol O Tiw ROIs To Segment ROI Name Settings The tool relies on settings selected by the user There are two levels of settings the Basic Settings explained below and Advanced Settings which should not need to be modified Basic Settings For the majority of users the Basic Settings tab contains all the settings that will need to be changed This is where the user can select the appropriate Reference Images appropriate Test Image ROIs to segment and probablilty threshold to use Adding to Reference Library 256 VS VivoQuant Manual 11 12 2015 Reference List Selection Selecting the proper Reference scan is imperitive to the proper functionality of the to
220. isplay a message in place of the MIP for uncompleted frames Color Palettes The default Color Palettes for the Reference and Input data sets can be changed using the drop down menus Maximum Intensity Projection 234 Data The Data panel contains options for data handling including data loading and quantification Display Data DICOM Network vivoScript Registration MinVoxSize Data Loading Disable MIP viewer Grow reference to input volume no V Ask Disable MIP Max voxsize ratio for vol 20 00 0 00mm Anchor input data at center Quantification Options Unit of Activity uCi w CSV Separator Comma Data Manager Y confirm moving T Show seconds in Browser V Apply default shift Data Loading Cancel Use the amp apos Data Loading amp apos panel to set loading options Max voxsize ratio for vol Data Check the box to disable the MIP viewer upon loading For large datasets this can improve the loading speed Check the box to enable VivoQuant to ask for your permission to initialize the MIP viewer upon loading For large datasets this can improve the loading speed Choose amp apos yes amp apos to allow the addition of zero padding to a reference image to match the volume of an input image or amp apos no amp apos to keep the reference image size static and potentially crop the input image if it is larger than the reference C
221. istry files automatically gathered example DICOM files a screenshot a comment file and a manually selected User file How to use the VQ Reporter Tool 359 VivoQuant Manual 11 12 2015 C Users KGOETT 1 AppData Local Temp rt 20151029 135203 792 bd 4 02 Session C Users KGOETT 1 AppData Local Temp session Request4Help zipacs 4 03 Registry Dump C Users KGOETT 1 AppData Local Temp rt 20151029 135203 792 reg C Users KGOETT 1 AppData Local Temp rt 20151029 135203 792 reg C Users KGOETT 1 AppData Local Temp rt 20151029 135203 792 reg C Users KGOETT 1 AppData Local Temp rt 20151029 135203 792 reg C Users KGOETT 1 AppData Local Temp rt 20151029 135203 792 reg C Users KGOETT 1 AppData Local Temp rt 20151029 135203 792 reg C Users KGOETT 1 AppData Local Temp rt 20151029 135203 792 reg 4 04 User comment C Users KGOETT 1 AppData Local Temp rt 20151029 135338 193 txt It is possible to review some low level items in the Content section by double clicking on them For example in the screenshot above all System Information collected for the report has been displayed Images with common extensions 1 e png jpg gif may also be previewed Double clicking on DICOM data will preview the DICOM header using the DICOM Dump tool It is also possible to rename entries in the Contect section by double clicking on the top level element File Help Components System Info Add Files OS Version Unknown Wind
222. it activity administered is estimated using the following area under the curve AUC method The tool uses a curve fitting algorithm which fits the experimental isotope s exponential decay curve to the percent injected dose per gram ID g vs time curve of the experimental data The AUC is calculated using trapezoidal approximations for experimental measurements and the remaining AUC is calculated using the analytical solution to the definite integral The data is then stored in a CSV file that can be copied into the OLINDA application NOTE Before continuing ensure that a Remainder Body ROI has been created This is a required data point for the OLINDA application Getting There To access the Dosimetry Calc tool the 3D ROI Tool must be active Go to the Advanced Modules tab then move down to Dosimetry Calc Advanced Modules ia SPECT ol fr CT gt Bed removal Whole Body Atlas gt Atlas NM CT analysis fMRI Tool Install Atlas Split ROI to DICOM Average body calculation Specify ROI center Specify ROI center 2 Upload tumor ROI TumorPK Model Dosimetry Calc gt Function Getting Started Start the tool by selecting Export Quantification AUC Calculation Export Quantification Dosimetry Calc 329 VivoQuant Manual 11 12 2015 Once the tool starts a spreadsheet will appear and request for you to fill in missing information from the study This can either be done in VivoQuant or in
223. ius parameter Smaller radii will result in smoother ROIs 3D Segmentation Tools 53 VivoQuant Manual 11 12 2015 Operator ax je lolow x e Classify input voxels to output ROI Low pass Smoothing gt Smooth the current ROI using low pass filtering Use a smaller radius for smoother Low pass radius px 20 5 Apply ROIs Ii x wm e P RightKidney x BEFORE NOTE Smoothing ROIs contained in images with large dimensions can take upwards of 30 seconds Modal Smoothing Use modal smoothing to reassign every voxel s ROI value to the mode of the surrounding region specified by the given radius The amount of smoothing can be controlled by the Mode Radius and Iterations parameters 3D Segmentation Tools 54 VivoQuant Manual 11 12 2015 Operator ax f h 0 e X 2 Classify input voxels to output ROI Modal Smoothing pe Reassigns every voxel s ROI value to the mode ofthe surrounding region specified by the given radius Mode Radius px 2 de Iterations 2 Apply ROIs xx WM F RightKidney y Bounding Cylinders The Bounding Cylinders tool can be used to generate cylindrical ROIs that encompass each animal of a multi animal image The number of animals is automatically determined and the cylinder radius can be configured This algorithm works best on NM images but may also work on some CT images Operator ax 1 o 2 Classify input voxels to output ROI
224. izes CT data and automatically sets it as the Reference VQ is capable of handling several file formats Getting There Three different methods exist for opening data The first method is to use the Replace Data or the Append Data thumbnails in the Main Window gt WV bi The second method is to go to Open Data under the File menu rs S Data Browser Ctri D id ny ml dh O bi Open Local Data gt lki Replace Data Ctri O 59 Save Image Ctrle 3 Append Data Ctrl N E Save Movie Ctrl M DICOM b Save Data Bruker MR Sn Sion gt Multiple Images VivoScript Ctrl Shift V EEF NRE Exit The third method is to use the keyboard shortcut Ctrl 0 For more on keyboard shortcuts in VQ please see Keyboard Shortcuts Function Selection of the Open Data option opens a navigation window from which the Reference data set may be selected Open Data 342 VivoQuant Manual 11 12 2015 t dh DEMO Search DEMO Organize v New folder gt mm de customers El Desktop Je Downloads PEJ y Recent places DEMO inp mhd DEMO inp raw DEMO ref mhd DEMO ref raw b a Homegroup p de Desktop gt E Documents test inp mhd test inp raw test ref mhd test ref raw gt de Downloads gt Jo Music gt E Pictures gt B Videos gt E Windows8_OS C v File name v Data files ras raw zraw bi v Coment File Formats VQ can handle a variety of file formats
225. kstation would require changing INVIVOSCOPE to something different like VQ WS2 For example let s say a 2nd workstation was being set up for the NS13 In the Client Panel of the DICOM Server Manager a client would be added as in Example 3 in the above table In the VQ on the 2nd workstation a new repository would be created with the following settings General Information Displayed Name NS13WS_DCMSRV Repository Type i Local folder DICOM server Pacs Local DICOM folder DICOM Server Calling AET IvS WS2 Called AET NS13WS_DCMSRV Hostname nanospecti3ws Port 104 Use localhost lower case for optimized local access Test OK Cancel Displayed NS13WS_DCMSRV or customer s Name e a o Type DICOM Server 1 Server Calling AET VQ WS2 Called AET NSI3Z3WS_DCMSRV Hostname _ nanospect13ws or IP Port 104 Troubleshooting e Double check the settings in VQ and the DICOM Server Manager Remember that they may be running on the same computer VQ on the WS computer talking to the WS DICOM Server or different computers VQ on the WS computer talking to the ACQ DICOM Server e Check the network connection between the two computers Can you ping the hostname configured in VQ from the computer running VQ Can you ping the hostname configured in the DICOM Server Manager from the computer running the DICOM Server If not try switching the hostname from the computer s name 1 e nanospect13ws
226. ktop Allows access to an online PACS system to Add DEMO PACS download example data and share your data with other users Adds a write only online PACS system reading requires password to allow you to comfortably Add Service iPACS send data to our service engineers Please see iPACS Service Repository for details When enabled VQ regularily checks for the availability of new versions and offers you to download and install them Please see Update Check for details Exports data required by VQ Run BatchTool Dump BatchFileGenerator from HiSPECT database BatchTool Generator Enable update check These options should be reserved for advanced users Reduces the amount of memory required Disable use of normalization in CT reconstruction however invalidates HU calibration for helical acquisition orbits Forces VQ to use only a single thread Disable multi threaded i e utility only single CPU or core for reconstructions reconstruction thus reducing efficiency on SMP systems Disable Hounsfield Turns off application of Hounsfield calibration calibration data Hounsfield Calibration Debugging These options allow us to debug problems in VQ Choose Install Location For the destination folder it is recommended to keep the default settings However if you would like to install multiple versions of VivoQuant on your system you can choose a different install location here Choose Components 10 VivoQuant Manual 11 12 2015
227. l e BatchTool Generator e Beta version e Bias Field Correction VQ Keywords 375 VivoQuant Manual e boot ini e Cache e Calibration failures e Calibration failures e Capture Viewer e Captures e Change Delay e Choosing the ROI type e Choosing the View Direction e Color Controls e Color Maps e Configuration e Confirm Configuration e Control e Control e Controls e Convert e Coronal e Cross hairs e CT Geometrical e Customize Analysis Pipeline e Cutting and Quantification Table Control e Data e Data e Data Browser e Data Browser Repository Panel e Data Formats e Data Loading e Data Manager e Data to Quanti Calc e Data to SpectAct Calc e Data to SUV Calc e DataL ist Object e DataManager Object e DB path e DCMDICTPATH e Debug e Delete an ROL e DICOM e DICOM e DICOM 11 12 2015 376 VivoQuant Manual e DICOM Cache e DICOM Dump e DICOM Editor e DICOM Peers e DICOM Repository e DICOM Repository e DICOM Secondary Capture e DICOM server e DICOM server e DICOM Settings e DICOM Settings e DicomRepository Object e Dictionary e Display e Displayed Name e Displays e Downloading Sample Library e ECG Split e ECMAScript e Edit e Edit an ROL e Enable Logfile e Expert Settings e File Formats e File Drop Down Menu e File Formats e File Menu e Filter e Find e Folder Filter e Function e Function e Getting There e Getting There
228. l const QString amp baseDir QStringList args QStringList bedRemoval const QString amp bedName QString getROIStats int datID int roiID combineFrames QStringList pngFiles const QString amp outfile int delay 40 bool deleteAfter false getNMCTWidget const QString amp name openNMCT setNMCTQuietModeOn runNMCTO getMPRWidget loadRGB int 1 QStringList imgFiles VivoQuant Manual 11 12 2015 gt float voxX float vox Y float voxZ int rebRep 4 sum bool forcePlanar true resume Q AbstractButton button mainWin Object Function setViewMode view op savelmage fileName type saveMovie fileName type dDataFromCommandLine const OStringList amp arguments openZIPACS fileName loadScript executeScript const QString file bool interactive false stopScript evalScript openReference openInput1 appendData openRaw mainWin Object Description Opens view and op e g VO mainWin setViewMode Tile View Navigation VO mainWin setViewMode Slice View 3D ROI Tool type e Slice Viewer 0 MIP 1 S 2 C 3 T 4 All 5 Everything e Tile Viewer 0 S 1 C 2 T 3 Screen 4 All See savelmage Opens the ZIPACS file at filename Terminates script Evaluates script Open data for Reference via dialog box Open data for Input 1 via dialog box Append data via dialog box Open raw images via dialog box 175 10 importBrukerMR con
229. larger as the threshold is lowered Select Images The middle pane of the GUI allows the user to select which images to use for the final Reference List These should already have been narrowed down by the user s previous selections in the Settings pane It is up to the user how many Reference Images to use however the time the tool takes to run is largly influenced by how many Reference Images are selected On the other hand performance is often influenced positively by increasing the number of Reference Images Run Tool and View Log Once the settings and Reference Images have been selected clicking Run in the lower right corner of the GUI will run the tool The Log will outline the steps being taken by the tool At its completion the tool will remain open but VivoQuant will navigate to the 3D ROI Tool where the new ROIs can be viewed and modified Settings 257 va VivoQuant Manual Downloading Sample Library A sample Reference Library is available depending on the user s VivoQuant license This is to be used for 11 12 2015 testing and learning how to operate the tool It can be downloaded from Tools gt Advanced Analysis gt Whole Body Atlas gt Download Sample Library File View Tools Advanced Modules Help scomm Display Downloading Sample Library SPECT gt J O BD ove we CT a Bed removal Whole Body Atlas Whole Body Segmentation Tool Atlas NM CT analysis Add To Library fMRI Tool
230. lating data including sorting finding and opening Data This pull down menu can limit the data displayed in the Study Browser to a single modality 1 e CT or data type 1 e reconstructions This button is used to open the data highlighted in the Study Browser If a single data file is highlighted it will be opened as the Reference image If an entire Study is highlighted the Open button recognizes which data file is the CT and sets it as the Reference Use of the Open button unloads data currently in VQ and replaces it with the highlighted data More information on the relationship between the Study Browser and the Open button can be found in the Study Browser documentation Show data type This button is used to append the data highlighted in the Study Browser to the data sets already loaded into VivoQuant For example 1f two data sets are selected in the Data Browser and three data sets are already loaded into VQ then appending the two highlighted data sets will cause them to appear as data sets 4 and 5 in the Data Manager Use the Open button to unload data currently loaded in VQ and replace it with the highlighted data Enables a search of the Study Browser by looking for user defined text in one of the available columns Patient s Name Study Date Study Description or patient ID Append Find Allows data from a local folder to be imported Import E into another local folder database or iPACS repo
231. les VTK Viewer Controler Object Function getRange int 1 getAlpha setAlpha f getDim setDim f getBalance setBalance f getIntensity 1 setIntensity 1 f 1sActive 1 setActive i on getFrom 1 getTo 1 setFrom i f setTo 1 f Controler Object Description Get the intensity value of the image at Input 1 Set the intensity of the image at Input 1 to f a value between O and 1 Get the intensity value of the Input 1 image Set the intensity of the Input 1 image to f a value between 0 and 1 Get the intensity value of the Input 2 image Set the intensity of the Input 2 image to f a value between 0 and 1 Get the intensity value for the image at the ith position Set the intensity value for the image at the ith position to f where f is a value between 0 and 1 Check whether the image at the ith position is active returns true or false If on is true makes the image at the ith position active otherwise makes the image inactive Get the current lower bound on the color palette range for the image at the ith position Get the current upper bound on the color palette range for the image at the ith position Set the lower bound on the color palette range for the image at the ith position to f where f is a value between 0 and 1 Set the upper bound on the color palette range for the image at the ith position to f where f is a value between O and 1 180 VS VivoQuant Manual 11 12 2015 setPos i
232. lick the Load from iPACS button The image data currently loaded must have been retrieved from an iPACS and there must be an ROI associated with that particular image already stored on the iPACS If only one ROI exists for the image that ROI will automatically be loaded If multiple ROIs exist the user will be given a drop down menu of available ROIs to choose from The choices can be distinguished by the ROI creator s iPACS username the date and time of creation and the region names for that file ROI kgoettler 2015 08 18T 17 48 15 Brain RightKidney LeftKidney Liver Heart Save an ROI to an iPACS To save an ROI to an iPACS click the Save to iPACS button The ROI will be automatically associated with the current image Unique filenames will be generated based on the creator s username and the patient name from the image header Previously saved ROIs will never be overwritten The files will be saved to a subdirectory of the current project on the WebDisk named roi Merge ROIs from an iPACS or disk If you wish to append previously stored ROIs to a set of ROIs currently open in the 3D ROI tool the merge ROIs function can be utilized as follows Operator ax rt o e As A w SR a k Store to disk k Load from disk M Merge from disk Store to iPACS f 3 l Load from PACS Y Merge from iPACS Larceny EP MB RightKidney E Heart wo O s Liver YM Oo ROI Loading Saving and Quantif
233. lows the user to view the images for that particular calibration in the Preview panel Details provides information about each calibration Run performs the analysis of that measurement Additionally the orbits from the 4 point calibration may be displayed using the Orbits button Aluminum Grid Measurement Linearity Check Data for the Aluminum Grid Measurement is collected with a device containing 16 carefully positioned holes The collimated beam source holder see NanoSPECT CT documentation is placed in each hole The resulting 16 point images are used to analyze the linearity of the detector Pees OU arid measurement Linearity Head1 7 Head3 7 Head2 uf Head4 7 CUECA SS a Resolutions Linearity s7 Collimator Depth The collimator depth phantom is used to collect data for the collimator depth calibration This calibration was once used to determine the distance from the detector plane to the pinhole plane however it is now out of date and is turned off by default It may be turned back on using the Enable ColDepth option found in the MMP Menus Headi N A Head3 N A Head2 N A Head4 N A Quality Nia Pinhole Offset Collimated Beam The Pinhole Offset calibration evaluates the deviation between the center of the pinhole plane and the center of the detector plane Pinhole offset Collimated bear Headi lt Head3 7 Head2 us Head4 7 Quality 7 Templates 320 VS VivoQuant Manual
234. ls General Information 4 Displayed Name iPACS Documentation Repository Type i Local folder DICOM server 8 Pacs Local DICOM folder PACS Username a Password Port 80 4 fies aralh art fimarar prann i far anor AA A Use loca ost lower case for optimized local access How to configure the NanoSPECT s DICOM Servers First open the Data Browser Find the Repository panel and either select the pre existing repository from the pulldown menu or select new to create a new repository For the standard access on the NS Workstation WS use General Information Displayed Name NSxx WS_DCMSRV Repository Type a Local folder 8 DICOM server Pacs Local DICOM folder DICOM Server Calling AET INVIVOSCOPE Called AET NSxxWS_DCMSRV Hostname localhost Port Use localhost lower case for optimized local access Test OK Name preference NSxxWS_DCMSRV _ _ Called AET INSxxWS_DCMSRV How to configure the NanoSPECT s DICOM Servers 25 VivoQuant Manual 11 12 2015 where xx is replaced with the NanoSPECT number typically no leading 0 for numbers lt 10 The local access VQ is able to access the DICOM Server directly so there is no need to add the VQ as a client on the DICOM Server However it does not hurt and is necessary when configuring an VQ for which access is not locally on the workstation See Adding VO as a DICOM Client for more information
235. m 0 000 mm _ Uniform Scaling 100 100 100 gt The buttons at the top of the operator window perform various functions within the operator Using the Tool 72 VivoQuant Manual 11 12 2015 vk Force re render of VTK Viewer s Reset VTK Viewer position T o oggle ability to perform reorientation in VTK Viewer O Resets current reorientation operation Y Apply current reorientation operation The Interpolator drop down menu designates which interpolator will be used during the transformation Linear 1s the default interpolator When manipulating atlases and other integer only datasets linear interpolation may be detrimental The Nearest Neighbor NNB interpolator is recommended to preserve integer values upon transformation The Quick Preview option enables VQ to generate a low resolution preview of an automatic registration and require the user to press the Apply Registration button to apply it 3D and 2D Manual Options 3D and 2D manual registration options can be found in the first two tabs of the operator Images ROIs can be rotated up to 360 degrees around their X Y and Z axis translated in any direction along their X Y and Z axis and scaled in any dimension Note that the reorientation will be performed on all images ROIs selected at the top of the operator window Operator Gx Ref Inp1 Inp 2 np v ROI v vk a Ov Interpolator Linear v Quick Preview 73D 020 R30 A2 M Be Rot
236. m the viewport through which the user is navigating To update these with information from another viewport there is a drop down menu in the upper left hand corner where the desired viewport may be selected Alternatively simply clicking on or navigating through another viewport in the Display will update the Viewer Control VC ax MultiView 1 y SliceView 1 SliceView 1 SliceView 1 Y Link Views co fe MultiView 1 2 MultiView 1 3 f TA co co 4 4 4 Color Controls Voxel Value Intensity Y Ref 49 2197 HU 100 Y Inp1 6 39116e 05 uCi 100 Y n Show ROIs By default the Viewer Control links all viewports in Multi View together This means any navigation through the slices in one viewport is reflected in all other viewports automatically Viewports may be unlinked by unchecking the Link Views checkbox in the upper right corner of the Viewer Control Unchecking this box will succesfully unlink the viewports and allow viewports to be navigated independently of one another File View Tools Advanced Modules Help SY SY M Eje Ba 0000 as o AOO Y ove me MM Multi View v Layout y d Quick Scripts gt 4 D 0 Y VC 8X Display MultiView1 7 mM C Link Views Sliders X 90 E Y 125 Z 294 Color Controls Voxel Value Intensity v Ref 290 051 HU 100 Y Inp1 0 000751932 uCi 100 Y _ Show ROIs Operator VC DM Resampling images to reference image took 0
237. mage Scales image by factor of f Checks for available VivoQuant update Forces check for available VivoQuant update Runs Crosstalk removal NanoSPECT module Opens Min Max Tool Shows histogram from Min Max Tool Runs Bed Removal module 176 10 showStartupDialogs setupLayout2x2 setupLayout1x4 setupLayoutMIP setupLayoutTrans setupLayoutSlice toggleCrosshair set ViewMode view op finishedCTReco tartCTReconstruction const OStringList amp files QStringList startBatchCT startIPACSSync startAppHomepage startOrgHomepage showConfig owCalibCTGeometrical showCalibMMP saveCalibrationTxt show UserData showNFFUniformity showNFFEnergy switchPatientName b switchPosLabel switchPosLabels bool b switchCrosshair bool b switchSliceNumber bool b switchAutoZoom bool b autoZoom showDICOMDump renameDICOM relabelDICOMStudies anonymizeDICOM getDataName int type operatorHasChanged update ViewPort updatePaletteHeight enableLogfile bool b startDbg View imageToCapture mainWin Object VivoQuant Manual 11 12 2015 Sets Main Display to Grid 2x2 view Sets Main Display to Grid 1x4 view Sets Main Display to MIP only view Sets Main Display to Transversal only view Sets Main Display to Slices only layout Toggles appearance of crosshairs Opens view and op e g VO mainWin setViewMode Tile View Navigation VO mainWin setViewMode Slice View
238. malSize ET a l ESA trl trl trl U g U trl Z Z ndo Operation Ctrl Shift Z 7 u E Redo Operation trl 1 Ctrl Shift D PSU ICOM Dum Ctrl Shift U o el trl Shift C H Hide VivoQuant Ctrl B oe Bas NanoSPECT Configuration Crl Q Q Quit MMP Calibration Tool Ctrl T T 213 Keyboard Shortcuts VivoQuant Manual Toggle between pre and post correction images in the Near Field Uniformity panel Scroll through slices in either the Slice View or Tile View fn Scroll through slices in either pee Race wane Slice View or Tile View 3D ROI Tool Specific Keyboard Shortcuts N N Naviagate to the Navigation tab in the 3D ROI Operator Naviagate to the Manual Painting tab in the 3D ROI Sju E O ee tab in the 3D ROL Operator ma se BS to the Magic Segmentation tab in the 3D ROI Operator O O to the Expert tab in the 3D ROI Operator Shift Shift E CRgsetthe active ROT EE EdittheaciveROl Edit the active ROI Rotate through the ROI list in the active ROI drop down Rotate through the ROI list in the active ROI drop down A Within the Spline tool confirm classification of voxels within contour to active ROI Return or Enter Within the Spline tool confirm classification of voxels within contour to active ROI and move to next slice Shift Return or Enter Within the Spline tool scroll through Spline Freehand Bully
239. multiple files may be opened into the Main Window simultaneously The Data Browser recognizes the files in the study and opens them accordingly setting the CT image as the Reference If extra data is found the Data Browser provides the message Ignoring extra data sets Patients Name StudyDate StudyDescription Patient ID IVS Documentation Example 1 2007 10 05 16 27 CT_Mouse SPECT_Tc99m ES 1S Documentation Example 2 h 2007 10 05 13 55 CT_Mouse SPECT_Tc99m 58 1YS Documentation Example 3 2007 10 05 12 35 CT_Mouse SPECT_Tc99m At the next level single data sets from a study may be selected for viewing Patients Name StudyDate StudyDescription Patient ID 53 1YS Documentation Example 1 2007 10 05 16 27 CT_Mouse SPECT_Tc99m Series Description Series Date E CT Example 1 2007 10 05 16 56 NanoSPECT NM Example 1 2007 10 05 16 27 NanoSPECT 58 1YS Documentation Example 2 2007 10 05 13 55 CT_Mouse SPECT_Tc99m 58 1YS Documentation Example 3 2007 10 05 12 35 CT_Mouse SPECT_Tc99m This nested structure continues depending on the format in which the data is saved For example for CT data saved in Single Frame format single slices may be selected for viewing Patients Name StudyDate StudyDescription Patient ID Series Description Series Date Modality Model name CT Example 1 2007 10 05 16 56 CT NanoSPECT CT Example 2 2007 10 05 16 56 CT NanoSPECT Image Type Image Date Dimensions InstanceNo
240. n Layout 157 VivoQuant Manual 11 12 2015 File View Tools Advanced Modules Help TI i vc ze Qeon mear gt S gt A Display Palette Grid 2x2 158 R update disabled Saving Image took 0 4 sec W Grid 1x4 In the Grid 1x4 layout the MIP and all three slices are laid out in a single row VivoQuant Manual 11 12 2015 File View Tools Advanced Modules Help e Qem os oWo t amp 2 Dow Display R update disabled i 4 p i A f gt 4 a SA x e 4 Saving Image took 0 4 sec Mc Mu Slice View 2 Palette its e a E MIP only In the MIP only layout only the MIP is visible the slices are not in view Grid 1x4 159 VivoQuant Manual 11 12 2015 File View Tools Advanced Modules Help e 99M0 5 coMoD e e Display R update disabled i i i 4 4 y f Saving Image took 0 4 sec o0 Slices only In the Slices only layout only the slices are visible the MIP is not in view MIP only 160 VS VivoQuant Manual 11 12 2015 File View Tools Advanced Modules Help ze 9398M Os cm t e 9 OB eve E E 6 Mu Sice view A Display con _Palette_ Slices only 161 Saving Image took 0 4 sec O Transverse only In the Transverse only layout only the transverse slice is in view VS VivoQuant Manual 11 12 2015 File View Tools Advanced Modules Help SY SY M T 23 000 08 L Y a O BD eee asd 1c Mu Slice View v 2
241. n Data e Append Data e Open raw dat e Open fromiPACS e Import Bruker MR Multiple Images RAW Capture Viewer e Save Data e Sessions onload javascript loadFrame gt File Management 333 Opening Data The Data Browser provides convenient access to files ina DICOM server or any other specified PACS Browser Reconstructions can be started from the data browser and files may also be exported e Getting There e Function Repository Filter Data Study Browser Getting There Three different methods exist for reaching the Data Browser The first method is to use the Data Browser thumbnail in the Main Window The second method is to go to Data Browser under the File menu e00 Open Local Data TTE EET Display i Session lt VivoScript The third method is to use the keyboard shortcut Ctrl D For more on keyboard shortcuts in VQ please see Keyboard Shortcuts Function The Data Browser s main window is split into four regions Repository Filter Data and Study Browser Opening Data 334 VivoQuant Manual 11 12 2015 Study Browser Repository SECURE Test Tumor moi PASS Aesting_wc qa_qc_exampledata EJES Ia _Data Show data type All data types a e 8 Y Apply default shift V Auto Start reconstruction _ Force planar Force 3D TIe TE Transfer O VVVVVVVVVVVVVVVVVVVVVVVVYVTVV STUDY1A2B3C555555 STUD
242. n arrows to edit the time point If Keep Data Steps is checked in the Output section of the tool then the registered data will be stored to the output directory with suffix anatreg Similarly if the Save QC box is checked then before and after registration QC images will be stored to the output directory as well as displayed under the anatomical registration tab as seen in image above Since the mean of the registered functional will be used for the QC images no QC images will be stored if the mean functional is used as the reference Brain Mask The brain mask tab provides options for skull stripping the input data smoothing 264 VivoQuant Manual 11 12 2015 Motion Correction Smoothing Anatomical Registration Brain Mask Atlas Registration GLM None Manual Do extraction in 3D ROI tool Provided Brain Mask 031020 14 2 brainmask rmha joey Automatic Otsu Thresholding Before After The user can choose from the following masking options e None Does not perform any brain masking e Manual Pauses the processing and prompts the user to manually segment the brain in the 3D ROI tool using automatic spline tool thresholding e Provided The user must provide brain segmentation RMHA file e Automatic Performs an Otsu thresholding on the brain If Keep Data Steps is checked in the Output section of the tool then the masked data will be stored to the output directory with s
243. nail in the Main Window The second method is to go to Slice Control under the Tools menu File View Tools Advanced Modules Help Vi tro FS l View contro a E E3 MIP contro FE Display Data Manager F7 Min Max Histogram Ctrl Shift H Workflow Assistant Pre processing Resample data DICOM Image amp Movie gt Update Check Ctrl Shift U Configuration Ctrl Shift E EB 8 D36 amp The third method is to use the keyboard shortcut F5 For more on keyboard shortcuts in VQ please see Keyboard Shortcuts Function The Viewer Control window provides a variety of options for manipulating the appearance of open data sets in the main window of the VQ Options include Sliders for slice selection Color Controls and Voxel Values Viewer Control 186 VivoQuant Manual vc iceVie a Y Sliders X Y Z Color Controls Voxel Value Y Ref 161 995 HU Y Inp1 1 32049e 05 uCi Y Sliders 11 12 2015 Intensity 100 100 Adjustment of the x y and z sliders in the Sliders section changes the sagittal coronal and transverse slices respectively that are displayed in the main window The slice numbers and crosshairs displayed on the main window also reflect the x y and z slider values Please see the view options for more on the display settings for the main window Sliders X Y Z Color Controls 63 87 4 4 4 204 The Color C
244. nalysis is rearrangement of tracer kinetic equations to yield a useful linear equation 1 Patlak analysis proposes that after some time t the plot of Co Sd Cape CAD vys Opt where Cy is the concentration of the tracer in the tissue and Cp is the concentration of the tracer in the metabolite corrected arterial plasma becomes linear with slope equal to the net influx rate constant K The rate constant K represents influx and trapping of the tracer into the tissue 1 2 70 y 2 028x 14 79 60 50 T C dt a0 cH 20 F 10 40 CH C 0 A N A G A le m Crit K fa Colrddr n K Coit Colt 40 69 BC 6 Cy dr Coy Media ona ESA In terms of a two tissue comparment model where k O because the tracer is irreversibly trapped K A Aik nib Model Assumptions This model makes the following assumptions Patlak Analysis Patlak Plot 112 VS VivoQuant Manual 11 12 2015 e The tracer binds irreversibly Crt ri a Pa After some time t the slope of the plot of vs sp approaches linearity Note Violation of any of these assumptions may produce biased parameter estimates While the model will still run in VivoQuant the estimated parameters may not accurately reflect the true tracer kinetics Required Inputs This model requires the following inputs e Metabolite corrected arterial plasma input curve e ROI s or voxels e t in scan time 4 Sele
245. natomical files If Keep Data Steps is checked in the Output section of the tool then the registered data will be stored to the output directory with suffix atlasreg Similarly if the Save QC box is checked then before and after atlas registration QC images will be stored to the output directory as well as displayed under the atlas registration tab General Linear Modeling Check the Enable box to perform modeling analysis Choose from pre defined Ramp Bolus Boxcar or Region ideal functions or import a custom design Motion Correction Smoothing Anatomical Registration Brain Mask Atlas Registration GLM Y lv Enable Image Time min F Ref 0 Save Residuals Y Voxel Maps Y Inpi 0 0333333 4 ROI Plots Add Regressor 3 j Import Design ia Y Inp6 0 2 Y Inp 2 0 0666667 Y Inp3 01 Y Inp 4 0 133333 Y Inp 5 0 166667 Y Inp 7 0 233333 Y Inp 8 0 266667 Y Inp 03 a EPA ha Customize the analysis and output materials with the following settings e Save Residuals Check this box to save a map of the residuals to the output folder The name of the map will be residuals e Voxel Maps Check this box to save parameter maps for the chosen regressors These files will be stores with suffix paramMap e ROI Plots Check this box to store all ROI plots in a folder within the specified output folder The name of th
246. ndarized uptake value with the Calc acquired data Submit ROI joa F 4 to iPACS Submits ROI the selected ROD to the iPACS Deletes the entire row of the corresponding selected cell Deletes all information from the table but not permanently The table can be reopened by right clicking and the data for the corresponding selection will reappear Remove line Plot data It is possible to plot the quantified data This function is useful to look at changes in activity concentration volume etc particularly in gated dynamic and longitudinal studies To plot data from the quantification tool select the column of interest 1 e Sum Mean etc right click on any element in the column and select Plot Data The plotted data will open in a new window and may be saved into an output PDF file Sum plot DEMO Data to Quanti Calc The calculator will automatically import the associated data Quantification Table Options 67 VivoQuant Manual 11 12 2015 0 000 E 1 1 2000 12 00 00 AM E 358 559 kCounts 1 1 2000 12 00 00 AM al E j si Decay factor aperture Quantification factor 0 000000 EWin 73 26 E Data to SpectAct Calc The calculator will automatically import the associated data amy ea BIO onssa v wue assa a rowe esm O vlae OOOO h SeeafeActwty 100 E Manel 6 19 2035 1200000 v Calculated values amant o m v Molarity dl soe Data
247. ndered in the MIP view automatically upon certain triggers When unchecked rendering will only occur when the VTK button is used For systems with less speed and memory it may be helpful to select a less demanding setting from the rendering quality combo box Segmentation To add a curvature flow smoothing preprocessing step to the segmentation methods check the Smoothing box Use the fields beside Segmentation to tune the parameters of the smoothing and various segmentation methods mouse over the each field to view the field name The Smoothing filter will use the Iterations and TimeStep settings the Confidence Connected Thresholding will use the Multiplier and NeighborRad neighborhood radius settings the Neighborhoood Thresholding will use the NeighborRad setting Crop Range To perform any of the thresholding segmentation methods on only a sub region of the input image follow these steps 1 Open the Cropping operator from the Operators drop down menu 2 Use the red sliders to select the desired region of the image 3 Do NOT click OK Instead go directly to the 3D ROI tool by selecting the 3D ROI operator from the Operators drop down menu see Getting There Clicking Cancel or the X in the upper right hand corner of the Cropping operator before opening the 3D ROI tool is also acceptable 4 In the Expert panel of the 3D ROI Operator mark the checkbox for Crop Range Expert Settings 57 VivoQuant Manual 11 12 2015
248. nel General Font Pal path Frame time 40 ms gt display Sync mode enabled Defaults Display Data DICOM Network vivoScript Registration Arial Crosshair transp open color shadow Orientation Radiologist RL Maximum Intensity Projection No of views 60 Frame delay 80 ms movies Requested Vol Renderer Smart Color Palettes Reference Input 1 Input 2 gray nih_fire2 x hotgreen OK Cancel Several font styles are available for display in the Main Window Controls the size of the displayed text in the Main Window A variety of cross hair styles are available for use in the Main Window Cross hair color options include red yellow magenta white green and blue different Color Palettes available in the VQ selections Provides option to view the data in the Radiologist Orientation View face to face or Neurologist View mirror Diagrams are used to show the difference 233 VS VivoQuant Manual 11 12 2015 Maximum Intensity Projection Sets the amount of time for which each MIP projection image is displayed in a saved movie Sets the delay time between MIP frames in a saved Sets the number of projection angles computed to construct the MIP With sync mode enabled only completed MIP frames will be displayed With sync mode disabled the MIP will freely rotate at all times but will d
249. nfdemo subproject2 bioscanfdemofsubproject3 Select any project to view only data associated with that project OO PACS Documentation i Patients Name StudyDate bioscan demo subproject1 esa 1YS Documentation Example 1 2007 10 05 16 27 bioscanfdemo bioscan demo subproject1 bioscanfdemo subproject2 Ibioscan demosubproject3 By default data will only be displayed when the project to which it belongs is selected from the second pulldown menu For example in this screenshot no data appears in the bioscan demo repository because all data within the larger repository belongs to individual projects Repository SECURE ES Training w fexampleproject therapeutic_ track 1 2013f Iratvart ff amp A Projects 28 28 Oo To simultaneously view all data belonging to a repository AND its projects place a at the end of the PACS Projects 244 VivoQuant Manual 11 12 2015 hostname during respository configuration The will cause all data within the repository and its projects to be displayed recursively This behvavior applies across all repository and project levels General Information 4 Displayed Name iPACS Documentation Repository Type i Local folder DICOM server 8 Pacs Local DICOM folder PACS Username a Password Port 80 4 fies aralh art fimarar prann i far anor AA A Use loca ost lower case for optimized local a
250. ngle SPECT projection data DICOM file into multiple projection data files along one of several DICOM fields Getting There The Split Projections tool is available in the Tools Menu under SPECT Tools File View Tools Advanced Modules Help e SY MA _NanoSPECT gt A Multi Pinhole SPECT iv Ne a cr r Spec Act Calculator NFF Uniformity QC f Bed removal SUV Calculator QuantiCalc Display Whole Body Atlas Crosstalk removal Atlas NM CT analysis Hi Split Projections fMRI Tool EKG split install Atlas Save Calibration bd Split RO te DICOM Show user data Sum projections Average body calculation eee Append projections Specify ROI center i Semi Stationary Data Processing Specify ROI center 2 Upload tumor ROI TumorPK Model Dosimetry Calc One specialized application for the Split Projections tool 1s the splitting of gated data In this case the data may be split directly from inside the Data Browser Study Browser Patients Name StudyDate StudyDescription Sp 2009 08 20 13 29 Gated Helical SPECT Topo CT Series Description Series Date Modality Helical Gated SPE 2009 08 20 15 02 NM Image Type Image Date Dimensions Pa M4 SOMBq Ap Open data Send to HISPECTNG gt Send to HISPECT Send to BatchTool EKG split Export to Open in Dump header Delete Data Function Upon selection of the Split Projections tool the Data Browser opens Select an appropri
251. nput 2 to perform a swap see image below Options Right clicking on a dataset brings up a menu with several data manipulation options Ordering Data 195 VivoQuant Manual 11 12 2015 DM ax Data List Loaded 3 Memory 16023MB Available Data Type CT CT Reconstruction Name DEMO DEMO 1 Desc DEMO Dim 176x176x452 Vox 0 200 20 mm 3 4920 Type NM NM Reconstruction Name DEMO DEMO 12 Desc DEMO Dim 176x176x452 Vox 0 200 20 mm nid yoke Wetoogrtiietls Use as Reference Use as Input 1 Annotate 0 00102 Copy Details DICOM Dump Save Data as b X Unload Data If one data set has been selected in the Data Manager 1t may be moved to either the Reference Input 1 Input 2 Allows an annotation to be added to the Annotate A data details Copes data set details to the clipboard from where they may be pasted into other files i e Word documents the selected data sets se TRaster Raw 4D or ITK image file More Information Many of the functions in VivoQuant are directed to specific images loaded in the Data manager so it is important to pay attention to the order in which data has been loaded into the Data Manager See How To Make a Dynamic Movie for a practical example that makes use of the Data Manager Options 196 Min Max Tool The Min Max Tool allows you to see and adjust the minimum and maximum values of all loaded studies Getting There The Min Max To
252. nt 2 50beta8 64bit DEMO DEMO NM DEMO Frame 03 NM DEMO Frame 04 NM DEMO Frame 05 a File View Tools Advanced Modules Help SY M ta 0000 os o gt A 9 Bove oe Mu Slice View Navigation y Quick Scripts AS O E 9 DM xX Display Data List Loaded 3 Memory 160 23MB X Available Data Type NM NM Reconstruction Name DEMO DEMO 1 Desc DEMO Frame 03 Dim 176x176x452 Vox 0 200 20 mm NN cara Type NM NM Reconstruction Name DEMO DEMO 12 Desc DEMO Frame 04 Dim 176x176x452 Vox 0 200 20 mm Type NM NM Reconstruction Name DEMO DEMO Desc DEMO Frame 05 Dim 176x176x452 Vox 0 200 20 mm O acoso 12 13 DM MM Downloading Annotations took 0 1 sec Ensure again that the minimum and maximum values are consistent across datasets How to make a dynamic movie 227 10 File View Tools Advanced Modules VivoQuant Manual VivoQuant 2 50beta8 64bit DEMO DEMO Help 99M os Bm GOr S e ope MM Min Max Min Reference 0 Input 1 0 Input 2 0 alt Hist 0 Tool min DM MM Max Unit 0 00101808 uCi 0 00101808 uCi 0 00101808 uCi te 0 max Downloading Annotations took 0 1 sec 11112 2015 NM DEMO Frame 03 NM DEMO Frame 04 NM DEMO Frame 05 O Mu Slice View y Navigation y Quick Scripts 4 D Y The newly loaded data sets are now properly prepared Save the images and data as in Steps 9 11 After sav
253. ntrol F6 Operator 4 Data Manager F7 f R Min Max lan A vt at Histogram Ctrl Shift H l Workflow Assistant E a E Pre processing ROI E Resample data pa lt gt DICOM E backgro 3 123 Image amp Movie W Update Check Ctrl Shift U 4 Configuration Ctrl Shift C The third method is to reach the Configuration panel using the Ctrl Shift C shortcut For more on keyboard shortcuts in VQ please see Keyboard Shortcuts Configuration Dialog The DICOM panel in the Configuration Tool provides the most in depth DICOM information available in VQ The DICOM panel consists of three sections DICOM Settings DICOM Cache and Capture DICOM Settings 19 VS VivoQuant Manual 11 12 2015 DICOM Settings DICOM Settings DB path D DicomDB Dicom ImageFiles ne Repositories Demo iPACS Y Y e 98 A aS XA Dictionary Rev Port 23104 V load palette DICOMDIR Folder Filter dem dc3 dicom IM_ S_ Override FOR No v Location of local DICOM database Allows optimized internal access to the Mediso DICOM database See Optimized local access for details List of available repositories The bank of buttons immediately beneath the pulldown menu operate on the selected repository in this field Y Check connection to DICOM repository Local folders are verified to exist and a C ECHO is sent to DICOM servers Add a new repository x Delete selected repository A Open
254. nually or by setting the text to the label of the field and the dates to a new date such as today The buttons Text to Label and Dates to Today will fill in these sections as described Selecting OK will apply the changes O Successfully anonymized 1 1 data sets Now the DICOM Dump will reveal no identifying information Rename DICOM Files The Rename DICOM function can be used to rename locally stored DICOM files according to information from selected fields of the headers Anonymizer 209 VivoQuant Manual 11 12 2015 Getting There DICOM files can be renamed by selecting Rename DICOM under the Tools gt DICOM menu Eile View Advanced Modules Help ve SY g View control F5 y ea O Dov MIP control F6 DM Data Manager F7 aS Display Data List Min Max Loaded Histogram Ctrl Shift H Workflow Assistant Pre processing Resample data me Dak He ii i DICOM a DICOM dump Ctrl Shift D SS Image amp Movie gt Anonymizer Type NM Update Check Ctrl Shifteu Rename DICOM N DEI 2 TE A Configuration Ctrl Shift C melas Study Dim 176x17 Function Template oF B PatientsBirthDate D StudyDate E AcquisitionDate I SOPInstanceUID J StudyID K AcquisitionNumber M Modality O ProtocolName P PatientsName S StudyDescription T StudyTime d SeriesDate e AcquisitionTime i InstanceNumber j SeriesNumber k AccessionNum
255. o File View Tools Advanced Modules Help M pE 0000 as O y ion 9 Pp ee ae ue Mu Slice View Navigation x E Quick Scripts gt D Y Display A Resampling images to reference image took 0 1 sec Scrolling through slices in the Slice View may be achieved using the scroll wheel on a mouse or by using the arrows and PageUp PageDown keys on your keyboard To learn how these keys control scrolling in the Tile View click here The keys control different views 1 e coronal sagittal or transversal depending on the current active view Click on a view to make it the active view In general the active view will be controlled by the Slice View 130 VivoQuant Manual 11 12 2015 PageUp PageDn keys while scrolling of the other two views 1s controlled by the arrow keys Scrolling Example E sj Y a JE SQ OS a Y MI AA EE ees E 8 EEIE 9 gt z pS K SAN JAN JAN at SAN sAN GY SAN A a E EN a 3 a Ds Oy Jl Q A _ an FE DD a fe e a b D B taba The arrow and paging PageUp PageDn keys may be used to scroll through slices in the Slice View The relationship of the keys with respect to scrolling is described by this example and further illustrated in the table below The crosshairs help to illustrate the scrolling properties of the arrow keys In the example image below the transversal view is the active view The and keys move the cross hairs tow
256. o register please fill out form and hit Register If you already have a license key please install it with Install key Show Key Install key HW Keys Registration 31 Operators VivoQuant offers several operators for performing a wide range of image processing tasks e Navigation e 3D ROI Tool e Quantification e Reorientation Registration e Time Series e Distance Annotation e Checkerboard e Cropping e Arithmetics e Filtering e Modeling Operators 32 Navigation The Navigation operator is automatically selected when VivoQuant is opened This tool enables you to manually scroll through the image slices and rotate the Maximum intensity Projection MIP Similar functionality is available via the Viewer Control tool Note this page is concerned with Navigation in Slice View While navigation is similar in other view modes the keystrokes and movements described below may not produce identical behavior For information regarding navigation in other view modes see the Tile View Multi View or MPR View pages Getting There To enter the panel select Navigation via the tool pull down menu on the VQ front panel File View Tools Advanced Modules Help ze 99M 55W60 t 9 Pw ola sos id B Quexscipts 1 Display 3D ROI Tool Quantification Reorientation Registration Time Series Distance Annotation Several methods exist for operating the slice control Navigator
257. o sections Network Settings and Auto Import Display Data DICOM Network VivoScript Registration Network settings Proxy Port 3128 Enable online check Please restart IVS after changes on this page Auto import Directory Repository y InviCRO PACS v Cancel The Network Settings section includes an option for enabling a proxy server for use with the VQ There are fields for entering a proxy and a port number associated with that proxy The Enable Online Check checkbox will automatically detect any available proxy servers If you believe a proxy server is needed please speak with your local IT representative The Auto Import settings may be used to designate a folder through which files may be automatically transferred into a Repository According to the setup in the above screenshot DICOM files placed in the VQ AutolImport directly will be automatically imported into the NSOOWS_DCMSRYV repository upon the next restart of the VivoQuant Network 250 Registration Getting There The registration panel may be reached from the Configuration Panel or 1t may be reached directly via the Help menu File View Tools Advanced Modules Help SY SY M ta MN Z Request Help Log out Ctrl Shift X DM W Registration Data List Enable Logfile Loaded 2 Memory Debug View Available Dati Hints Type CT CT Reconstruction Manual FL Name SegmentationExample 1007 W About 1 CT Date 2010 05 19 18 34 03
258. oadData int startIndex int numberToUnload applicationName buildIDO zipTool evalDialog const QString amp text QString mergeROIs const QString amp out const QScriptValue amp map splitROIZDICOM int id IsDir const QString amp dir const QString amp filter QString frand suspend getHash const QString amp key const QString amp def QString getHashKeys setHash const QString amp key const QString amp val clearHash storeHash const QString amp fileName loadHash const QString amp fileName ipacs translateUnit const QString amp type float value const QString amp input const QString amp output repairSlice int dataset int pos int off 0 int thick 1 getEnv const QString amp key const QString amp defaultValue QString VQ Object VivoQuant Manual 11 12 2015 Writes or appends text to a file with name fileName Returns a Brukerlmporter object See examples loadBruker vgqs for an Centers the crosshair in the field of view Returns an IPACSWebDisk object for the repository specified by rep See bel Saves a png of the loaded image to the path specified by fileName Unloads data from num sequential indicies starting at index from Using num Returns VivoQuant versionNumber Returns VQ Build ID Returns a ZipArchive object see below Suspends execution of current script and generates dialog box User must select script 174 10 startTool const QString amp too
259. oaded in the Data Manager Inp1 is the second etc and the thickness of the tool in the bully tool and for the following three tools as well Freehand tool A freehand region may be drawn by moving the mouse while holding down the left mouse button The region may be drawn in segments through a series of L clicks and closed with a right click 2D Thresholding tool Use the Percentage selector field to set a threshold for the ROI Specify the image on which to base the thresholding using the drop down menu Apply Spline Path to ROI and move to next slice Creates 2D ROI within spline path and moves to next slice Apply Spline Path to ROI Creates 2D ROI within spline path Clear Spline Path Clears spline path and all points 3D Segmentation Tools The 3D Segmentation Tools located in the tab denoted by the magic wand icon can be used to apply different thresholding techniques across input images and user defined ROIs as well as advanced ROI processing Note an ROI must be added before utilizing the segmentation tools 3D Segmentation Tools 50 VivoQuant Manual 11 12 2015 Operator ax le le l e 4 2 Classify input voxels to output ROI Global Thresholding E Global Thresholding A Pa il Connected Thresholding hd Neighborhood Thresholding Otsu Thresholding v Confidence Connected ROI Connected ROI Max Size Low pass Smoothing Bounding Cylinders Interpolate Slices s Apply ROIs Aa WM HB Br
260. obble as it rotates around its axis The CT Geometrical calibration measures this wobble and generates a file that is used to correct for the wobble in the reconstruction The calibration data is also used to assess the severity of the wobble and to insure that it does not exceed 0 5mm CT Geometrical Calibration 312 VS VivoQuant Manual 11 12 2015 A CT Geometrical measurement consists of a set of projection data collected in a circular CT measurement of the Geometrical CT phantom The orbits of the three metal balls embedded in the Plexiglas of the phantom are used to assess the wobble in the gantry Example settings for this measurement include 55kVp 360 projections 1000ms The protocol needed to run this measurement is called CT Geometrical and can be found in the Service Protocols section of the Nucline After collecting the measurement data it may be loaded into the CT Geometrical calibration panel using the Open button described below NanoSPECT CT Geometrical Calibration PROJECTIONS pees trans pxl MU N y o wo Co O 0 o 100 150 axial pxl mms 2010 O Erretor 0 4 0 3 offset mm bd 3a o o MI o Rh ri 1 oO QJ 150 200 angle r G pee eo MSE 47 31 Rs 213 0mm Sy 0 0mm Dy 0 6 mm Show Calib Quality Please repeat Rd 64 7 mm Sz 1 7 mm Dz 0 0mm alit The CT Geometrical calibration panel is divided into five sections Projections Orbits 2nd Order Corrections
261. odel makes the following assumptions e The tracer binds reversibly e Tracer concentration in all regions or voxels of interest as well as the reference region see below can be represented by a 1 tissue compartment model e A region tissue exists which is devoid of the target site receptor We call this region the reference region It represents the concentration of the tracer which is free in tissue and or bound to off target sites non specific binding An ideal reference region is a devoid of the target site receptor and b has the same concentration of tracer free in tissue and nonspecifically bound as the ROI Note Violation of any of these assumptions may produce biased parameter estimates While the model will still run in VivoQuant the estimated parameters may not accurately reflect the true tracer kinetics 2 SRTM is currently implement in VivoQuant using a basis functio nmethod approach and unweighted fitting 3 Required Inputs This model requires the following inputs e Reference tissue curve e ROI s or voxels Outputs Region level analysis e Plot of data from each ROI with SRTM fit e BPuyp R k k and mean squared error MSE of fit are shown when the cursor is hovered over the model fit plot e BPxp R k k and mean squared error MSE data and SRTM fit for each ROI can be saved out to CSV Voxel level analysis e Plot of data for each voxel with SRTM fit Select the voxel for which you d like to see
262. of evenly distributed gradations placed across all color bars 4 Smart labels colorbars with separate sets of gradations for each color bar incremented with respect NO ik Function 11 12 2015 125 VivoQuant Manual 11 12 2015 to the units of each color bar Set whether the image file will be stored as a local image file or as a DICOM via Secondary Capture Function 126 Docks The Viewer Control MIP Control Data Manager and Operators are automatically placed into docks upon opening Docks may be dragged and dropped into and out of the Main Window display and multiple Controllers are dockable at any given time Using docks The three controllers MIP Viewer and Data Manager are opened into docks automatically when used Also any individual operator 1 e reorientation cropping etc is opened into a dock upon use Operator ax Ref inp1 np 2 Inp ROI v wk Mm 1 Ov Interpolator Linear vw Quick Preview 93D Q2 A3 A2 B30 B2d Rotation X axis Y axis Z axis 0 00 0 00 0 00 Translation 0 000 mm 5 0 000 mm 0 000 mm _ Uniform Scaling 100 100 100 F DM A Xx Data List Loaded 2 Memory 10682MB Available Data Type CT CT Reconstruction Name DEMO DEMO Desc DEMO Dim 176x176x452 Vox 0 20x0 20 mm Type NM NM Reconstruction Name DEMO DEMO Desc DEMO Dim 176x176x452 Vox 0 20x0 20 mm 2 NM Any controller or op
263. of iterations for each resolution level can be adjusted Drop down preferences include Fast Symmetrical Demons Symmetric Demons Diffeomorphic Demons and Demons To show the deformed grid overlaid or a heatmap of the Deformable vector field over of the image use the toggle buttons To learn more about the Non Linear Registration techniques please visit the link below e http www insight journal org browse publication 154 Automatic Non Linear Registration 77 VivoQuant Manual 11 12 2015 Operator a x Ref Inp1 Inp 2 inp RO vw vk Ov Interpolator Linear v Quick Preview 3p 020 A370 A Bso A2 Automatic Non linear Registration Fast Symmetric Demons y Std Dev 1 00 px Register Automatic Slice by Slice Non Linear Registration The 2D Automatic Slice by Slice Non Linear Registration tool provides deformable registration of the data by computing individual transformation matrices for each voxel of data represented After selecting your preference from the dropdown the number of iterations for each resolution level can be adjusted To learn more about the Non Linear Registration techniques please visit the link below e http www insight journal org browse publication 154 Operator ax Ref inp1 inp 2 Inp RO vk y Ov Interpolator Linear vw Quick Preview 930 092 R A2 G3 Q20 Automatic Slice by Slice Non linear Registration Fast Symmetric Demons Select n Fast S
264. ol The settings selected by the users that factor into the images used are outlined in the table below mance This the the image in the Data Manager that will be the 8 basis of the ROIs generated The species of the animal being segmented This is based on the available options in the Reference Library The Low and High parameters for the voxel size of the Reference Images available The default low is 0 00 mm and the default high is the voxel size of the data loaded It is not recommended to use Reference Data with a lower resolution than the data that has been loaded as this will compromise the quality of the Reference ROI This list will display the protocols present in the Reference Library Changing the protocols included will narrow the Reference List It is suggested to only include Reference Images with the same protocol as the image loaded in the Data Manager This list will display the possible ROIs to generate based on those present in the Reference Library Only those selected will be generated by the Tool Other Basic Settings The other setting that can be edited by the user is the Probability Threshold Following the registration of each Reference Image to the image in the Data Manager each voxel is assigned a probability that it belongs in the ROI Only voxels with a probability greater than the threshold set by the user will be mapped to the ROI The default for this setting is 0 5 and typically the ROI will become
265. ol is available via the Tools menu e View contro FS MIP contro FE Date Manager F7 Min Max y Histogram Ctrl Shift H Workflow Assistant a Pre processing Resample data DICOM Image amp Movie gt Update Check Ctrl Shift U Configuration Ctrl Shift C The Min Max Tool can also be accessed by clicking on the Min Max Tool thumbnail in the Main Window ie Function The Min Max Tool displays the minimum and maximum values with units for the Reference Input 1 and Input 2 MM ax Min Max Min Max Unit Reference 1000 9360 56 HU Re calc Input 1 0 0 00101808 uCi Reset Input 2 NIA at Hist do 0 do 0 Tool k min max Y Apply The minimum and maximum values are used to calculate the colors for each voxel in the Display by way of a mapping from voxel values to the colors in the color palette Any values below the minimum will return the lowest color e g black in the gray palette while any values above the maximum will return the highest color e g white in the gray palette The Min Max tool makes use of a cache feature whereby minimum and maximum values for inputs are stored in a cache and used by the color mapping until the user forces the tool to recalculate them The advantage to this is it enables users working with multiple datasets to if they wish keep the color scale Min Max Tool 197 VS VivoQuant Manual 11 12 2015 consistent across multiple
266. old Ref 0 30 Es og HE eee cerco SEE HE EEES piii HE or Per Ln EB Ho id a CD T sum 49 74217 85mm 1178 Help Global Rotate Shift Wheel Scale Alt Wheelf Submit Right when closed Points Drag Left Remove Mid Open curve Shift Mid F Curve Drag Shift Left Add point Double Click Close Right E Bully Add start point inside curve Remove outside curve a Resampling images to reference image took 0 1 sec Choosing the View Direction The ROI may be drawn in either the transverse default coronal or sagittal plane To toggle between these options use the View menu in the Quantification panel File View Tools Advanced Modules Operator Help ss w es sja q Save table Ctri S a EN Hh Append to table Ctri A oo Clear table Display Mode Options a Eb Load RO Ctri Shift L 2 i Save ROI Ctri Shift S O Submit to iPACS O Threshold Ref Ey E View gt OF Y BulyRad 12p v Cut outside ALL EEE Cut R lv Transversal Help tus Global Rotate Shift Wheel Scale Alt Wheel Submi Cy Select FOV Points Drag Leff Remove Mid Open curve Shift Mid Curve Drag Shifi Lef Add point Double Click Close Right Bully Add start point inside curve Remove outside curve Using the tool 61 A 6 VivoQuant Manual 11 12 2015 In this example using the default settings the axial sliders determine the extent of the ROI in the axial direction The region or pre defined shape described bel
267. ommand VQ getWidget widgetName can then be used to interact with these elements For example to determine the name of the button in the 3D ROI Tool that resets all ROIs click on the peek icon then click on the button in the 3D ROI Tool A yellow box containing the class and name of the selected button will be displayed Operator ax E eo xX 2 A vik y E ROI H a background C One can then use the command VQ getWidget buttonResetROIs click to click the button and reset all ROIs VQScript Examples Included with VivoQuant are 30 VQScript example scripts to help you get started working with VQScript These scripts illustrate some of the many ways VQScript may be used to streamline workflows in VivoQuant To learn more about each files see the VOScript Example Scripts page Adding Script Shortcuts to the Toolbar 170 VQScript Objects and Object Methods VO Object Function debug text mainWin dataManager dataList sliceViewer mipViewer controler mipControler vtkController vtk Viewer quit counter c s showMessage text ask YesNoQuestion const QString amp msg progressDialog label cancel min max getDouble title label value 0 min 214748364 max 2147483647 decimals 1 getInt title label value 0 min 214 7483647 max 2147483647 step 1 Description Writes text to VQ s debug console e g the Windows debugger a Unix termi The text look
268. ompartment a nodisplaceable tracer Function 100 VivoQuant Manual 11 12 2015 Cao Concentration in specifically bound S gt compartment CO Concentration in plasma P compartment Transfer of ligand from arterial plasma to K mL cm min R 8 P ne Transfer of ligand from tissue to arterial ee plasma Transfer of ligand into specifically bound compartment k min Transfer of ligand out of specifically bound l compartment For tracers for which a compartmental model is appropriate estimation of the rate constants provides valuable information about tracer uptake and binding 1 Due to the difficulty of reliably estimating all four parameters of the 2TCM lumped or macroparameters are often employed Macroparameters are rate constants which are functions of individual microparameters e g K k kz and k4 One such macroparameter that is estimated by the 2TCM is the total volume of distribution Vy k min When the 2TCM is applied to image data with a reference region the distribution volume ratio DVR can be calculated DVR V Vynp where Vyp is the estimated distribution volume in a region that is devoid of the target site or receptor often called the reference region or nondisplaceable region Binding potential BPyp can then be calculated by BPyp DVR 1 Model Assumptions This model makes the following assumptions e The tracer binds reversibly e Nonspecifically bound ligand equilibrates ra
269. on begins the reconstruction As the reconstruction is running it can also be used to stop the reconstruction The first checkbox autostart will automatically begin a reconstruction when the CT panel is called from the Data Browser The second checkbox autosave will automatically save a reconstruction once completed Preview and Color Panel Preview and Color Panel 303 VivoQuant Manual 11 12 2015 Preview Color Panel 36 6 The Preview panel displays the CT reconstruction as it is being calculated The Color Panel provides several color map options File Menu CT Reconstruction r1 140 A Settings Help Load DICOM data Load local data Sawe data Transfer to IYS Algorithm Exact Cone Beam FBP v FEF filter typejcut off Frequency SheppLogan vw fi 100 2 Identical to the function of amp apos Ctrl D amp apos this option opens the Data Browser window from where a set of CT projection data may be loaded Note that the Browser opens with the amp apos CT Projection amp zapos data filter set Identical to the function of amp apos Ctrl L amp apos this option opens a Windows Explorer browser window A properly chosen CT projection data set is then loaded into the CT Reconstruction tool File Menu 304 VivoQuant Manual 11 12 2015 Sane Allows the user to save the data in DICOM format both into the selected repository and a local folder The reconstruction is opene
270. on of any of these assumptions may produce biased parameter estimates While the model will still run in VivoQuant the estimated parameters may not accurately reflect the true tracer kinetics Required Inputs This model requires the following inputs e Metabolite corrected arterial plasma input curve e ROI s or voxels e t in scan time Selection of t The Logan plot as implemented in VivoQuant requires that the user inputs the t which defines the time at which the plotted data become linear In VivoQuant the default rt value is 0 This is likely not the appropriate value for your experiment 1 values are tracer dependent For characterized tracers we suggest reviewing the literature to see which 1 values have been used in Logan method The simplest way to select a reasonable t value for your data is to run the model once with the default 1 value review the Logan plots to find the point at which they become linear t then re run the model with the appropriate in scan time value Outputs Region level analysis e Logan plot with line fit for each voxel Select the voxel for which you d like to see the Logan plot by clicking on it within the image viewer e V fitted line intercept and mean squared error MSE of fit are shown when the cursor is hovered over the Logan plot e Parameter maps for Vy fitted line intercept and MSE Logan Graphical Method Logan Plot 105 VS VivoQuant Manual 11 12 2015 Referenc
271. on of the red sliders is displayed in the Cropped Area section of the operator window To apply the crop once the red sliders are in the desired positions click the button To reset the crop range sliders to their original positions click the button The Cropping dialog provides information about the pixel location of each red slider x y z and current and cropped image size information in both voxels and mm The embed function will pad background slices to increase the dimensions of the image The auto crop feature starts its search the end slices of the image and adjusts the sliders towards the center of the image until a non background voxel is detected from all 6 faces Example of an image before it has been cropped Example of image after it has been cropped Using the tool 91 Arithmetics The Arithmetics operator can be used to add subtract multiply divide average or merge multiple images Additionally a scalar multiplier or addend can be applied to all voxels of an image with the Arithmetic operator Getting There The Arithmetics operator can be accessed via the tool pull down menu on the VQ front panel Eile View Tools Advanced Modules Help SOOM O amp Bom GOs 2 2 Bie0e SH E Me sicevien gt aan 3D ROI Tool Quantification Display Reorientation Registration Time Series Distance Annotation Checker board Cropping Arithmetics z x Quick Scripts 4 D Y Using
272. ontrols display information about the datasets loaded at the Reference Input 1 and Input 2 positions Color Controls Voxel Value lt a a e np npz Ref 161 995 HU Inp1 1 32049e 05 uCi Intensity 100 100 100 The checkboxes on the left toggle the visibility of the datasets in the Display Next to these the voxel values of each dataset at the current slice are displayed along with their respective units Note 1f given proper Hounsfield or quantification calibration the voxel values will be given in Hounsfield units or MBq On the far right are spinboxes labelled Intensity which control the relative transparency of the dataset decreasing the intensity value increases the transparency of the image Viewer Control in Multi View Multi View enables users to customize the layout of viewports in the Display When in Multi View additional controls become available in the Viewer Control which extend its normal functionality to the Multi View Display Users may also select whether navigation is linked across viewports or if viewports may be navigated independently of one another Function 187 VS VivoQuant Manual 11 12 2015 For more on setting up the Display in Multi View see the Multi View page The general functionality of the Viewer Control does not change in Multi View However in Multi View information in the Sliders and Color Controls is automatically updated to reflect information fro
273. ool Overview The NMPT Tumor Segmentation tool is used in conjunction with the iPACS to display the results of processed job groups whose jobs constitute a longitudinal study particularly those utilizing a xenograft tumor model For more information on this module download the quickguide Tumor Segmentation Tool 268 LumiQuant Overview LumiQuant is a hardware and software solution from Aspect Imaging to improve spatial localization and quantification of luminescent signal along with providing 3D anatomical co registration with compact MRI For more information on this module visit Aspect Imaging LumiQuant 269 SPECT Tools The SPECT Tools sub menu contains features primarily associated with improving SPECT quantification e QuantiCalc e Specific Activity Calculator e SUV Calculator e Crosstalk Removal e Biodist Visualization e Split Projections File View Tools Advanced Modules Help Display SPECT Tools CT gt Spec Act Calculator Bed removal SUV Calculator SPECT gt NanoSPECT gt Whole Body Atlas Atlas NM CT analysis fMRI Tool install Atlas Split ROI to DICOM Average body calculation Specify ROI center Specify ROI center 2 Upload tumor ROI TumorPK Model Dosimetry Calc 270 QuantiCalc The Quantification Calculator enables a feature unique to the NanoSPECT CT imaging system the ability to perform absolute quantification in small animal SPECT imaging Getting
274. oradiography Calibration Intensity Area Bkgd Std Conc Recalc Conc PSL mm2 nCi mg nCi mg Std 1 524 538 109 110 804 Error Weights 1 x 2 Output Unit nCi mg Background dia Std 3 195 131 41 41 1488 de E Bor Read Values from Image Std 4 115 314 23 24 271 Std 5 68 5727 16 14 3873 a Seve Std 6 73 7707 15 15 4864 Use ROI Name Std 2 323 187 68 68 227 Std7 39 7201 8 3 8 28621 Slope 4 7 Intercept 0 53 R2 0 999 E lt x 2o ea g S 40 60 Concentration nCi mg Ready for Calibration Image Calibration 218 Image Magick The Image Magick suite 1s used to manipulate image frames and movies within the VQ These options are particularly useful for generating appealing and informative dynamic movies for use in conferences and presentations Getting There Image Magick may be reached via the Tools menu Function File View Tools Advanced Modules Help View contro FS JT P Y ev sex E D MM Slice Vier i MIP contro ES Date Manager F7 Min Max Histogram Ctrl Shift H Workflow Assistant Pre processing Resample data DICOM gt E Image amp Movie gt Split movie into frames Update Check Ctrl Shift U AE STE TE E 6 DS amp Configuration Ctrl Shift C Change movie delay Image to Capture The Image Magick options available in VQ provide an excellent tool for generating informative movies for dynamic and gate
275. ort See queryStudies for more examples loadRepository const QString Kname etListOfRepositories const QString amp type QString abort Stops execution of the script returning to VQ queryStudies rep patName patID Performs query of DICOM repository rep for studies matching argument criter dRange studyDesc dRange studyDesc are strings meten arco ae query of DICOM repository rep for series matching argument criterii queryImages rep studyInstanceUID Performs query of DICOM repository rep for images matching argument crite seriesInstanceUID seriesInstanceUID are strings downloadImages rep Downloads a full series sopInstanceUID empty or individual image Retu studyInstanceUID DICOM cache seriesInstanceUID VQ Object 172 VS VivoQuant Manual 11 12 2015 sopInstanceUID Returns the data point associated with rep type UID and formname f lt iPACS such as quantification metadata SubjectInformation or tumor_analysis point such as images or project queryDataPoints rep type UID formname submitDataPoint DicomRepository rep const QString amp uid const QScriptValue amp data dicomBrowserLoad DicomRepository rep const QString amp studyInstanceUID const QString amp seriesInstanceUID bool append false queryStudyPlan DicomRepository rep const QString amp plan const QString amp cohort const QString amp group const QString amp animal const QString amp modality const QStrin
276. ow determines the bounds of the ROI in the transverse plane T sum 59 20 6 43mm t64 By using the View pulldown menu it is also possible to draw ROI boundaries in the sagittal plane Choosing the View Direction 62 6 VivoQuant Manual 11 12 2015 S sum 19 32 4 13mm t41 or coronal plane Choosing the View Direction 63 A 6 VivoQuant Manual 11 12 2015 C sum 25 12 4 81mm t48 m j ND En Q 3 Choosing the ROI type Four ROI types labeled as Modes are available e Spline Points are defined and smooth curves are drawn in between The base points can be moved by using the left mouse button to drag them Additionally points can be deleted middle click point or added double click position on curve Once a shape has been closed right mouse button it can be re opened by using Shift middle click on a point e Freehand A freehand region may be drawn by moving the mouse while holding down the left mouse button The region may be drawn in segments through a series of L clicks eE Bully Push lines out or into the object with a circle shaped cursor The size of the cursor is defined by the Bully Rad field in the quantification table s Opt ions section This mode provides an efficient way to fine tune an ROI made in Spline or Freehand mode e X Threshold A reference voxel is determined with a L click in the transverse window The ROI is determined by finding the region of voxels surrounding the
277. ows AMD64 8 proc 64 bit Hostname Add DIcOM QT Version 4 8 IPaddr F E5A3 FE80 462 193C 53EF E5A3 FESO 5EFE AC10 1A5C App Version kgoettler Staton UKN Add Screenshot Content 4 01 System Info C Users KGOETT 1 AppData Local Temp rt 20151029 135203 792 bdt 4 02 Session C Users KGOETT 1 AppData Local Temp session Request4Help zipacs 4 03 Registry Dump C Users KGOETT 1 AppData Local Temp rt 20151029 135203 792 reg C Users KGOETT 1 AppData Local Temp rt 20151029 135203 792 reg C Users KGOETT 1 AppData Local Temp rt 20151029 135203 792 reg C Users KGOETT 1 AppData Local Temp rt 20151029 135203 792 reg C Users KGOETT 1 AppData Local Temp rt 20151029 135203 792 reg C Users KGOETT 1 AppData Local Temp rt 20151029 135203 792 reg e MERA O C Users KGOETT 1 AppData Local Temp rt 20151029 135338 193 bd Controls 19 INVICRO reag evis 0 Softee Your name Demo User Your mail address demoEworldwideweb com How to use the VQ Reporter Tool 360 VS VivoQuant Manual 11 12 2015 Once all of the necessary files screenshots comments and images have been loaded into the report press Send to zip the file and submit it for review by the appropriate inviCRO team member We also recommend use of the Save button to save a copy of the report for internal use If there are difficulties in sending the file from within the Reporter please save
278. pidly with free tissue ligand e Compartmental model assumptions 4 The tracer kinetics or behavior can be represented by a compartmental model Tracer concentration within each compartment is well mixed and does not vary spatially First order kinetics can describe exchange of ligand between compartments Note Violation of any of these assumptions may produce biased parameter estimates While the model will still run in VivoQuant the estimated parameters may not accurately reflect the true tracer kinetics The 2TCM is currently implemented in VivoQuant using a basis function method approach 2 and unweighted fitting In this basis function method Required Inputs This model requires the following inputs e Metabolite corrected arterial plasma input curve e ROI s or voxels Two Tissue Compartment Model 2TCM 101 VS VivoQuant Manual 11 12 2015 Outputs Region level analysis e Plot of data from each ROI with 2TCM fit e Vr K ky K3 ky mean squared error MSE of fit and are shown when the cursor is hovered over the model fit plot e Vr Ky ky ky ky mean squared error MSE data and 2TCM fit for each ROI can be saved out to CSV References 1 A quantitative model for the in vivo assessment of drug binding sites with positron emission tomography Mintun et al Ann Neurol 1984 Link 2 Kinetic modelling using basis functions derived from two tissue compartmental models with a plasma input
279. play Several appearance features of VivoQuant may be customized in the Display panel including General display information Maximum Intensity Projection attributes and Color Palette defaults General Display Option Font Style Font Size Cross hair style color Pal Path Preview Panel General Font Pal path Frame time 40 ms gt display Sync mode enabled Defaults Display Data DICOM Network vivoScript Registration Arial Crosshair transp open color shadow Orientation Radiologist RL Maximum Intensity Projection No of views 60 Frame delay 80 ms movies Requested Vol Renderer Smart Color Palettes Reference Input 1 Input 2 gray nih_fire2 x hotgreen OK Cancel Several font styles are available for display in the Main Window Controls the size of the displayed text in the Main Window A variety of cross hair styles are available for use in the Main Window Cross hair color options include red yellow magenta white green and blue different Color Palettes available in the VQ selections Provides option to view the data in the Radiologist Orientation View face to face or Neurologist View mirror Diagrams are used to show the difference 13 10 VivoQuant Manual 11 12 2015 Maximum Intensity Projection Color Palettes Sets the amount of time for whic
280. please see Hounsfield Calibration Allows user to enable multiple threads 1 2 3 4 6 or 8 for performing the CT Reconstruction Note that it only makes sense to enable as many threads as there are cores available in the computer amp zapos s processor Defines the priority given to the CT Reconstruction with respect to other tasks being performed by the CPU Allows the user to disable the use of normalization in the reconstruction Disabling normalization prevents the use of Hounsfield Calibration but reduces the memory usage required for the reconstruction For users imaging with the Minerve bed system this option will automatically remove the Minerve bed from the CT during reconstruction Help Menu Settings Menu 289 VivoQuant Manual 11 12 2015 CT Reconstruction r1 140 File Settings Mi EEEL Expert settings E ata Resolution Algorithm Exact Cone Beam FBP v FEF filter typejcut off Frequency SheppLogan v flio a The primary feature of the Help Menu is the Expert Settings panel This panel is only for advanced users and allows several key parameters in the CT reconstruction to be overwritten including voxel size voxel volume both axially and transaxially Z offset sampling threads and Up scaling Mc Expert Settings 5 Voxel size 0 40 0 40 mn volume 10 2 10 ox 4 0 E 4 0 2 mm z offset 0 00 2 mm i A Sampling 1 gt Allows the user to choos
281. processing needs Therefore periodic Update Checks are recommended to insure that you have the latest and greatest software available Getting There Update Check may be reached via two methods The first method is through the Tools menu File View Tools Advanced Modules Help g View control FS y ati MIP contro FE 4 Date Manager F7 E3 Min Max Histogram Ctrl Shift H Workflow Assistant Pre processing Resarnple data DICOM gt Image amp Movie gt dl M k m amp ii E Update Check Cris Shift U Configuration Ctri Shift C The second method is to press Ctrl Shift u on the keyboard For more information on Keyboard Shortcuts see Keyboard Shortcuts Function If an update is available the Update Check will present a window providing an option for downloading the new version You may either choose to download Yes not to download No or to ignore entirely Ignore If the new version is downloaded you will be prompted to follow several straightforward installation steps For more on installation see the Install Guide A new version of VivoQuant is available Installed 2 50alpha8 Update 2 5beta8 Would you like to download the new version Please note Your ability to upgrade this product may be subject to a valid service contract Ignore Update Check 231 VivoQuant Configuration The VivoQuant Configuration window has several panels providing access to customizable features as
282. put compartmental models Vesa Oikonen Turku PET Center website Link Logan Non Invasive Graphical Method Logan reference plot The Logan non invasive graphical method 1 was developed for reversibly bound traceres based on the Logan graphical method and Patlak method for irreversibly bound tracers 2 3 The Logan reference method proposes that after some time t the plot of Pee yai Poe sak b Cp t jdt do Ca tjal a a where Cy is the concentration of the tracer in the tissue and C is the concentration of the tracer in the reference region becomes linear with slope equal to the distribution volume ratio DVR Binding potential BPxp is related to DVR by BPyp DVR 1 70 y 3 752x 11 47 60 50 3 CHOdt 40 CAD The Logan plot is a rearrangement of tracer kinetic equations to yield a useful linear equation However the mapping of transformed variables is nonlinear in C t and this results in an underestimation of DVR which becomes more pronounced with larger true DVR and increased noise 1 4 Therefore the Logan graphical method may not be the best method to use when data are noisy and other methods should be considered Method Assumptions This model makes the following assumptions e The tracer binds reversibly e A region tissue exists which is devoid of the target site receptor We call this region the reference region It represents the concentration of the tracer which is free in tissue and or bound to of
283. r 1t may be reached directly via the Help menu File View Tools Advanced Modules Help SY SY M ta MN Z Request Help Log out Ctrl Shift X DM W Registration Data List Enable Logfile Loaded 2 Memory Debug View Available Dati Hints Type CT CT Reconstruction Manual FL Name SegmentationExample 1007 W About 1 CT Date 2010 05 19 18 34 03 series 2010 05 19 Contents The Registration panel includes VQ user information The panel includes fields for Institution Department Contact email address enabled VQ options license status and license expiration date The panel is also used for registering the VQ upon start up Three buttons Install key HW Keys Register assist the user in registering the VQ Registration of the VQ is required to unlock most of the VQ features Please see the Registration Quick Guide for details on registering the VQ a E Display Data Dicom Network vivoScript Registration License Key Institution Department Contact address exportDICOM exportimages exportMovies importBruker importRaw mprView multiThread multiView op3DROI opCropping opCutting opDistance_Measure opIsoCount opOthers Options opQualification opReorientation opTimeSeries registration segAtlasNMCT segAtlasfMRI segTumorAnalysis segWholeBody sessions tileView toolsCT toolsDICOM toolsSPECT tripleView vendorINVICRO volRender vascrint Expires 2028 12 31 T
284. r local administrator for assistance To open and change the boot ini file please follow these instructions 1 On the Desktop right click on My Computer and then Properties 2 Go to the Advanced tab 3 Click on Settings under the Startup and Recovery panel 4 Where it says To edit the startup options file manually click Edit click ob 5 Add 3GB slash 3 G B to the end of the line as shown above After this change the system has to be restarted For a detailed description of the 3GB switch see Microsoft s knowledge base A description of the 4 GB RAM Tuning feature and the Physical Address Extension switch Windows 64 bit The memory available to VQ is only limited by the physically available RAM in your PC Mac OS X The Mac OS X version of VQ is also making use of 64 bit wide addressing and thus the limit available 1s only limited by the physically available RAM in your Mac Memory configuration 372 Debug At the time of installation the Debugging option may be selected This option allows the maintenance of a logfile that may be used to help troubleshoot problems that occur while using VQ Getting There To enable debugging go to the Enable Logfile option under the Help Menu File View Tools Advanced Modules Help y 22 DO py Request Hel e 98M GO ool err 00 Log out Ctrl Shift X DM Wa Registration Data List B Enable Logfile Loaded 2 Memory 106 8 Debug View Available Data Hints
285. r operations the result replaces the original image and no new image will be loaded For all other arithmetic operations the result is appended as a new image at the end of the Data Manager distinguished by a modality set to OT and a description of the operation in the Desc field DM BA Data List Loaded 3 Memory 160 31MB E O EAN NN NN NN NN NN Available Data Type CT CT Reconstruction Name SegmentationExample 1007 1 f Date 2010 05 19 18 34 03 series 2010 05 19 21 27 13 Desc CTReco s bed removed DEMO Dim 192492380 Vox 0 20x0 20 mm Type NM NM Reconstruction Name SegmentationExample 1007 2 MM Date 2010 05 19 18 34 03 series 2010 05 19 21 31 43 Desc NM Reco Co Registered DEMO Dim 192x192x380 Vox 0 20x0 20 mm Type OT CT Reconstruction Name SegmentationExample 1007 13 CT Date 2010 05 19 18 34 03 series 2010 05 19 21 27 13 Desc Multiply Ref Inp1 CTReco s bed removed DEMO Dim 192492380 Vox 0 20x0 20 mm Units are not considered by the Arithmetics operator and a warning will be displayed if an attempt is made to add subtract multiply divide or average two images of differing units though the operation will still be carried out Using the tool 93 Filtering Tool The Filtering Tool offers a variety of smoothing filters with configurable input parameters and can be applied to either the Reference or input images or both Getting There The F
286. r which data will be stored in the DICOM Cache default 14 Life Time lear Empties the DICOM Cache Captures Defauit Repository Default Format Not yet implemented please check back soon Data Browser Repository Panel The DICOM Repository panel in the Data Browser is the most convenient location for adding and editing repositories including DICOM Servers local folders and PACS Servers DICOM Cache 21 VivoQuant Manual 11 12 2015 Repository SECURE fexampleproject therapeutic_track_1 20 134 A EN Projects 28 28 30 List of available repositories The bank of buttons immediately beneath the pulldown menu operate on the selected Repositories repository in this field Please click here to learn more about the DICOM repository section of the DICOM browser Check connection to DICOM repository Local folders are verified to exist and a C ECHO is sent to DICOM servers Add a new repository T Open the DICOM Editor Opens a Windows Browser that can be used to select a local folder as a Y Fetch all DICOM meta data l Remove repository from list DICOM Editor The DICOM Editor is used to add repositories including DICOM Servers PACS Servers or local folders General Information Displayed Name DOCUMENTATION DEMO i 300 ie OS C Repository Type Wir Local folder DICOM server 8 PACS EEE Calling AET Local DICOM folder Called AET Ho
287. raining ipacs invicro com 443 User testUser Direction To iPACS Local C Users User i Desktop New foider Remote fwebdisk projects invicro_lab petstudyi SSH Port 22 di Save job name New folder The Sync job is now created and will be run immediately Further settings can be configured as described in the following sections Configuring Additional Settings The PACS Sync Config window allows you to manually create new Sync jobs and edit the configuration settings of existing jobs To access the iPACS Sync Config window click on the wrench icon on the left side of the main window Create a Sync Job using the Wizard 364 VivoQuant Manual 11 12 2015 iPACS Sync File Jobs Help Logfile Job test v cr AA 2014 08 04 17 44 27 ipac 2014 08 04 17 44 34 Nurr 2014 08 04 17 44 34 Tota 2014 08 04 17 44 34 ipac 2014 08 04 17 59 27 ipac 2014 08 04 17 59 33 Nur 2014 08 04 17 59 33 Tota 2014 08 04 17 59 33 ipac x Select the job to configure from the Open drop down or enter a name and click Create to create a new Sync job Load Create Jobs Open test2 New de Create IPACS Setup Make a job active or inactive Specify the iPACS URL or IP address in the Hostname field Data transfers adhere to the roles associated with an iPACS user s account If the username and password information are not provided here the application will prompt for a username and password before every
288. rame sag png Frame tra png Frame8 cor png Frame8 mip pna Frame8 sag png Frames tra pna Framet all png Framel all pna Frame2 all y Files of type Image files png bmp pea pa tif Y 16 Type in a name for the movie file The default file format is gif ImageMagick Select Output Save in O MovieFrames A 2 My Recent Documents n Desktop My Computer My Network File name Places Save as type Movie files gif mna mpeg mpg Y c m fo e EA HowTo MovieT Cancel 11 12 2015 17 Use the Image Magick Change Movie Delay option to speed up or slow down the movie frame rate File View Tools Advanced Modules Help View contro MiP contro P Ll Ot Display Date Manager Min Max Histogram Workflow Assi E 6BDSE HSE iis How to make a dynamic movie Pre processing Resample data DICOM gt image amp Movie gt Split movie into frames Update Check Ctrl Shift U Join frames to movie Configuration Ctri Shift C Change movie delay FS FE E O B sse LA He Mi Slice View Y F7 Ctrl Shift H stant Image to Capture 229 VS VivoQuant Manual 11 12 2015 18 Congratulations Just double click to open and watch the new movie How to make a dynamic movie 230 Update Check VQ is frequently updated to provide users with more and better tools for all of their post
289. re are icons along the left side of the window for manipulating the batching process Job List The job list provides a list of the X ray projection data to be reconstructed Information about each individual scan is divided into a number of sections Mod Provides information on the modality used 1 e CT Displays the batch number ID the number of Details projections used and the name of the reconstruction as it will appear when loaded into VQ Patient his is the name of the folder from which the X ray Patient nobus projection data was taken Provides information on the status of the reconstruction If the status is Running then the reconstruction is underway if it is Waiting then the reconstruction has yet to begin The status section will also indicate when it is storing a completed reconstruction and when it is about to start a new reconstruction Job List 308 VivoQuant Manual Status 11 12 2015 The status of the current reconstruction job along with the total number of scans to be reconstructed is displayed in the Status bar and indicates the percentage of data remaining to be reconstructed Log file File Menu The file menu in the main window offers the following functions in the BatchCT application Batch CT Status 1 57 AGE Jobs Help Hide Ctrl H Quit Ctri Q Details Patient Hounsfield calibration Stop service Ctr T 505072353640 ct exp time Start service J CT Helical Scan Topogram CT a opr 2
290. reference voxels that share similar values to the reference voxels The threshold value establishes how near in value the boundary voxels must be to the reference voxel ROIs can be rotated by using Shift the mouse wheel scaled by using Alt the mouse wheel or moved by using Shift the left mouse button Choosing the ROI type 64 VivoQuant Manual 11 12 2015 Once the desired ROI has been defined a right click may be used to fill in an entry in the main table of the Quantification Table This table contains a wide range of information as described below Note that the unit used for measuring CT attenuation is the Hounsfield Unit HU while the unit used for measuring activity in the NM MR PET and SPECT images is Mega Becquerel MBq kilo Becquerel kBq or micro Curie uCi Click the Clear gt button in the Options section of the quantification table in order to clear the current ROI and begin drawing another VQ maintains the most recent ROI until a new ROI is defined Each ROI for which data is collected is assigned a new color Note for example that editing a ROI following data calculation results in a change to the color of the ROI Also the MIP reflects the currently selected ROI by shading the region encompassed by the ROI according to the appropriate color The Quantification Table After defining the ROI and R clicking the quantification table will fill the following fields ROI Patient Series Modality Color Voxel
291. rl M DICOM Save Data Bruker MR Session gt la es A Saas ES VivoScript Ctri Shift v Raw Data Exit Selection of the Open raw data option opens a navigation window from which the raw data may be selected Pob DEMO Organize New folder es E Favorites y customers EN Desktop Je Downloads ME El Recent places a Homegroup E This PC k Desktop El Documents Je Downloads m Music E Pictures E Videos E Windows8_OS C w File name Open Raw Data DEMO np mhd DEMO mp raw test inp mbd test Inp raw DEMO ref mhd DEMO ref raw va El test ref mbhd test ref raw Data files ras raw zraw bi w Cancel 346 VivoQuant Manual 11 12 2015 Once the raw data has been highlighted a Raw Data Importer window appears which contains information about the data The dimensions voxel size data type and file information are all included The raw data 1s imported to VivoQuant by clicking Load Data type Patient Info signed byte unsigned byte PatientsName DEMO signed short D unsigned short ee signed integer unsigned integer float Scaling factor Series Date 20131107 PatientID DEMO Series Desc DEMO Series Time 174102 Data order pa big endian 0 little endian _ comp CopyDCM Voxel sizes File info X 0 2000 mm z File size 5
292. ro com Port 80 and leaving Username and Password blank iPACS servers also enable the use of Projects a useful tool for organizing DICOM data Optimized local access To use the optimized local DICOM access much faster use localhost all lower case otherwise a normal DICOM connection is used as the host name Additionally you have to define the DB path see above PACS Projects The PAGS repositories permit the use of projects Projects represent a directory structure for DICOM repositories Data may be stored and accessed via different projects aiding organization of DICOM data In DICOM Editor 243 VivoQuant Manual 11 12 2015 this example an iPACS repository for bioscan demo is being configured The bioscan demo repository contains three projects on Displayed Name iPACS Documentation Repository Type Mb Local folder DICOM server Pacs Local DICOM folder lt Username Password Hostname ipacs invicro com bioscan demo Cancel If any projects are present within a configured iPACS repository a second pulldown menu will appear in the Repository panel of the DICOM browser All projects within that repository are available via the second pulldown menu The three projects associated with the bioscan demo repository are shown in the screenshot below Repository PACS Documentation bioscanfdemo subproject1 bioscan demo subproject1 Ibiosca
293. rter DO ic 356 IPA CS SYNG ao A 362 Batch Transfer Data to and from the IPACS cid 362 Download WebDisk files in batch usingiPACS SYDCo oocccccccncconononononnnnnononononononononnnnonnnnnnnnnnnnnnnnnnnnnnss 362 Download individual files from the iPACS via iPACS SYDCo occcccccccccnnnnnnnnnnnnnnnnnnonnncnnnnnnnnnnnnonnnnnnnnnos 362 COMMUTE a melo AAA 363 Create a Sync JOO Usine tHe Wiz dd nos 363 Come Unie Addon LS SUNMOS ias 364 A eee ere Meee ee Nid eee ee renee ne me ees anne reser re ean eae Sere enter ee 365 Direction SOLU os A aptahaeosuces a sO eaceaatancsnstuacatualatantaanteenceaes 365 A A A E TN NRO 366 AO A SIR E A A A NOT 366 PME AIC lts casas 367 SOL ol O A Ue Pe rE vC ene E Caton eek E 368 DRS Simce CUE caida 369 A ssa ac i eaat ta a O agen a aero lenatescan an teceaneenentsaets 369 TC OSS CTA ONS o o ES SP ace ese acaaadua idan bana casstesale etek cashes aces sen aoes tvaaseleuaanedensaaas 369 OUK SVIC ss oes Site beta to an daar dain O A Melanin 369 TE POUDICSNOOUING AA a 371 Trouble SHOOUNS Cate notes cid ti is 371 SEVICE REO o e a A o edo 371 Memory gi ticcidelaacecosnenscdeucouecoucaseaganccsesesoucesvensunssetenseueuecuasearsactecusccuseuseusetuucasoeoseacavsatuvavenceaces 372 NINA oats cee agceeed atee nace es ana a ue seeianeb cates cua taeeaaneatenen 312 Windows OA Diten A A A A TN 372 Mac OS emer oe eer IE PPT CS te PE EO 372 xiii VivoQuant Manual Table of Contents DOIG tds 373 A O Oe neyo een ome O eater rece
294. s Region level analysis e Logan plot with line fit for each ROI e DVR fitted line intercept and mean squared error MSE of fit are shown when the cursor is hovered over the Logan plot e DVR fitted line intercept and transformed Logan space data for each ROI can be saved out to csv Voxel level analysis e Logan plot with line fit for each voxel Select the voxel for which you d like to see the Logan plot by clicking on 1t within the image viewer e DVR fitted line intercept and MSE of fit are shown when the cursor 1s hovered over the Logan plot e Parameter maps for DVR fitted line intercept and MSE References 1 Distribution volume ratios without blood sampling from graphical analysis of PET data Logan et al JCBFM 1996 Link 2 Graphical analysis of reversible radioligand binding from time activity measurements applied to N 11C methyl cocaine PET studies in human subjects Logan et al JCBFM 1990 Link 3 Graphical evaluation of blood to brain transfer constants from multiple time uptake data Patlak et al JCBFM 1983 Link Logan Non Invasive Graphical Method Logan reference plot 111 VS VivoQuant Manual 11 12 2015 4 Effects of Statistical Noise on Graphic Analysis of PET Neuroreceptor Studies Slifstein and Laruelle JNM 2000 Link Additional Resources Multiple Time Graphical Analysis MTGA Vesa Oikonen Turku PET Center website Link Patlak Analysis Patlak Plot Patlak a
295. s be less than 0 5mm to enable successful correction of the gantry motion in the CT reconstruction 0 4 offset mm o Oo o o o y oa AAN O Ly 0 50 100 150 200 250 300 350 angle The Results panel provides further calibration results including a mean square error MSE value that represents the deviation of the fiducials from their ideal trajectories A one word Quality assessment is provided as well as numerical values for other parameters including the radius of the source Rs radius of the detector Rd offsets of the source axially Sz and transaxially Sy and offsets of the detector axially Dz and transaxially Dy MSE 47 31 Rs 213 0 mm Sy 0 0 mm Dy 0 6 mm Quality Please repeat Rd 64 7 mm Sz 1 7 mm Dz 0 0mm Function 315 VivoQuant Manual 11 12 2015 The Control panel houses four buttons including a Show Calib e Open Opens the Data Browser where a CT Geometrical data set may be selected for analysis e Close Closes the CT Geometrical panel e Save Calib Saves the existing calibration in the format used by the NanoSPECT CT e Show Calib Function 316 Calibration MMP SPECT This tool can be used to evaluate SPECT geometrical calibration data Getting There The MMP SPECT Calibration tool is available in the Tools Menu File View Tools Advanced Modules Help e sm NanoSPECT P A Multi Pinhole SPECT ET d Spec Act Calculator a NFF Uniformity
296. s in a WebDisk folder follow these steps 1 Navigate to the desired WebDisk folder on the iPACS 2 Click iPACS Sync URL under Other Links on the right side of the page 3 Copy the URL to the clipboard PACS Sync GUI 369 VivoQuant Manual 11 12 2015 4 In the iPACS Sync client go to Jobs gt Quick Sync then paste the URL 5 Select a folder where the iPACS files will be saved 6 The iPACS Sync client will run a job to transfer all files and folders from that WebDisk folder to the specified location Other links Edit header footer sidebar Public links jPACS Sync URL Trigger Indexing To download select files from the iPACS follow these steps 1 Select the desired files from the Browser or WebDisk then right click one of them and select iPACS Sy ic 2 A browser irsync file will be downloaded 3 In the iPACS Sync client open the browser irsync file by going to Jobs gt Quick Sync File then selecting the file 4 Select a folder where the iPACS files will be saved 5 The PACS Sync client will run a job to transfer the selected files to the specified location Project PACS Testing WC ipacssync testing_wc ipacssync Reigadl IMebiski mode non recursivel Select AR Cleas Quick Sync 370 Troubleshooting Should you run into any issues with VivoQuant please contact us at lt support vivoquant com gt consider using our Service Reporter and check out the list of trouble
297. s like Script 1234 text with 1234 being the time in ms since the script started Returns VQ s Main Window object see below Returns VQ s Data Manager object see below Returns VQ s Slice Viewer object see below Returns VQ s MIP Viewer object see below Returns VQ s View Contoller object see below Returns VQ s MIP controler object see below Returns VQ s VTK controller object see below Returns VQ s VTK viewer object see below Asks VQ to quit in an interactive session the user is asked for confirmation wl terminates without further ado Convenience function e g used for fileNames that returns a O padded counter counter 3 5 would return 00003 Shows text to the user Please note that the user has to confirm the message al Shows QString to user in Yes No dialog box Returns a boolean value 1 yes Returns a progress dialog which can be used to show the current state of a long var progress VQ progressDialog Saving Images Cancel 0 for var x 0 x amp lt dm getDimX x set posi progress setValue x progress hide Shows input window to ask for a floating point number e g Var radis VO lt getDouble Smocthing Radius 3 241 220 Defaults are shown above and these parameters are optional e g this will also VO getDouble Some Value See getDouble however returns an integer value Lets a user pick an item out of a list e g VQScript Objects and Object Me
298. s paa Sum Unit Conc Conc Unit Mean StdDev Min Max ZRange 1 M ROI 1 DEMO DEMO CT red 37720 301 76 1 05032e 06 HU 3480 65 HU mm 27 8452 139 166 794 793 2250 42 54 55 63 85 2 M ROI 2 DEMO DEMO NM red 37720 301 76 15 2599 pCi 0 0505696 uCi mm 0 000404557 0 000286029 1 13096e 05 0 00101808 54 55 63 85 Field available for comments ROI names A OI L click in the field will activate and allow comments to be entered atient The patient Name for this particular study The specific data set in the Study from which this Series data was calculated Displays the modality from which the data values for that row were calculated Modality olor The color of the ROI as drawn in the display Total number of voxels contained in the selected ROL Volume The volume of the selected ROI in units of cubic mm millimeters Voxels The total amount of attenuation activity in the selected ROI for CT and NM MR PET or SPECT data sets respectively Hounsfield units HU are used for CT data The SPECT units used by the Quantification panel may be specified in the Data Panel of the Configuration Tool Options include MBq kBq mCi and uCi Concentration The total amount of attenuation activity in the selected ROI for CT and NM MR PET or SPECT data sets respectively divided by the ROI The Quantification Table 65 VivoQuant Manual 11 12 2015 Hounsfield units HU mm are used for CT data The SPECT units used by the Quantifica
299. se of the unit should match what is listed in the Information window Convert supported units to from uptake and or concentration units If converting to from SUV please provide Weight and Injected Dose information note units must be specified defaults NM PT Convert unit Generates and stores quality control image of preprocessed image Results stored in the project webdisk of the repository specified below Save image data being preprocessed to specified iPACS repository below Specifies formats in which the data will be saved The numbers 0 1 and 2 correspond to multi frame MF module multi frame MF function groups and single frames one Z slice per file formats respectively For multiple data sets formats are separated by a comma as seen in image above The current formats of the loaded data sets will be displayed in this section upon opening the tool as well as in the Information section The second section 1s Storage Options where users may designate the PACS repository and Project folder where preprocessed datasets will be saved note Store data must be checked Repository Specify the repository Repositories can be configured in the DICOM tab of Configuration window Function 203 VivoQuant Manual 11 12 2015 Consult the DICOM settings page in the help guide for more information Specify the sub project GPACS or sub folder local path to which data will be saved Copy and paste pr
300. se through the different chapters which provide an in depth explanation of all of the post processing functions and instructions on their use The different sections covered in the manual are as follows e Installation e File Management o View e Post Processing e Tools e Help e Keyboard Shortcuts Manual 353 VivoQuant Manual 11 12 2015 a VivoQuant Manual 4 vivoquant com files manual index htm VQ Home page VivoQuant Installation VQ Manual Index Installation Quick Guide Keyword Index a Installation Details i Configuration E VivoQuant Manual z El Installation Memory Configuration Installation Quick Guide Installation Details Configuration Troubleshooting E Main Window Docks E View Modes Slice View Tile View Multi View MPR View E File Management Open DICOM data Open Reference Open Input 1 2 Open raw data Rename DICOM Save Image Save Movie Save Data Session VQ Script Print View Tools Help VQ Reporter Tool VQ Calibration Application Keyboard Shortcuts iPACSSync Tool The sections on the left can be viewed in detail by left clicking on them This will open up sub sections which can be viewed on the right Function 354 About Getting There To open the About section go to About under the Help menu Advanced Modules Help ee OO my et Request Hel C5 00 S See osa X Logout Ctrl Shift X W Registration B Enable Logf
301. seeeseeeeeeeeees 245 Addie VC asa DICOM Chenes a a a 247 A e o sauce abel decesetesetiaeaeoncuseee 248 UNC OW ORG aos 250 Registration nnani O O 251 GCC TNC PRE UU o O esas 251 A 0 oan ir eee NG ORS Wr ee PE ORR TC PE OREO OSI NPDE OR ON SNR E AAA ORL TUCO OUTER EE 251 Advanced Modules A A 252 Pl s m Modulis na AA A iA 253 Whole Bodt AOS RdA AAA a A EENE 254 A E N T E E ic uae hisece esrb aancaeeaancaseneat 254 Cetine Theressa A A 254 Admito Reference DA a a a a a E 255 sesmentins WMI NEToo sia duces dedeucaseseucuneats 256 EE E I E AA E EI E N A A E E A E E OEA A E E 256 NAAA E a AA 257 ROTOK Nd VIEW DOn bal a 257 Downldadino Sample IDE tii tt ia 258 SD Bran O AN 259 A A DT OP eT ee 259 IMRI Bram Atlas Segmentation Doo AAA EEA 260 A O 260 SAMA a e dd 260 E cer ee Mace Mt Sev roeenre ene eerree eye ome mn menee Trem Sen ere reser ser tert Srey sre ateMr cr arene Teter eater 260 Edad Data WhO te ROO sra ae eos ete oca coco poca cion S 261 Sel ectan Output REDOS ONY ii id 262 Customize Analysis Pipe as 262 MOHON CO CC UO IN tddi cestas 263 A sae E 263 VivoQuant Manual Table of Contents MRI Brain Atlas Segmentation Tool A atomical RE O18 Tl AU ON lla 264 Y A E 264 Adas REg GR AU O e Po a o OP non aay see la sted dat dome aes seotmesa seeds 265 General Lmear Modelo crac nicas 266 AS A 267 Tumor Segmentation TOOK a A Aereo EREET 268 DA O O O O scion A E 268 Eunice 269 As 269 SEE CTO SA id 270 A A O
302. series 2010 05 19 Contents The Registration panel includes VQ user information The panel includes fields for Institution Department Contact email address enabled VQ options license status and license expiration date The panel is also used for registering the VQ upon start up Three buttons Install key HW Keys Register assist the user in registering the VQ Registration of the VQ is required to unlock most of the VQ features Please see the Registration Quick Guide for details on registering the VQ a E Display Data Dicom Network vivoScript Registration License Key Institution Department Contact address exportDICOM exportimages exportMovies importBruker importRaw mprView multiThread multiView op3DROI opCropping opCutting opDistance_Measure opIsoCount opOthers Options opQualification opReorientation opTimeSeries registration segAtlasNMCT segAtlasfMRI segTumorAnalysis segWholeBody sessions tileView toolsCT toolsDICOM toolsSPECT tripleView vendorINVICRO volRender vascrint Expires 2028 12 31 To register please fill out form and hit Register If you already have a license key please install it with Install key Show Key Install key HW Keys Registration 251 AdvancedModules The Advanced Modules Menu contains a wide range of tools available for a variety of post processing applications e SPECT Tools e QuantiCalc Specific
303. sitory Allows data to be copied to a local folder If checked a pre defined shift will be applied to Apply default jreconstructed SPECT data when it is opened See shift Reorientation for more details on setting default If checked CT and NM reconstructions will begin automatically when the Open button is applied to projection data in the Study Browser Auto start reconstruction 338 VivoQuant Manual 11 12 2015 z dimension than in the x and y dimensions will be interpolated to have isotropic voxels when the Open button is applied To prevent interpolation from being performed on data with non isotropic voxels check Force planar Data Formats Data with dcm dc3 or dicom extensions are supported in the Data Browser by default To edit this setting and to configure loading in extension less data from the Data Browser navigate to the DICOM Settings page Study Browser The Study Browser displays the data found in the selected Repository The Filter Show Data Type and Find options can be used to limit the data displayed in the Study Browser In all cases the data is opened with either the Open button or the Append button The Open button will unload data currently open in VQ and load the highlighted data as Reference Input 1 Input 2 etc The Append button will leave the currently loaded data unchanged and append the highlighted data This appended data may be accessed via the Data Manager At the top level
304. st QString amp directory QString importMultiIMHD openRGBSliceViewer openDICOM openDICOMLocal print zoomIn zoomOut zoomOut normalSize toggleFullScreen setGlobalMinMax b toggleShowRGB bool b setRGBChannel about showManual requestHelp registration savelmage fileName type saveMovie fileName type scaleImage float f enableOpt int mod bool b showImagePreview int idx checkForUpdate bool verbose false forceCheckForUpdate loadDicomFromBrowser artCTRecoFromBrowser crosstalkRemoval showMinMaxTool showHistogram bedRemoval activeChanged int selection bioDistVis update Window Title unloadedData loadedData int idx showHints mainWin Object VivoQuant Manual 11 12 2015 Open BrukerMR file via dialog box Open MultiMHD file via dialog box Opens Data Browser to load data from DICOM repository Opens dialog box to load data from local DICOM repository Print images Instead of zoomIn please use VQO currentView setScaleFactor x Instead of zoomOut please use VQO currentView setScaleFactor x Auto zooms to original size Toggles Full Screen mode Opens About VivoQuant Opens VivoQuant Manual Opens Request Help tool Opens Registration tab of Configuration menu Saves image with fileName types are listed below type e Slice Viewer 0 MIP 1 S 2 C 3 T 4 All 5 Everything e Tile Viewer 0 S 1 C 2 T 3 Screen 4 All See savel
305. stance Measures sinaloa lola 85 Polen O A A NUTETIET 85 Landmark based Co RegilstratlON oooooncccnnccnnccnnnnnnnnnnnnnnonononononnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnonnnnnnnnnnnnnns 86 TPC GC Ci ai Nodes aes oes oes ainia ic 88 Gen NCS ges hse tt iets a cid 88 RISTO SENG A a a taneous acct oataeceusaceumenstaanemtecn setae 88 COPOS tOdO TE AEAEE AE AREE E A T 90 GENS De eenen aaa an a stone a A 90 RIS IM OO oen Setscsstaceraciadtetotiaciausctostoagsuin taagiactsce nosct cn tasseaasensbabael doutiseteselacune otseeseases 90 ATOMO aaa ida 92 TTS EN CP E el etvcnen ats se aloes aan UO antes ap hensive erodes eevee 92 RIS OES WOO APO PPP no A A canoe emanates 92 A caseuubvaweceiavenssseausouaues 94 Ge TT NC ease sata sata eat sonia hee tae oe cegecewen oes oon ata E A 94 A A e oo nn a O Po nobcce nley suaatee siediet docinen sdetantia sotede esos 94 A A O Soa tate 97 MOI ANNE 99 A ee reee nartrae trew reset rer Tey ree stem ter umraner tee ree nr ret tier pr amen e eeenter ro ren nr Mere ever errr 99 o RO 99 AO O A A A INE INT 100 TWo Tissue Compartment Model 2 FCM hace a posi 100 One Tissue Compartment Model 1TCMDioooooonnnnnnnnncconononononononcnnnnnnnonononononononnnnnnnnnnnnnnnnnnnnnnnnnnnnss 102 Logan Graphical Method Logan Plot 104 VivoQuant Manual Table of Contents Modeling Simplified Reference Tissue Model SRTM cccccccccccccccecceeceeeeeeeeeeeeeaeaeeeessseesssseseeseeeeeeeeees 106 Simplified Reteren
306. stname Port Use localhost lower case for optimized local access Test OK Cancel mm ES 7P gt Pp I qdlI A Username Password Hostname demo ipacs spect ct com Port 80 Use localhost lower Y for optimized local access Name as shown in the repository selection box Can contain any alphanumeric Data Browser Repository Panel 22 VivoQuant Manual 11 12 2015 Repository Local folders are simple directories Type available on the local computer also via a shared network Such directories with many files take rather long to scan in this case the performance of a DICOM server 1s Superior Such DICOM servers are network services on the local or a remote computer They provide a database to efficiently browser study data An PACS server 1s an online PACS server a regularly used picture archiving and retrieval system for medical images Select a local directory All sub folders will be displayed as projects in the second repository drop down window Username and password are specific to the user for their site s iPACS system Hostname will be the site of the server for the PACS and Port is the communication channel through which the iPACS server communicates DICOM server A DICOM server is specified by a calling AET application entity title a called AET as well as a TCP address consisting of a host name and a port the default settings are localhost 104 The AETs have
307. t then the cropping function can be used to trim away the blank areas of the image Getting There The Cropping Tool can be accessed via the tool pull down menu on the VQ front panel File View Tools Advanced Modules Help e 98M0 Wgl t 2290 5 de Sco ew gt A B QuexScipis 4 O O 00 A Display Quantification Reorientation Registration Time Series Distance Annotation Checker board Arithmetics Filtering Modeling Using the tool Upon selection of the Cropping tool the standard view options disappear and red sliders are displayed in their File View Tools Advanced Modules Help oo ve ae 4 3 e SY M 88 0000 08 E y O SB ese m Slice View Cropping v E Quick Scripts gt 4 DO Y Operator amp X Display Palette Cropped Area Xx Y Z From 21 37 1157 To 153 1129 259 Embed 176 176 1452 Information Voxel mm Old size 176x176x452 35 2x35 2x90 4 New size 133x93x103 26 6x18 6x20 6 Auto crop Ref v Set Ov Resampling images to reference image took 0 1 sec Two red sliders appear for each view direction 1 e coronal sagittal and transversal The red sliders may be moved using the mouse click and hold on a slider and then move the mouse to move the slider or by using Cropping tool 90 VivoQuant Manual 11 12 2015 the arrow keys in the cropping dialog Manipulation of the red sliders creates a three dimensional rectangangular cropping volume The current voxel positi
308. t O 330 CAM O cess 333 Openin Dita ASAS A ANA A 334 Cetina Ehete ry man rar MeO Ce Om nents arrest re inne eae mae ee nan ee var 334 UCU OM acai titan OU O 334 A ON are a cea ease a senate scaeteseacamnscearnacss 335 A ge ane ass TET EAEE E AEE TE A E AEA E ERE tata SETENE TEE E AAA E 336 Dalee a A 338 SU BTOWS CE e E E taee tans eeeea me sauaasecomuaemucncgee 339 PRIN Re Cl Os tds 340 Within Database or IPACS Severa ice 340 Mithma Local REPOSTO Sioa E ane Muatadabnaid desi Gitvaats 341 A ea eat esac cascdca tase saa aeeus sce wannateu sacauuseaccedeuseuceuseasuccocauascaicuctenuseeulucstau AE EN 342 GCN TNC A PS E o PO PO UPS UE E R 342 A A A TN 342 A O E A UT 343 APPENA Dit SA 344 A A er nin ee vere 344 UCU ON e a ictats ieee etter teetG hal lee ed ese uae ita aU lla ee ia be a a at ith aa 344 A seseaae taama an Taee aa coencu tase ae a a eewte eases 345 AAA AA e En cute 346 Gettin Tte osa 346 A No A 346 SES A A E 348 Gens TN Is 348 A Lit oah cusuot casa E lado saesncnn oaneetasoueemtntaasee aaa ueanieentenson ace 349 j a E I PAP o oo A A EA E T E AE A 351 xii VivoQuant Manual Table of Contents DEDUS asne EEEE E N 352 Geine THET sane a A ANN 352 A A 352 Manual AS AAA E A AS AA 353 CT A ann vere 353 EU a a Sonera TN aE ee 353 ADOU Ls iis 355 A A a A ener perm ren nen N 355 AN a Ct 7 PP VOPR VOR Yor nae may ean oe CTI UTE 355 VO RED ORCC I vsin odes a tetas tecns vaca ES E T N aes A a 356 Howto MISE the VO Repo
309. t an Output Repository The Output section in the upper right corner of the GUI window allows the user to select an output folder and manage the format and number of output files Keep Data Steps Correlation Matrix Save QC Folder voi once a poe folder is selected oy the user which the user can select a local output folder Provide a prefix optional to be added to all output file names Adding a prefix 1s useful when performing multiple analyses that are being saved to the same output folder prefix Keep Data Check this box to save intermediate analysis results Steps including the original data set Correlation Check this box to save a region of interest Matrix correlation matrix spreadsheet Check this box to save before and after motion correction smoothing anatomical registration brain mask and or atlas registration QC movies and images Before After Customize Analysis Pipeline The pipeline section of the fMRI tool allows the user to fully customize their data analysis workflow Pipeline Motion Correction Smoothing Anatomical Registration Brain Mask Atlas Registration GLM The user can choose to enable or disable any of the following processing modules Select an Output Repository 262 VivoQuant Manual 11 12 2015 e Motion Correction e Smoothing e Anatomical Registration e Brain Mask e Atlas Registration e General Linear Modeling Depending on which processes
310. t can be used to measure the size of a tumor by measuring its length depth and width One of the most powerful options available with the distance measure 1s the capability to perform landmark co registration Getting There The Distance Annotation Tool can be accessed via the tool pull down menu on the VQ front panel File View Tools Advanced Modules Help SY SY M T aa 0000 08 T gt O BD eve ae oi Mu Slice View v oe i d Quick Scripts Y AS O avigation A Display 3D ROI Tool Quantification Reorientation Registration Time Series Using the tool Upon selection of the distance annotation tool the Distance Annotation operator is displayed The physical distance between two points can be measured by clicking on the green plus symbol to add an object To measure distance left click on two points of the image A line is displayed between the two points to show what 1s being measured In the Distance Annotation operator each line is identified by a unique color tag For each line the 3D start and end points of the line are displayed as well as the length of the line in mm Multiple distances can be measured on the same image and are easily distinguished by their unique color The results can be saved into an Excel file by clicking Save The Profile function enables a graphic plot of the distance to be displayed for both the reference and the input data Operator F a kL amp 9 amp TE Input Label
311. t location for adding and editing repositories including DICOM Servers local folders and PACS Servers DICOM Cache 241 VivoQuant Manual 11 12 2015 Repository SECURE fexampleproject therapeutic_track_1 20 134 A EN Projects 28 28 30 List of available repositories The bank of buttons immediately beneath the pulldown menu operate on the selected Repositories repository in this field Please click here to learn more about the DICOM repository section of the DICOM browser Check connection to DICOM repository Local folders are verified to exist and a C ECHO is sent to DICOM servers Add a new repository T Open the DICOM Editor Opens a Windows Browser that can be used to select a local folder as a Y Fetch all DICOM meta data l Remove repository from list DICOM Editor The DICOM Editor is used to add repositories including DICOM Servers PACS Servers or local folders General Information Displayed Name DOCUMENTATION DEMO i 300 ie OS C Repository Type Wir Local folder DICOM server 8 PACS EEE Calling AET Local DICOM folder Called AET Hostname Port Use localhost lower case for optimized local access Test OK Cancel mm ES 7P gt Pp I qdlI A Username Password Hostname demo ipacs spect ct com Port 80 Use localhost lower Y for optimized local access Name as shown in the repository selection
312. ta int 1 updatedData int 1 unloadedData changedActive setupLayout int type 0 resetLayout linkControls bool on paletteRangeUpdateO float from float to Sets Reference palette range paletteRangeUpdate 1 float from float to Sets Input 1 palette range paletteRangeUpdate2 float from float to Sets Input 2 palette range paletteNameUpdateO const QString amp name Sets Reference color palette to name SliceViewer Object 179 10 paletteNameUpdatel const QString amp name paletteNameUpdate2 const QString amp name palettelnvertedO paletteInverted1 paletteInverted2 toggleShowReference toggleShowInput1 toggleShowInput2 newDataComing int type newDataLoaded int type 1ewerConcurrentTasks VivoQuant Manual 11 12 2015 Sets Input 1 color palette to name Sets Input 2 color palette to name Inverts Reference color palette Inverts Input 1 color palette Inverts Input 2 color palette Toggles display of Reference Toggles display of Input 1 Toggles display of Input 2 callQuantiCalc int mod float activity QString actUnit callSpecActCalc int mod float activity float volume const Opens SPECT Act Calculator module and QString amp actUnit inputs activity volume and actUnit callSUVCalc int mod float activity const QString amp actUnit Opens SUV Calculator module and inputs float volume renderVTK enable VTK bool toEnable activity actUnit and volume Forces re render of VTK Viewer Enab
313. tatus is Running then the reconstruction is underway if it is Waiting then the reconstruction has yet to begin The status section will also indicate when it is storing a completed reconstruction and when it is about to start a new reconstruction Job List 292 VivoQuant Manual Status 11 12 2015 The status of the current reconstruction job along with the total number of scans to be reconstructed is displayed in the Status bar and indicates the percentage of data remaining to be reconstructed Log file File Menu The file menu in the main window offers the following functions in the BatchCT application Batch CT Status 1 57 AGE Jobs Help Hide Ctrl H Quit Ctri Q Details Patient Hounsfield calibration Stop service Ctr T 505072353640 ct exp time Start service J CT Helical Scan Topogram CT a opr 20070912 MoveUp MoveDown Current job MMM F EditJob DeleteJob 2008 04 30 15 02 47 Welcome to batchCT 1 57 2008 04 30 15 02 48 BatchCT started 2008 05 05 07 23 54 Job added batch 0505072353640 ct exp time CTReco CT Helical Scan 2008 05 05 07 23 54 Job started batch 0505072353640 Hide Hides the Batch CT window from the desktop Also reached using the Ctrl H keyboard shortcut Quit Quits the Batch CT application Also reached using the Ctrl Q keyboard shortcut Stop Stops the Batch CT application Also reached using Service the Ctrl T keyboard shortcut eae Starts the Bat
314. th the activity concentration to calculate the SUV Units for these entries are user selectable SUV Calculator Activity 20 0000 MBq Patient Weight 30 0000 Volume 0 5000 mil vw Injected dose 15 0000 Concentration 40 000000 MBg ml v SUY 88 8889 Amount of isotope as measured oli me in a dosimeter or with the NanoSPECT activity Concentration kBq ml The ratio of activity to volume MBq ml SUV Calculator 275 VivoQuant Manual 11 12 2015 The amount of R successfully injected into the subject The specific uptake value SUV given the patient weight activity concentration and injected dose specified in the other fields mg ml g ml kg ml g l g mm kg mm Function 2 6 Crosstalk Removal The Crosstalk Removal tool is used to remove crosstalk photons in dual isotope SPECT images The limits in energy resolution inherent to SPECT imaging result in some overlap between the energy spectra of isotopes with relatively similar peak energies For example in dual isotope I 123 and Tc 99m imaging some I 123 photons will spill over into the Tc 99m window and vice versa The Crosstalk Removal tool is applied to projection data to remove these spill over photons or crosstalk This function will soon be implemented into the HiSPECT reconstruction software solution Getting There Crosstalk Removal is available in the Tools Menu in SPECT Tools File View Tools Advanced Modules Help SY
315. the zip file to a local machine and then please email support invicro com with a link to your report NOTE A contact email must be included to Save or Send the report Controls Your name Demo User Your mail address demo worldwideweb com Save Send Please contact support invicro com should you have any questions How to use the VQ Reporter Tool 361 IPACS Sync The PACS Sync application is designed for batch two way data transfers between the WebDisk of a specific PAGS project and a local storage location Directories and files are synchronized between the source and destination locations and data transfers are authorized by an PACS user s account permissions Batch Transfer Data to and from the PACS Browse the following links to learn more about using iPACS Sync to batch transfer data e Download latestiPACS Sync Application e Run a Sync Job e Configure a Sync Job Download WebDisk files in batch using iPACS Sync To execute a one time download of all WebDisk data for a particular project locate the project on the WebDisk and click on iPACS Sync URL located under the Other Links header on the right side of the page Other links Edit header footer sideba Public links PACS Sync URL Copy the URL that is provided and open the iPACS Sync client Go to Jobs gt Quick Sync and paste the URL into the window that appears and click OK The user will be prompted to select a folder to which the data can be downloaded
316. thods 171 VS VivoQuant Manual 11 12 2015 getItem title label value items var item VQ getItem Some Item item 1 item two current 0 a ean Cee Allows user to input a line of text returned by this function getLocalPath caption startdir Allows the user to select a local directory after being presented with the messag getSavePath const QString amp caption QString getLocalFiles const QString amp caption Select files const QString amp startDir QString getVivoScriptDir Returns VivoScript directory mkdir path subdir Creates the subdirectory subdir at the path specified by path fileExists path If the file specified by path exists returns true otherwise returns false minMaxTool Returns the VQ Min Max Tool object see below Returns whether the script is started interactively or non interactively by using isInteractive command line switch See also setInteractive and quit setInteractive b Sets interactive or non interactive mode is TestMode setTestMode bool b true lumiQuantMaster dicomBrowser DicomRepository rep Creates and returns a DICOM repository object e g var folderUnix VO dcmRep folder path to dir var folderWin VO dcmRep folder c path to dir dcmRep repURL var ipacs VQ dcmRep ipacs username password ipacs invicr var ipacss VQ dcmRep ipacss username password ipacs invi var dicom VO demRep dicom calling called dicom host p
317. tically In these cases the nondisplaceable and bound tissue compartments may be collapsed into one compartment that represents both the nondisplaceable and specifically bound tracer within the tissue 2 In these cases apparent transfer of ligand from tissue to arterial plasma is represented by the parameter k and Vy K K When a tracer that specifically binds to a target can be represented by a 1TCM as above and has a reference region the distribution volume ratio DVR can be calculated DVR V Vyp where Vyp is the estimated distribution volume in the reference region Binding potential BPyp can then be calculated by BPyp DVR 1 Model Assumptions This model makes the following assumptions e The tracer binds reversibly e Nonspecifically bound ligand equilibrates rapidly with free tissue ligand e Compartmental model assumptions The tracer kinetics or behavior can be represented by a compartmental model Tracer concentration within each compartment is well mixed and does not vary spatially 4 First order kinetics may be used to describe exchange of ligand between compartments Note Violation of any of these assumptions may produce biased parameter estimates While the model will still run in VivoQuant the estimated parameters may not accurately reflect the true tracer kinetics Required Inputs This model requires the following inputs e Metabolite corrected arterial plasma input curve e ROI s or voxels Outpu
318. tion panel may be specified in the Data Panel of the Configuration Tool Options include MBq mm kBg mm mCi mm and uCi mm The average amount of attenuation activity in the Mean selected ROI The standard deviation is a measurement of the variability in attenuation activity in the selected ROI from voxel to voxel The smaller this value the more uniform the distribution of attenuation activity in the ROI Min The minimum attenuation activity value of the voxels in the selected ROI Max The maximum attenuation activity value of the voxels in the selected ROI Specifies via slice numbers the distance spanned ZRange l by the axial sliders Quantification Table Options Right click on any one or any number of entries in the Quantification Table to view the following various options Volume 3 Sum Unit Conc Conc U mm Voxels 35793 286 344 3 28615e 06 HU 11476 2 HU mm 35793 286 344 Ci 0 0337488 pCi m 35875 287 4 56228e 06 HU 15896 4 HU mm 35875 287 Ci 0 00650698 pCi m Plot data Data to Quanti Calc Data to SpecAct Calc Data to SUV Calc Q Submit RO 6 to iPACS M Remove line Y Cleartable Plot data Plots the selected data on a line graph Quantification Table Options 66 VivoQuant Manual 11 12 2015 Data to Calculates the Quantification factor with the Quanti Calc acquired data Calculates the specific activity with the acquired Data to SUV Calculates the sta
319. tional inputs For more on keyboard shortcuts in VQ please see Keyboard Shortcuts Function Selection of the append data option opens a navigation window from which the input data set may be selected Append Data 344 VivoQuant Manual 11 12 2015 t dh DEMO Search DEMO Organize v New folder gt mm WY Favorites A de customers El Desktop Je Downloads PEJ y Recent places DEMO inp mhd DEMO inp raw DEMO ref mhd DEMO ref raw 2 Homegroup de Desktop E Documents test inp mhd test inp raw test ref mhd test ref raw Je Downloads db Music E Pictures B Videos E Windows8_OS C v File name v Data files ras raw zraw bi v Coment File Formats VivoQuant is capable of handling a variety of file formats The default options include 1 DICOM dem dicom 1 2 TRaster ras res bin 3 Raw raw 4 Image Files png tif tiff jpg jpeg bmp 5 Other img nii mhd mha fdf dc3 vol There also exists an option for displaying All Files and not just those with the above formats Function 345 Open Raw Data This option is used to load the raw data from studies Getting There To load raw data go to Open raw data under the File menu File View Tools Advanced Modules Help Function Data Browser Ctrl D 2mm 9f1s Open Local Data gt W Replace Data Ctrl 0 caos Ctrl 3 Append Data Ctrl N Save Movie Ct
320. to the currently selected ROI in the ROIs drop down menu near the bottom of the window If you would like the voxels that are being added or removed from the ROI to be put in an ROI other than the one currently selected mark the Map to checkbox and choose the ROI to put the new voxels in from the drop down menu to the right To perform the erosion or dilation click the green checkmark button Painting Tools 48 VivoQuant Manual 11 12 2015 Operator a x eo wv 10312 Use a sphere or circle to paint ROI over data a O Sphere _ 2D only O Cylinder 12 px Cube C Sync Pos Erode Dilate to remove add layers of voxels to an ROI C Map to Liver e 5 Dilate 4 Dilate 3 Dilate 2 Dilate 1 Dilate 1 Erode 2 Erode 3 Erode 4 Erode 5 Erode C Current Slice only 11111 Do H Brain v Operator a x Rojo x z Use a sphere or circle to paint ROI over data O Sphere C 2D only O Cylinder 12 px 5 O Cube C Sync Pos Erode Dilate to remove add layers of voxels to an ROI 5Dilate v Mapto ROI 6 gt Y C 2D only C Current Slice only Re render ROI wytk ROls xx WM Brain z 2D Drawing Tools The 2D drawing tools match the options available within the Quantification Tool Operator Gx Use the drawing tools to make 2D ROI perimeters and apply them when ready Global Rotate Shift Wheel Scale Alt Wheel Po
321. totais 146 A OMIA CNG apc tans AS 147 A ESPACE ESN EN ROR EET A ETC RETO ORIN 147 Mae VVC pass ciao si 148 View MENU AAA A AAA 149 Sice NUMDEE ii AAA RE Ra 150 Greta oral O PE PO E O 150 o O 150 Cross TALES ii ii 151 A e OP iO II IS 151 NIN 151 Position Labels ina Ai 152 Geine ales owmeeeerre eeeecen ee treme rer unre A 152 AO 152 Patient Name ai cd 153 GEE Te he ta ca PP oo studs sto ocsab sattacted bts tasters Custos way come eau scene seapaneansanucetadsaaanasce chun deta escucassseucateess 153 O EE AELIAN AA daar eo tee PATIA EI TET E AAEE ANE 153 Active Indicator A A a 155 Geine THES cr eeerrt tT eeer Meath orr meer er rate ner res eeee eer eennire hr erenee nT omen nner er Teen eros 155 o eases e E A E se eaeaas 155 La OMG na cd 157 Cerna ENE tags o nO e II IS 157 EA A 157 A RERUN STC NNEC UENCE Te ET NET Me TORT mene eer Ee On Renee enn eee 157 A e e ls eo ARENT nee rate 158 MERGIS CO sSeee dataset O um aostaaaamedcnaatsaaaiatecasatacs 159 SEE SOIL ss ahh A O E 160 ESAS A aa wade teoalah A AAN 161 VivoQuant Manual Table of Contents LOMA iaa 163 A A ner rer 163 O A 164 LOON aida sais edit See 164 AN AC 164 A eee A a TANI Re ATR eT Teen SERS CRC A mS eerie ren ene ee 165 AS AA A eee NT Ney eater a nae eee 165 PUNO ZO ONG esas yates O O A O oem nom nea ana ienatreag saat ease tame 165 OOM A ON 167 VOS CEDE o A A AA A 168 TavaScrpEstructte Sana ciao 168 A Massey tates 168 PUIG LOM ssi A A DS lel las Wt sal
322. tracer and the experiment For characterized tracers we suggest reviewing the literature to see how the fixed k has been selected in different studies and the effect of the method to fix k on SRTM2 parameter estimates Generally k can be fixed to the median value estimated by a Simplified Reference Tissue Model 2 SRTM2 108 VivoQuant Manual 11 12 2015 first pass of SRTM from all voxels with a BPND value gt a set minimum 3 4 or all voxels with a BPND value within a given range 5 The idea behind using BPND values to select voxels for inclusion in the median is to exclude voxels which maybe represent noise or have poor SRTM fit For most tracers there is a range of physiologically relevant BPND values Values outside of that range may be non physiological Other studies have fixed k to the population average value estimated from a 1 tissue compartment model fit to the reference region 3 or estimated k for each subject by a simultaneous SRTM fit including all target regions with coupled k 3 6 SRTM fit with coupled k is not currently available in VivoQuant Outputs Region level analysis e Plot of data from each ROI with SRTM2 fit e BPup R k gt and mean squared error MSE of fit are shown when the cursor is hovered over the model fit plot e BPxp R k gt and mean squared error MSE data and SRTM2 fit for each ROI can be saved out to CSV Voxel level analysis e Plot of data for each voxel with SRTM2
323. truction calibration and configuration features Help content including registration information and the manual are available in this menu Docks The Viewer Control MIP Control Data Manager and Operators are automatically placed into Docks upon opening Docks may be dragged and dropped into and out of the Main Window display and multiple controllers operators are dockable at any given time Thumbnails A bank of thumbnail icons is located below the Menus These icons provide fast access to features Function Icon Opens the Data Browser Opens a browser that will unload currently loaded data and replace it with the data selected in the Opens a browser that will append data to currently loaded data Opens the Save Image window Opens the Save Movie window B8 Changes the display layout to a 2 x 2 grid layout Changes the display layout to a 1 x 1 grid layout Changes the display layout to show the sagittal coronal and transverse data slices but not the MIP Changes the display layout to show only the transverse data slices Changes the display layout to show only the MIP Resets the zoom and pan within each viewport in the display Zooms in 25 Auto zooms to fit data to screen se Opens RGB color options Opens the Min Max Tool panel Menus 116 VivoQuant Manual 11 12 2015 El Opens the VivoScript Evaluation window Edits the VivoScript file selected in t
324. ts 12 380 o Filter Study Browser Patients Name A 4 ADC_M1_1_48h ADC_M1_1_48h gt _M1_1 3h ADC_M1_1_24h ADC_M1_1_144h Patients Name Patient ID Description Study Date 7 Data Show data type All data types 7 eae eB _ Apply default shift Auto Start reconstruction Force planar Stack 3D gt Append Open Transfer O Close StudyDate 2010 07 22 11 25 Open data Append data Export to Open in Delete Data FileType dem StudyDescription Patient ID Topo CT SPEC Topo CT SPEC Topo CT SPEC Topo CT SPEC Topo CT SPEC 11 12 2015 Finally using the keyboard shortcut Ctrl L will open the Reconstruction panel For more on keyboard shortcuts in VQ please see Keyboard Shortcuts Function The CT Reconstruction panel controls the parameters available for generating tailored CT reconstructions Getting There 284 CT Reconstruction File Help po RECONSUMUCLCION Parameters i Resolution CE 6 CET Algorithm Fast Cone Beam FBP v FBP filter typejcut off Frequency SheppLogan v 8 100 E ss Study Details Patientname Na volume 0x0x0 mm Yoxel Pixel size 0 0 mm Filter SheppLogan 100 0 frequency Estimated time 00 00 00 0 0 KOntrols O autostart autosave Reconstruction Parameters VivoQuant M
325. ts Region level analysis e Plot of data from each ROI with 1TCM fit e Vr K k and mean squared error MSE of fit are shown when the cursor is hovered over the model fit plot e Vr K k and mean squared error MSE of fit data and 1TCM fit for each ROI can be saved out to CSV Voxel level analysis One Tissue Compartment Model 1 TCM 103 VivoQuant Manual 11 12 2015 e Plot of data for each voxel with 1TCM fit Select the voxel for which you d like to see the model fit by clicking on 1t with the image viewer eV K k and mean squared error MSE of fit are shown when the cursor is hovered over the model fit plot e Parameter maps for Vy K k and mean squared error MSE References 1 Kinetic modeling in positron emission tomography Morris et al In Emission Tomography The Fundamentals of PET and SPECT Eds wermick MN Aarsvold JN 2004 2 Comparison of methods for analysis of Icinical 11C raclopride studies Lammerstsma et al JCBFM 1996 Link 3 Kinetic modelling using basis functions derived from two tissue compartmental models with a plasma input function general principle and application to 18F fluorodeoxyglucose positron emission tomography Hong et al Neurolmage 2010 Link Additional Resources Compartmental Models Vesa Oikonen Turku PET Center website Link Logan Graphical Method Logan Plot The Logan graphical method 1 was developed for reversibly bound tracers
326. uant Manual 11 12 2015 ROIs can be drawn freely on any of the three slice views The view currently being drawn in will be denoted Active in the upper left corner Each voxel can only belong to a single ROI Painting over an existing ROI with a new ROI will place the painted voxels in the new ROI unless the existing ROI is immutable See Editing an ROI to learn how to make an ROI immutable To erase voxels from an existing ROI paint over the existing ROI with the ROI selector set to Background Alternatively set the ROI selector to the existing ROI from which to erase voxels and hold down the Shift key while drawing The Shift key activates the background ROI for the painting tool even if another ROI is set in the ROI selector Sync Pos If Sync Pos is checked then the non Active slice views will be updated in real time to match the position of the drawing tool on the Active slice When this box is checked drawing times will typically be slower Operator Gx e ole lx ls Use a sphere or circle to paint ROI over data Sphere 2D only 3 A Cylinder 12 px 2 O Cube Y Sync Pos Erode Dilate to remove add layers of voxels to an ROI 5Dilate Mapto Live y _ 2D only _ Current Slice only Re render ROI ytk ROIs AS x Y D 68 Brain Erode Dilate The Erode Dilate tool can be used to remove or add up to 5 layers of voxels from the input ROL The erosion or dilation will be applied
327. uantification table table Submit to Submit the quantification data as a Data Point to the iPACS associated image on the iPACS Closes the Quantification panel and returns the VQ to Close et the Navigation screen The View Menu See Choosing the View Direction Cutting and Quantification Table Control The Options menu of the Quantification Panel provides a Cutting option and miscellaneous ROI functions File Menu 69 VivoQuant Manual 11 12 2015 File View Tools Advanced Modules Operator Help Append to table Ciri A Operator Clear table e Display Mode Options E W Load RO Ctrl Shift L v DO Save ROI Ctri Shift S O R F Submit to iPACS O Threshold Ref E View gt Ofc Ye BullyRad 12p Cut outside ALL Cut gt E Help inside Fa Global Rotate Shift Wheel Scale Alt Whee Submi LJ Select FOV outside Points Drag Left Remove Mid Open curve Shift Mid samira tities dd eii Curve Drag Shifi Lef Add point Double Click Close Right Buliv Add start point inside curve Remove outside curve Apply ROI to all slices selected slices Slices outside the set axial range will be cleared entirely Clears all voxels inside outside the ROI within the currently selected slices depending on which direction inside outside is selected Slices outside the set axial range will not be affected Apply ROI E Apply ROT a tios the ROI to every slice in the
328. ues of image at index i Returns dimension of voxel along X axis Returns dimension of voxel along Y axis Returns dimension of voxel along Z axis Returns key meta information for data at index id Updates meta information for data at index id e g set source to be such as 3D ROIs ar dm setDesc 0 __repository_url dcmRepURL dm setDesc 0 __ project projectName 178 VS VivoQuant Manual 11 12 2015 fill DICOMFromDesc Fills DICOM header with meta information getSOPUID nt 1 Returns SOPInstanceUID string for image at index i getSeriesUID nt 1 Returns SeriesUID as string for image at index i getStudyUID int 1 Returns StudyUID as string for image at index i setUniqueStudyID inti Sets setDataTypeAll int type getDataDetailsString int 1 0 getHeaderSummary nt 1 0 isEmpty Returns boolean t rue if Data Manager is empty hasData int 1 0 Returns boolean t rue if index i has data unloadData from num Unloads data from num sequential indicies starting at index from Using num 1 unloac swapData int a int b Swaps data at index a and b moveData QList amp lt int amp gt list int dst toggleDefaultShift bool on signalDataChange int 1 signalDataUpdated int 1 signalOptEnabled int 1 bool b nalDataAboutToChange int 1 SliceViewer Object Function Description setMinMaxCache id min cutOff setOperator AbstractOperator op updateDisplay forceUpdateDisplay updateDisplay changedDa
329. ues stored in the Min Max Tool For more on changing the minimum and maximum values see the Min Max Tool page The color palettes for a single frame of data can be edited in the Data Manager by right clicking on the color palette To edit multiple at once use ctrl or shift to select multiple frames then right click on one of the palettes and all will be edited together This technique can also be used for editing the Min Max for the palettes of multiple frames at once Using the Data Manager 194 Ordering Data VivoQuant Manual 11 12 2015 m DM cardiac Data List m cool Loaded 6 Memory cty4 Z default Available m exp Type CT CT Reconstruction mM flow Name 012610 saline Ml ge color y encata gl Dim 170x170x72 Vox 0 40x0 40 mm gray M green greenhot w hot hotblue m hotgreen E linear E linw m log lm nih nih fire Bl nih_fire2 E nih_ice phase prism ZE prism2 Z prism3 pto E ratio2black E red M smat E sokolov stepl0 Data may be rearranged into any order in the Data Manager A convenient drag and drop function allows users to quickly move data between positions Simply click on a dataset and drag it to the desired position A prompt will appear confirming the move Click OK to complete the move Data can also be quickly swapped with data in the Reference Input 1 or Input 2 positions Right click on a dataset and select Use as Reference Input 1 I
330. uffix masked Similarly if the Save QC box is checked then before and after masking QC images will be stored to the output directory as well as displayed under the brain mask tab as seen in image above Atlas Registration Check the Enabled box to co register the input data to an atlas Motion Correction Y Smoothing Anatomical Registration Brain Mask Atlas Registration GLM A l Enabled Data to Atlas El Atlas invicroRatAtlas54 Allow Inter Slice Interp Custom Atlas Before After The user can customize the atlas registration by adjusting the following settings e Data to Atlas Atlas to Data Choose to register the atlas to the data or vice versa Brain Mask 265 VivoQuant Manual 11 12 2015 e Atlas This should populate with the correct provided atlas based on the header information from the loaded data set e Key Choose to perform hemisphere Left Right or whole brain analysis using all regions in the provided atlas or using a mapping of all regions to a smaller number of larger regions e H F Flip Check this box to flip the data or atlas in the head foot direction before registration e Affine Check this box to allow the tool to scale and shear the data or atlas during registration if necessary e Allow Inter Slice Interp Check this box to allow the tool to interpolate the data or atlas between slices e Cutsom Atlas Check this box to provide custom atlas RMHA and a
331. utton A window will appear in which the user can edit the script Adding Script Shortcuts to the Toolbar 169 VivoQuant Manual 11 12 2015 Edit VivoScript C Users kgoettler Documents Projects misc tool vqs indude ipacs vqs indude VQSTools vqs var dm VQ dataManager var mw VQ mainWinQ var ctl VQ controler mw setViewMode Slice View 3D ROI Tool var roi VQ currentOp Create ROI for Processing roi addROICROI Pre Comp red VQ getWidget qt_tabwidget_tabbar setCurrentindex 1 roi setCurrentROI roi numROIs 1 jI Allow user to place ROI VQ suspend Place ROI Apply Connected Components on ROI VQ getWidget qt_tabwidget_tabbar setCurrentindex 3 VQ getWidget MagicSegmentationSelector setCurrentIndex 11 roi applyConnectedCompQ Create final ROI roi addROICROI Final red roifinal roi numROIs 1 ji Dilate 1 and map to new ROI VQ getWidget gt_tabwidget_tabbar setCurrentIndex 1 VQ getWidget cbMagicEDRadius setCurrentIndex 4 VQ getWidget cbErodeMapTo setChecked true VQ getWidget cbLayerROT setCurrentIndex roifinal VQ getWidget cbROIs setCurrentIndex 0 VQ currentOp applyErode Delete all but new ROI vari 1 while i lt roi numROIsQ 1 roi deleteROI i 0 Y Using the Peek Tool The Peek tool is used to reveal the names of elements called widgets in the operator GUIs for use in scripts The c
332. val Sets slice number in i view to val Fori 0 X 1 Y 2 Z Set the lower and upper bounds on the color palette range for the image at the ith setRange 1 from to position to the specified from and to values respectively where from and to are values between O and 1 setPal 1 palname Set the color palette for the image loaded in the ith position where palname is the name of an available color palette e g gray or nih_fire2 invertPalette 1 Invert the color palette for the image loaded in the ith position updatelmage adjustActiveState Better to use setAct ive see above palChange0 palChangel palChange2 MinMaxTool Object Function putePercentileCutoff int imageldx double percent clipMin0Q clipMax0 clipMinMin clipMaxMax apply Values resetValues recalc Values PercentileToImageVal centileButtonEnabled int imageldx copy ToMax aveNewPercentilesCS V appendPercentilesCS V showTable bool appendRow removeRow updateEnabledImages int imgldx show updateMIP updateDisplay updateAll showHistogram updateROIList MinMaxTool Object Description Sets all values below minimum to 0 Sets all values above maximum to 0 Sets all values below minimum to minimum Sets all values above maximum to maximum Applies current values Restores values from cache Recalculates actual minimum and maximum values Opens dialog box that allows user to save percentiles to
333. w The Whole Body Atlas Tool generates ROIs by registering a series of images in a Reference Library to the image that has been loaded in the Data Manager The Reference Images must each have a corresponding ROI The tool registers the images in the Reference Library to the loaded data and applies the same transform to the corresponding ROI The tool then works on a voxel by voxel basis classifying a voxel to the new ROI if a greater percentage of the reference sets classified that voxel as within the ROI than the threshold percentage set by the user Important factors that influence performance include image contrast animal positioning consitancy and the size of the reference library Probability 1 0 0 0 Getting There The Whole Body Atlas Tool 1s accessed by navigating to Tools gt Advanced Analysis gt Whole Body Atlas Here there are three options Whole Body Segmentation Tool Add to Library and Download Sample Library Whole Body Atlas 254 VivoQuant Manual 11 12 2015 File View Tools Advanced Modules Help y b i res w fi soom De op an LE tr CT En Display Bed removal Whole Body Atlas b Whole Body Segmentation Tool Atlas NM CT analysis Add To Library fMRI Tool Download Sample Library instali Atias Split RO to DICOM Average body calculation Specify ROI center Specify ROI center 2 Upload tumor ROI TumorPK Model Dosimetry Calc Adding to Reference Library The Reference Li
334. w percentile value with Patient Name Paitent ID Acquisition Time Percentile Cutoff Value and Units information from image metadata Load calculated percentile value into table Highlight the row to delete from table with left click and click the red X button 199 Histogram The Histogram tool is used to plot a histogram of the voxel values in a loaded data set Getting There The Histogram tool may be reached via the Tools Menu or by using the keyboard shortcut Ctrl Shift H See VO Keyboard Shortcuts for a complete list File View Tools Advanced Modules Help View contro FS S E MIP contro F6 Data Manager F7 Min Max Histogram Ctrl Shift H Workflow Assistant Pre processing Resample data DICOM gt Image amp Movie d Update Check Ctrl Shift U A Configuration Ctrl Shift C Function The Histogram Tool is operated via two control panels Data Controls and File Controls Data Controls Histogram Plot Data set 01 CT DEMO No bins 100 350 000 0 300 000 Max File Controls 250 000 PDF ee 200 000 a 150 000 100 000 50 000 2 000 3 000 HU Histogram 200 VS VivoQuant Manual 11 12 2015 Data Controls This pulldown menu allows the selection of the data set Data Set to be histogrammed No bins Sets the number of bins into which to divide the data Sets the minimum value for which data will be displayed The Set button automatically loads th
335. ymmetric Demons Symmetric Demons Diffeomorphic Demons Low 1 Demons resoluti Std Dev 1 00 px Register Automatic Slice by Slice Non Linear Registration 78 VS VivoQuant Manual 11 12 2015 How to Set a Default Image Shift One of the most powerful features of the NanoSPECT is its ability to automatically register SPECT and CT data to create anatomically and functionally valuable fused images Imaging without the application of any transformation typically results in data that are fused well within 1 5mm in any direction However taking the time to set up a default image shift can help insure that all image acquisitions are perfectly fused Make a simple phantom but one that breaks symmetry along multiple directions A syringe with an air bubble placed in the bed at an angle works well Collect an image CT of the phantom It is recommended that standard reconstructions or better are used for both the image and the CT to enable more precise transformation settings Uncheck the Apply Default Shift box located in the DICOM browser Data Show data type All data types x Bm E Y Apply default shift Y Auto Start reconstruction _ Force planar _ Force 3D Append Open Transfer O Close Stor Load the data into the VQ How to Set a Default Image Shift 79 10 VivoQuant Manual 11 12 2015 Use the reorientation tool to shift and or rotate the image data set Input 1 so that the image

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