VivoQuant User Manual

Version: Tue Oct 24 19:32:14 UTC 2017

 VivoQuant Manual

Table of Contents
VivoQuant Manual.............................................................................................................................................1

VivoQuant Installation.......................................................................................................................................2

Installation Quick Guide....................................................................................................................................3

1. Downloading........................................................................................................................................3
2. Installing..............................................................................................................................................4
A. Windows.......................................................................................................................................4
B. Mac OS X.....................................................................................................................................4
C. Linux.............................................................................................................................................5
3. License Registration.............................................................................................................................5
I. Active Accounts.............................................................................................................................5
II. Trail Accounts.............................................................................................................................5
4. Installing License Key.........................................................................................................................8

Installation Details..............................................................................................................................................9
Choose Components................................................................................................................................9
Choose Install Location.........................................................................................................................10

VivoQuant Configuration................................................................................................................................11
Configuration Panels..............................................................................................................................11
Getting There.........................................................................................................................................11

Display................................................................................................................................................................12
General...................................................................................................................................................12
Maximum Intensity Projection..............................................................................................................13
Color Palettes.........................................................................................................................................13

Data....................................................................................................................................................................14
Data Loading..........................................................................................................................................14
Quantification Options...........................................................................................................................16
Data Manager.........................................................................................................................................17

DICOM Settings................................................................................................................................................18
Getting There.........................................................................................................................................18
Configuration Dialog.............................................................................................................................18
DICOM Settings..............................................................................................................................19
DICOM Cache.................................................................................................................................20
Captures...........................................................................................................................................20
Data Browser Repository Panel.............................................................................................................20
DICOM Editor.................................................................................................................................21
iPACS Projects................................................................................................................................22
How to configure the NanoSPECT's DICOM Servers..........................................................................24
Adding VQ as a DICOM Client......................................................................................................26
Troubleshooting...............................................................................................................................27

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Network..............................................................................................................................................................29

Registration.......................................................................................................................................................30
Getting There.........................................................................................................................................30
Contents.................................................................................................................................................30

File Management...............................................................................................................................................31

Opening Data.....................................................................................................................................................32
Getting There.........................................................................................................................................32
Function.................................................................................................................................................32
Repository.......................................................................................................................................33
Filter................................................................................................................................................34
Data.................................................................................................................................................36
Study Browser.................................................................................................................................37
Right-Click function..............................................................................................................................38
Within Database or iPACS Server..................................................................................................38
Within a Local Repository.............................................................................................................39

Open Data..........................................................................................................................................................40
Getting There.........................................................................................................................................40
Function.................................................................................................................................................40
File Formats.....................................................................................................................................41

Append Data......................................................................................................................................................42
Getting There.........................................................................................................................................42
Function.................................................................................................................................................42
File Formats.....................................................................................................................................43

Open Raw Data.................................................................................................................................................44

Getting There.........................................................................................................................................44
Function.................................................................................................................................................44

Sessions...............................................................................................................................................................46
Getting There.........................................................................................................................................46
Session Manager....................................................................................................................................47

Operators...........................................................................................................................................................49

Navigation..........................................................................................................................................................50
Getting There.........................................................................................................................................50
Function.................................................................................................................................................50
Scrolling.........................................................................................................................................51
Zooming.........................................................................................................................................51
Panning...........................................................................................................................................51

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Navigation
Resetting Viewport.........................................................................................................................51
MIP-Specific Function..........................................................................................................................51
VTK MIP........................................................................................................................................51
Classic (non-VTK) MIP.................................................................................................................52
Tooltip............................................................................................................................................52

3D ROIs..............................................................................................................................................................54
Overview................................................................................................................................................54
Getting There.........................................................................................................................................55
ROI Creation and Deletion....................................................................................................................56
ROI Loading, Saving, and Quantification Tools...................................................................................60
Painting Tools........................................................................................................................................66
2D Drawing Tools..................................................................................................................................68
3D Segmentation Tools.........................................................................................................................69
Expert Settings.......................................................................................................................................75
Undo/Redo Functionality.......................................................................................................................77

Quantification++...............................................................................................................................................79
Getting There.........................................................................................................................................79
Using the tool.........................................................................................................................................79
Choosing the View Direction..........................................................................................................80
Choosing the ROI type....................................................................................................................83
The Quantification Table.................................................................................................................84
Quantification Table Options..........................................................................................................85
File Menu........................................................................................................................................87
The View Menu...............................................................................................................................88
Cutting and Quantification Table Control.......................................................................................88

Reorientation/Registration Tool......................................................................................................................90
Getting There.........................................................................................................................................90
Using the Tool.......................................................................................................................................90
3D and 2D Manual Options.............................................................................................................92
3D and 2D Automatic Options........................................................................................................93
Menu Options........................................................................................................................................95
Automatic Non-Linear Registration......................................................................................................96
Automatic Slice-by-Slice Non-Linear Registration...............................................................................97
How to Set a Default Image Shift..........................................................................................................97

Time Series......................................................................................................................................................101
Getting There.......................................................................................................................................101
Using the Tool.....................................................................................................................................101
Saving a Movie....................................................................................................................................101

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Distance/Annotation Tool...............................................................................................................................103
Getting There.......................................................................................................................................103
Using the tool.......................................................................................................................................103
Goto with-in the object..................................................................................................................104
Removing Distance Measures.......................................................................................................104
Profile............................................................................................................................................104
Landmark-based Co-Registration..................................................................................................105

Checkerboard..................................................................................................................................................107
Getting There.......................................................................................................................................107
Using the tool.......................................................................................................................................107

Cropping tool...................................................................................................................................................109
Getting There.......................................................................................................................................109
Using the tool.......................................................................................................................................109

Arithmetics......................................................................................................................................................111
Getting There.......................................................................................................................................111
Using the tool.......................................................................................................................................111

Filtering Tool...................................................................................................................................................113
Getting There.......................................................................................................................................113
Using the tool.......................................................................................................................................113
Bias Field Correction...........................................................................................................................116

Modeling..........................................................................................................................................................118
Getting There.......................................................................................................................................118
Function...............................................................................................................................................118
Models................................................................................................................................................119
MR Models...................................................................................................................................119
Pharmacokinetic Models..............................................................................................................119

Main Window..................................................................................................................................................120
Menus...................................................................................................................................................120
Docks...................................................................................................................................................121
Thumbnails..........................................................................................................................................121
View Modes........................................................................................................................................122
Operators.............................................................................................................................................122
Display.................................................................................................................................................123
Projections vs. Reconstructions.....................................................................................................124

Save Image Data..............................................................................................................................................126

Getting There.......................................................................................................................................126
Function...............................................................................................................................................126

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Save Movie.......................................................................................................................................................129
Getting There.......................................................................................................................................129
Function...............................................................................................................................................129

Docks................................................................................................................................................................132
Using docks..........................................................................................................................................132

Displays............................................................................................................................................................134

Slice View.........................................................................................................................................................135
Getting There.......................................................................................................................................135
Using the Slice View Display..............................................................................................................135
Scrolling Example.........................................................................................................................136
Scrolling Shortcuts Table..............................................................................................................137
Other Slice View Tools................................................................................................................138

Tile View..........................................................................................................................................................139
Getting There.......................................................................................................................................139
Using the Tile View Display................................................................................................................139

Multi View.......................................................................................................................................................142
Getting There.......................................................................................................................................142
Setting Up the Multi View Display.....................................................................................................142
Using the Multi View Display.............................................................................................................146
Navigation....................................................................................................................................146
Viewer Control in Multi View.....................................................................................................146

MPR View........................................................................................................................................................148
Getting There.......................................................................................................................................148
Using the MPR View Display.............................................................................................................148

Capture Viewer...............................................................................................................................................150
Getting There.......................................................................................................................................150
Function...............................................................................................................................................150
Info................................................................................................................................................151
Convert..........................................................................................................................................152
Edit................................................................................................................................................152
Image View...................................................................................................................................153

View Menu.......................................................................................................................................................154

Slice Number...................................................................................................................................................155
Getting There.......................................................................................................................................155
Function...............................................................................................................................................155

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Cross-hairs.......................................................................................................................................................156
Getting There.......................................................................................................................................156
Function...............................................................................................................................................156

Position Labels................................................................................................................................................157
Getting There.......................................................................................................................................157
Function...............................................................................................................................................157

Patient Name...................................................................................................................................................158
Getting There.......................................................................................................................................158
Function...............................................................................................................................................158

Active Indicator...............................................................................................................................................160
Getting There......................................................................................................................................160
Function...............................................................................................................................................160

Layout..............................................................................................................................................................162
Getting There.......................................................................................................................................162
Layout Options....................................................................................................................................162
Grid 2x2........................................................................................................................................162
Grid 1x4........................................................................................................................................163
MIP only........................................................................................................................................164
Slices only...................................................................................................................................165
Transverse only..........................................................................................................................166

Zoom.................................................................................................................................................................167
Getting There.......................................................................................................................................167
Function...............................................................................................................................................168
Zoom In.........................................................................................................................................168
Zoom Out......................................................................................................................................168
Normal Size...................................................................................................................................169
Full Screen.....................................................................................................................................169
Auto Zoom....................................................................................................................................169

Tools.................................................................................................................................................................171

VQScript..........................................................................................................................................................172
JavaScript structures............................................................................................................................172
Loop...............................................................................................................................................172
Function.........................................................................................................................................172
Array..............................................................................................................................................172
Hash...............................................................................................................................................172
The VQScript Toolbar.........................................................................................................................172
Adding Script Shortcuts to the Toolbar.........................................................................................172
VQScript Examples............................................................................................................................174

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VQScript Objects and Object Methods........................................................................................................175
VQ Object............................................................................................................................................175
MainWin Object...................................................................................................................................180
DataManager Object............................................................................................................................183
SliceViewer Object..............................................................................................................................184
Controler Object...................................................................................................................................185
MinMaxTool Object............................................................................................................................186
MultiViewer Object.............................................................................................................................187
IPACSWebDisk Object.......................................................................................................................188
ZipArchive Object...............................................................................................................................188
DataList Object....................................................................................................................................188
MIPViewer Object...............................................................................................................................189
MIPController Object..........................................................................................................................189
VTKController Object.........................................................................................................................190
VTKViewer Object..............................................................................................................................191
DicomRepository Object.....................................................................................................................191
3D ROI Operator Object......................................................................................................................191
Cropping Operator Object....................................................................................................................192
Reorientation/Registration Object.......................................................................................................192

Viewer Control................................................................................................................................................193
Getting There.......................................................................................................................................193
Function...............................................................................................................................................193
Sliders............................................................................................................................................194
Color Controls...............................................................................................................................194
Viewer Control in Multi-View.............................................................................................................194

MIP Controls...................................................................................................................................................197
Getting There.......................................................................................................................................197
Function...............................................................................................................................................197
Playing a MIP Movie....................................................................................................................198
VTK Viewer..................................................................................................................................198

Data Manager..................................................................................................................................................200
Getting There.......................................................................................................................................200
Using the Data Manager.....................................................................................................................200
Ordering Data................................................................................................................................202
Options..........................................................................................................................................202
More Information..........................................................................................................................203

Min/Max Tool..................................................................................................................................................204
Getting There.......................................................................................................................................204
Function...............................................................................................................................................204
Histogram......................................................................................................................................205
Percentile Tool..............................................................................................................................205

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Histogram........................................................................................................................................................207
Getting There.......................................................................................................................................207
Function...............................................................................................................................................207
Data Controls.................................................................................................................................208
File Controls..................................................................................................................................208

Preprocessing Tool..........................................................................................................................................209
Getting There.......................................................................................................................................209
Function...............................................................................................................................................209

Resample Data.................................................................................................................................................212
Getting There.......................................................................................................................................212
Using the tool.......................................................................................................................................212

DICOM............................................................................................................................................................213
DICOM Dump.....................................................................................................................................213
Getting There.................................................................................................................................213
Function.........................................................................................................................................214
Anonymizer..........................................................................................................................................216
Getting There.................................................................................................................................216
Function.........................................................................................................................................216
Rename DICOM Files.........................................................................................................................216
Getting There.................................................................................................................................217
Function.........................................................................................................................................217
Relabel Study.......................................................................................................................................217
Getting There.................................................................................................................................218
Function.........................................................................................................................................218

Rename DICOM Files....................................................................................................................................219

Getting There.......................................................................................................................................219
Function...............................................................................................................................................219

Keyboard Shortcuts........................................................................................................................................220

Autoradiography Calibration........................................................................................................................223
Getting There.......................................................................................................................................223
Function...............................................................................................................................................223
Getting Started...............................................................................................................................223
Image Calibration..........................................................................................................................224

Image Magick..................................................................................................................................................226
Getting There.......................................................................................................................................226
Function...............................................................................................................................................226
Split Movie Into Frames...............................................................................................................226
Join Frames to Movie....................................................................................................................226

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Image Magick
Change Delay................................................................................................................................227
Image to Poster..............................................................................................................................227
Image to Capture...........................................................................................................................227
How to make a dynamic movie....................................................................................................227

Update Check..................................................................................................................................................238
Getting There.......................................................................................................................................238
Function...............................................................................................................................................238

VivoQuant Configuration..............................................................................................................................239
Configuration Panels............................................................................................................................239
Getting There.......................................................................................................................................239

Display..............................................................................................................................................................240
General.................................................................................................................................................240
Maximum Intensity Projection............................................................................................................241
Color Palettes.......................................................................................................................................241

Data..................................................................................................................................................................242
Data Loading........................................................................................................................................242
Quantification Options.........................................................................................................................244
Data Manager.......................................................................................................................................245

DICOM Settings..............................................................................................................................................246
Getting There.......................................................................................................................................246
Configuration Dialog...........................................................................................................................246
DICOM Settings............................................................................................................................247
DICOM Cache...............................................................................................................................248
Captures.........................................................................................................................................248
Data Browser Repository Panel...........................................................................................................248
DICOM Editor...............................................................................................................................249
iPACS Projects..............................................................................................................................250
How to configure the NanoSPECT's DICOM Servers........................................................................252
Adding VQ as a DICOM Client....................................................................................................254
Troubleshooting.............................................................................................................................255

Network............................................................................................................................................................257

Registration.....................................................................................................................................................258
Getting There.......................................................................................................................................258
Contents...............................................................................................................................................258

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AdvancedModules...........................................................................................................................................259

Plug-In Modules..............................................................................................................................................260

Whole Body Atlas............................................................................................................................................261

Overview..............................................................................................................................................261
Getting There.......................................................................................................................................261
Adding to Reference Library...............................................................................................................262
Segmenting With The Tool..................................................................................................................263
Settings..........................................................................................................................................263
Select Images.................................................................................................................................264
Run Tool and View Log................................................................................................................264
Downloading Sample Library..............................................................................................................265

3D Brain Atlas Tool........................................................................................................................................266

Overview..............................................................................................................................................266

fMRI Brain Atlas Segmentation Tool...........................................................................................................267

Overview..............................................................................................................................................267
Install Atlas..........................................................................................................................................267
Getting There.......................................................................................................................................267
Load Data into the Tool......................................................................................................................268
Select an Output Repository................................................................................................................269
Customize Analysis Pipeline...............................................................................................................269
Motion Correction.........................................................................................................................270
Smoothing.....................................................................................................................................270
Anatomical Registration................................................................................................................271
Brain Mask....................................................................................................................................271
Atlas Registration..........................................................................................................................272
General Linear Modeling..............................................................................................................273
Run the Tool........................................................................................................................................274

Tumor Segmentation Tool.............................................................................................................................275

Overview..............................................................................................................................................275

Pharmacokinetic Modeling...........................................................................................................................276
Getting There......................................................................................................................................276
Function..............................................................................................................................................276
Input/Reference Function.....................................................................................................................276
Parent/Plasma Fraction..................................................................................................................277
Arterial Input Function..................................................................................................................278
Reference Tissue Compartment....................................................................................................279
Saving and Loading of Fraction, AIF, and Reference Region Data..............................................279
Additional Resources....................................................................................................................280
Models.................................................................................................................................................280

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Pharmacokinetic Modeling
Two-Tissue Compartment Model (2TCM)...................................................................................280
One-Tissue Compartment Model (1TCM)....................................................................................282
Logan Graphical Method (Logan Plot).........................................................................................284
Simplified Reference Tissue Model (SRTM)...............................................................................286
Simplified Reference Tissue Model 2 (SRTM2)..........................................................................288
Logan Non-Invasive Graphical Method (Logan reference plot)...................................................290
Patlak Analysis (Patlak Plot)........................................................................................................292

SPECT Tools...................................................................................................................................................295

QuantiCalc.......................................................................................................................................................296
Getting There.......................................................................................................................................296
Function...............................................................................................................................................296
Quantification Database................................................................................................................297

Specific Activity Calculator...........................................................................................................................298

Getting There.......................................................................................................................................298
Function...............................................................................................................................................298

SUV Calculator...............................................................................................................................................300
Getting There.......................................................................................................................................300
Function...............................................................................................................................................300

Crosstalk Removal..........................................................................................................................................302
Getting There.......................................................................................................................................302
Function...............................................................................................................................................302

Biodist. Visualization......................................................................................................................................303
Getting There.......................................................................................................................................303
Function...............................................................................................................................................303

Split Projections..............................................................................................................................................305
Getting There.......................................................................................................................................305
Function...............................................................................................................................................305

CT Tools...........................................................................................................................................................307

CT Reconstruction..........................................................................................................................................308
Getting There.......................................................................................................................................308
Function...............................................................................................................................................309
Reconstruction Parameters............................................................................................................310
Study Details, Progress, and Controls...........................................................................................310
Preview and Color Panel...............................................................................................................312
File Menu......................................................................................................................................313

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CT Reconstruction
Settings Menu................................................................................................................................314
Help Menu.....................................................................................................................................314
BatchCT Tool......................................................................................................................................316
Job List..........................................................................................................................................317
Status.............................................................................................................................................318
Log file..........................................................................................................................................318
File Menu......................................................................................................................................318
Jobs Menu......................................................................................................................................318

Hounsfield Calibration...................................................................................................................................320

CT Reconstruction..........................................................................................................................................324
Getting There.......................................................................................................................................324
Function...............................................................................................................................................325
Reconstruction Parameters............................................................................................................326
Study Details, Progress, and Controls...........................................................................................326
Preview and Color Panel...............................................................................................................328
File Menu......................................................................................................................................329
Settings Menu................................................................................................................................330
Help Menu.....................................................................................................................................330
BatchCT Tool......................................................................................................................................332
Job List..........................................................................................................................................333
Status.............................................................................................................................................334
Log file..........................................................................................................................................334
File Menu......................................................................................................................................334
Jobs Menu......................................................................................................................................334

Calibration.......................................................................................................................................................336
Getting There.......................................................................................................................................336
Function...............................................................................................................................................336

CT Geometrical Calibration..........................................................................................................................337
Getting There.......................................................................................................................................337
Function...............................................................................................................................................337

Calibration - MMP SPECT............................................................................................................................342

Getting There.......................................................................................................................................342
Function...............................................................................................................................................342
Templates.....................................................................................................................................344

Near-Field Uniformity....................................................................................................................................350
Getting There.......................................................................................................................................350
Function...............................................................................................................................................350

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Dosimetry Calc................................................................................................................................................354
Getting There.......................................................................................................................................354
Function...............................................................................................................................................354
Getting Started...............................................................................................................................354
Using the AUC Calculation...........................................................................................................355

Help..................................................................................................................................................................358

Debug...............................................................................................................................................................359
Getting There.......................................................................................................................................359
Function...............................................................................................................................................359

Manual.............................................................................................................................................................360
Getting There.......................................................................................................................................360
Function...............................................................................................................................................360

About................................................................................................................................................................362
Getting There.......................................................................................................................................362
Function...............................................................................................................................................362

VQ Reporter....................................................................................................................................................363
How to use the VQ Reporter Tool.......................................................................................................363

iPACS Sync......................................................................................................................................................369
Batch Transfer Data to and from the iPACS.......................................................................................369

Configure a Sync Job......................................................................................................................................370

Create a Sync Job using the Wizard....................................................................................................370
Configuring Additional Settings..........................................................................................................371
iPACS Setup........................................................................................................................................372
Directory Setup....................................................................................................................................372
Scheduler..............................................................................................................................................373
Notifications.........................................................................................................................................373
Advanced.............................................................................................................................................374
Store Job..............................................................................................................................................375

iPACS Sync GUI.............................................................................................................................................376

Run a Sync Job....................................................................................................................................376
Icon Descriptions.................................................................................................................................376
Quick Sync...........................................................................................................................................376

Troubleshooting..............................................................................................................................................378
Trouble shooting categories.................................................................................................................378
Service Reporter...................................................................................................................................378

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Memory configuration....................................................................................................................................379
Windows 32-bit....................................................................................................................................379
Windows 64-bit....................................................................................................................................379
Mac OS X............................................................................................................................................379

Debug...............................................................................................................................................................380
Getting There.......................................................................................................................................380
Function...............................................................................................................................................380

Saving 3D ROI Images/Movies......................................................................................................................381

Known issues with graphics card.........................................................................................................381

VQ Keywords..................................................................................................................................................382
.............................................................................................................................................................382
/ 2 3 A B C D E F G H I J K L M N O P Q R S T U V W Z..............................................................382
/............................................................................................................................................................382
2...........................................................................................................................................................382
3...........................................................................................................................................................382
A...........................................................................................................................................................382
B...........................................................................................................................................................382
C...........................................................................................................................................................383
D...........................................................................................................................................................383
E...........................................................................................................................................................384
F...........................................................................................................................................................384
G...........................................................................................................................................................385
H...........................................................................................................................................................385
I............................................................................................................................................................385
J............................................................................................................................................................385
K...........................................................................................................................................................385
L...........................................................................................................................................................386
M..........................................................................................................................................................386
N...........................................................................................................................................................386
O...........................................................................................................................................................386
P...........................................................................................................................................................387
Q...........................................................................................................................................................387
R...........................................................................................................................................................387
S...........................................................................................................................................................388
T...........................................................................................................................................................388
U...........................................................................................................................................................389
V...........................................................................................................................................................389
W..........................................................................................................................................................389
Z...........................................................................................................................................................389

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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's
iPACS® data management platform for bi-directional data transfers.

VivoQuant Manual 1
VivoQuant Installation
• Installation Quick Guide
• Installation Details
• Configuration
• Memory Configuration

VivoQuant Installation 2
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.

Development releases are available for download here listed in the Download section on the left side.

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:

Class Description
stable release

Installation Quick Guide 3

 VivoQuant Manual 10/24/2017

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 have undergone testing by inviCRO and are
send to our partnering expert users for evaluation.
release Depending on the feedback of actual users release candidates are
candidates 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.
beta versions
You can use these versions are your own risk.
Beta versions have a limited life time of 30 days.
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 10/24/2017

Double-click the VivoQuant installer package to start the installer.

The only step necessary to complete the installation is to select the disk VQ 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
I. 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 VivoQuant licenses Click Here.

II. 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

• Download the latest stable version of VivoQuant. Once you have successfully installed VivoQuant,
you will be prompted to register your computer. Click 'Yes'.

• 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 10/24/2017

• After clicking 'Register', your Internet Browser will load and navigate to the license registration
confirmation page.

Click 'Submit' and a trial license will be sent to you shortly.

b. Pre-approved Licenses

• 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

II. Trail Accounts 6

 VivoQuant Manual 10/24/2017

the license key. After the software has been successfully installed, you will be prompted to register
your computer for a license. Click 'Yes'.

• Enter the company code provided in the email along with the email address to which the registration
email was sent.

• 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.

II. Trail Accounts 7

 VivoQuant Manual 10/24/2017

• After you click 'Submit', the system will validate the request. If successful, the below page will
appear.

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 ->
Registration within VivoQuant and click on 'Install key'. Your VQ is now registered and fully operational.

If you experience any problems, please contact [email protected].

4. Installing License Key 8

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 it is typically safe to accepts the default settings,
though.

Choose Components

Component Description
Unless you already have Qt installed on your system, it is highly
Qt4 libraries
recommended that you use the version coming with VQ.
Installs the IM programs mpeg2encode (required for generation of
ImageMagick
MPEG movies) and convert (general tool to convert image formats,
binaries
not required by VQ).
After installation, the manual is available by pressing <F1> on the main
VQ screen, or using the Help|Manual menu.
Manual
Alternatively, you can also find the manual online at
http://www.vivoquant.com/manual/index.html.
BatchCT Install the BatchCT service, allowing reconstruction of CT data sets
service without further user interaction.
Experimental options to allow VQ to be used in an 21 CFR part 11
21 CFR part 11
environment (FDA's electronic record keeping regulations).
Options Shortcut on desktop Install an VQ icon on Windows desktop.
Place a quick start icon for the CT
CTReco shortcut on
reconstruction module on desktop. CT
desktop
Reconstruction
DicomBrowser Allows starting of VQ with opened
shortcut on desktop DicomBrowser quickly. Open DICOM data
Add local DICOM Adds an example DICOM folder to the list of
folder repositories.
Add DEMO iPACS

Installation Details 9
 VivoQuant Manual 10/24/2017

Allows access to an online PACS system to

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
Enable update check
download and install them.
Please see Update Check for details.
Exports data required by VQ
Run BatchTool-Dump BatchFileGenerator from HiSPECT database.
BatchTool Generator
These options should be reserved for advanced users.
Reduces the amount of memory required
Disable use of normalization in CT reconstruction, however,
matrix invalidates HU calibration for helical
acquisition orbits.
CT Disable
Forces VQ to use only a single thread
options
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 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:

• Display
• Data
• DICOM Settings
• Network
• Registration
• 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.

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 11
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
Option Description
Several font styles are available for display in the
Font Style
Main Window.
Controls the size of the displayed text in the Main
Font Size
Window
Cross-hair A variety of cross-hair styles are available for use in
style the Main Window.
Cross-hair Cross-hair color options include red, yellow,
color magenta, white, green, and blue.
Pal files hold the color map information for the
Pal Path
different Color Palettes available in the VQ.
Preview Displays a preview of the font and cross-hair
Panel 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.

Display 12
 VivoQuant Manual 10/24/2017

Maximum Intensity Projection

Option Description
Frame
Sets the amount of time for which each MIP
Time -
projection image is displayed in a saved movie.
Display
Frame
Sets the delay time between MIP frames in a saved
Delay -
movie.
Movie
With sync mode enabled, only completed MIP frames
will be displayed. With sync mode disabled, the MIP
Sync mode
will freely rotate at all times but will display a
message in place of the MIP for uncompleted frames.
Color Palettes
Option Description
Sets the method for determining the range of the color
Type palette. Options are to set the Window Min/Max or the
Window Level/Width
The default Color Palettes for the first three loaded
Palette volumes of each Modality are set. Inputs beyond the third
of a particular modality follow the palette of third.

Maximum Intensity Projection 13

Data
The Data panel contains options for data handling, including data loading and quantification.

Data Loading
Use the &apos;Data Loading&apos; panel to set loading options.

Option Description
Check the box to disable the MIP viewer upon
Disable MIP
loading. For large datasets, this can improve the
viewer
loading speed.
Check the box to enable VivoQuant to ask for
Ask Disable your permission to initialize the MIP viewer upon
MIP loading. For large datasets, this can improve the
loading speed.
Choose &apos;yes&apos; to allow the addition of
zero-padding to a reference image to match the
volume of an input image, or &apos;no&apos; to
Grow keep the reference image size static (and
reference to potentially crop the input image, if it is larger
input volume than the reference). Choose &apos;ask&apos; to
allow a window to appear upon loading in an
input 1 data set that is larger than the image in the
reference position.
Max voxsize Specify the maximum pixel ratio (largest pixel
ratio for vol. dimension / smallest pixel dimension) by which a

Data 14
 VivoQuant Manual 10/24/2017

data set is interpolated as a volume image file.

Specify the minumum allowed voxel width. Data
will be resampled upon loading if their voxel
MinVoxSize 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
Anchor input
be anchored at the following options: center,
data
head, or foot.

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, i.e. MaxVoxSizeRatio < 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 15
 VivoQuant Manual 10/24/2017

If the pixel ratio of the loaded image is less than the given threshold, i.e. MaxVoxSizeRatio > 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,

• If the &apos;Force Planar&apos; check box is checked in the Data Browser, then the image will
load in planar mode regardless of the value set for MaxVoxSizeRatio.
• If the &apos;Force Planar&apos; check box is unchecked in the Data Browser, then the image will
load in the appropriate mode according to the value set for MaxVoxSizeRatio.

Quantification Options
Use the &apos;Quantification Options&apos; panel to set options used by the Quantification++ Operator and
the 3D ROI Operator.

Option Description
Select the unit to be used for quantifying SPECT
data. Options include MBq, kBq, mCi, and µCi. Note:
Concentration units (e.g. nCi/cc) will not be
Units of
converted to the unit of activity specified. The Tumor
Activity
Segmentation and NM/CT Brain analysis plugin
modules do support converting from concentration
units to units of µCi.
CSV Choose the CSV file delimiter of their choice, applied
Separator when saving Quantification data.

Quantification Options 16
 VivoQuant Manual 10/24/2017

Data Manager
In the "Data Manager" panel, there is a checkbox to enable or disable a confirmation message when moving
data.

Option Description
confirm Check to enable a confirmation message when
moving rearranging data in the Data Manager
Show Check to display the seconds in the study date
seconds in column in the DICOM browser. VQ has to be
Browser restarted to configure this change.
Check to apply a default reorientation to data being
Apply
loaded into VQ. The default shift can be defined in
default
the Reorientation/Registration operator. For more on
shift
this, please see the Reorientation/Registration page

Data Manager 17
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.

The second method is to select the Configuration option in the Tools menu and to then click on the DICOM
panel.

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 18
 VivoQuant Manual 10/24/2017

DICOM Settings

Option Description
Location of local DICOM database.
Allows optimized internal access to the
DB path
Mediso DICOM database. See
Optimized local access for details.
List of available repositories. The bank
of buttons immediately beneath the
Repositories
pulldown menu operate on the selected
repository in this field
Check connection to DICOM
repository. Local folders are verified to
exist and a C-ECHO is sent to DICOM
servers.
Add a new repository
Delete selected repository
Open the DICOM Editor
Shows list of additional dictionaries used
by the DICOM library. Please set
Dictionary environment variable DCMDICTPATH to
set this value. For more on the DICOM
dictionary, see DICOM Dump
Port over which the DICOM peer sends
Rcv Port
data.
When this box is checked, the palette
window will be loaded in accordance
load palette with the image data. When this box is
% not checked, the palette window will be
set to whatever the window was set to
last.
Checking this box enables support for
DICOMDIR
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 19
 VivoQuant Manual 10/24/2017

DICOM Cache

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.

Option Description
Size in Mb of the data currently stored in the
Current DICOM Cache. The percentage to the right
Size of the field indicates how close the cache is
to capacity.
Maximum amount of memory that can be
Max
made available for the DICOM Cache
size
(default = 1000.0 MB).
Length of time over which data will be
Life
stored in the DICOM Cache (default = 14
Time
days).
Clear Empties the DICOM Cache
Captures

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 20
 VivoQuant Manual 10/24/2017

Option Description
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.
edit: Open the DICOM Editor.
Opens a Windows Browser that can be
used to select a local folder as a
repository.
Fetch all DICOM meta data.
Remove repository from list.
DICOM Editor
The DICOM Editor is used to add repositories, including DICOM Servers, PACS Servers, or local folders.

Option Description
Name as shown in the repository selection
Displayed
box. Can contain any alphanumeric
Name
character.

Data Browser Repository Panel 21

 VivoQuant Manual 10/24/2017

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
is superior.
Such DICOM servers are network
services on the local or a remote
computer. They provide a database to
efficiently browser study data. An iPACS
server is an online PACS server, a
regularly used picture archiving and
retrieval system for medical images.
Local Select a local directory. All sub-folders
DICOM will be displayed as projects in the second
folder repository drop-down window.
DICOM
server
Username and password are specific to
the user for their site's iPACS system.
iPACS Hostname will be the site of the server for
server the iPACS 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.

iPACS server

An iPACS 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).

iPACS Projects
The iPACS 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 22
 VivoQuant Manual 10/24/2017

this example, an iPACS repository for "bioscan/demo" is being configured. The "bioscan/demo" repository
contains three projects.

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.

Select any project to view only data associated with that project.

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.

To simultaneously view all data belonging to a repository AND its projects, place a * at the end of the

iPACS Projects 23
 VivoQuant Manual 10/24/2017

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.

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:

Option Description
Displayed NSxxWS_DCMSRV (or customer's
Name preference)
Type DICOM Server
Calling AET INVIVOSCOPE
Called AET NSxxWS_DCMSRV

How to configure the NanoSPECT's DICOM Servers 24

 VivoQuant Manual 10/24/2017

Hostname localhost
Port 104

where xx is replaced with the NanoSPECT number, typically no leading 0 for numbers < 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 VQ 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.

Options Description
Displayed ACQ_NSxx_DCMSRV (or customer's
Name preference)
Type DICOM Server
Calling AET INVIVOSCOPE
Called AET NSxx_DCMSRV
Hostname nanospectxx
Port 104

where xx is replaced with the NanoSPECT number, typically no leading 0 for numbers < 10.

In place of hostname (i.e., nanospectxx), it is also possible to use IP addresses (i.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 25

 VivoQuant Manual 10/24/2017

Adding VQ as a DICOM Client

Start C:\Program Files\Mediso\DICOM Server\DICOMServerMgr.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.

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

Host Port
(AET)
HiSPECT LOCALHOST 3104
HiSPECT_BATCH LOCALHOST 3105
INTERVIEWXP LOCALHOST 11112
INVIVOSCOPE 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.

Example
Computer Calling AET Hostname Port
Number
Example NS5 ACQ
INVIVOSCOPE NANOSPECT5WS 23104
#1 Computer
Example NS13 WS
INVIVOSCOPE LOCALHOST 23104
#2 Computer
NS13 2nd IP Address or 2nd
Example
WS VQ-WS2 WS Computer 23104
#3
Computer Name

Adding VQ as a DICOM Client 26

 VivoQuant Manual 10/24/2017

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.

Option Description
Displayed NS13WS_DCMSRV (or customer's
Name preference)
Type DICOM Server
Calling AET VQ-WS2
Called AET NS13WS_DCMSRV
Hostname nanospect13ws (or IP)
Port 104

Troubleshooting
• 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).
• 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 (i.e., nanospect13ws) to the computer's IP address.
• Check the DICOM Server logfiles (on the computer that you want to access), located in C:\Program
Files\Mediso\DICOM Server\logs.

Troubleshooting 27
 VivoQuant Manual 10/24/2017

• Enable debugging in the VQ and collect output while trying to access the DICOM Server.

Troubleshooting 28
Network

The Network panel consists of two sections: Network Settings and Auto Import.

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-AutoImport directly will be automatically imported into the NS00WS_DCMSRV repository upon the
next restart of the VivoQuant.

Network 29
Registration
Getting There
The registration panel may be reached from the Configuration Panel or it may be reached directly via the Help
menu.

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.

Registration 30
File Management
The Data Browser contains a variety of options for loading, saving, publishing, and printing data. Options
include:

• Data Manager
• Open Data
• Append Data
• Open raw dat
• Open from iPACS
• Import
♦ Bruker MR
♦ Multiple Images
♦ RAW
♦ Capture Viewer
• Save Data
• Sessions

File Management 31
Opening Data
The Data Browser provides convenient access to files in a DICOM server or any other specified iPACS
Browser. Reconstructions can be started from the data browser and files may also be exported.

• Getting There
• 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.

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 32
 VivoQuant Manual 10/24/2017

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
Description Example
Option
Reduces project
list to all Type 'exampledata' in the projects
projects that filter to reduce the projects list to all
word
contain the projects with the word 'exampledata' in
given word in their path.
their path.
!word

Function 33
 VivoQuant Manual 10/24/2017

Reduces project Type '!exampledata' in the projects

list to all filter to reduce the projects list to all
projects that do projects that do not contain
not contain the 'exampledata' in their path.
given word in
their path.
An example of a commonly used
regular expression** is the choice
Reduces project operator, |, which matches either the
list to all expression before or the expression
projects that after the operator. For example, if the
&regexp
match the given user types '&exampledata|test' in the
regular 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.

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 to refresh the Study Browser.
Want to view all of the data again? Simply hit the clear filter button to empty the fields and hit 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 I123, enter *I123* 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.

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 VivoQuant Manual 10/24/2017

Before expansion:

After one click of the "X button":

After the second click of the "X" button:

Filter 35
 VivoQuant Manual 10/24/2017

Expanding large numbers of datasets can take several minutes.

Data
The Data section provides several functions for manipulating data, including sorting, finding, and opening.

This pull-down menu can limit the data displayed

Show data
in the Study Browser to a single modality (i.e.,
type:
CT) or data type (i.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
Open 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.
This button is used to append the data
highlighted in the Study Browser to the data sets
already loaded into VivoQuant. For example, if
two data sets are selected in the Data Browser
and three data sets are already loaded into VQ,
Append
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
Find available columns (Patient's Name, Study Date,
Study Description, or patient ID).
Allows data from a local folder to be imported
Import into another local folder, database, or iPACS
repository.
Export Allows data to be copied to a local folder.
If checked, a pre-defined shift will be applied to
Apply default reconstructed SPECT data when it is opened. See
shift Reorientation for more details on setting default
shift values.
If checked, CT and NM reconstructions will
Auto-start
begin automatically when the Open button is
reconstruction
applied to projection data in the Study Browser.
Force planar By default, data with voxel widths greater in the

Data 36
 VivoQuant Manual 10/24/2017

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, 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."

At the next level, single data sets from a study may be selected for viewing.

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.

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"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.

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 (i.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, highlight 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

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.

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Allows the data to be opened in an external

Open in...
Application.
Sends the file to the DICOM dump tool, which
Dump
displays the information contained in the DICOM
Header
headers.
Within a Local Repository
When working in a local repository (i.e., a local folder as opposed to data from a database or iPACS server),
the right-click button may also be used to delete data.

Within Database or iPACS Server 39

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 (i.e., from the Data browser), VQ
recognizes 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.

The second method is to go to "Open Data" under the File menu.

The third method is to use the keyboard shortcut "Ctrl+O". 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.

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File Formats
VQ can handle a variety of file formats. The default options include

1. DICOM: *.dcm, *.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 41
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 (i.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.

The second method is to go to "Append Data" under the File menu.

The third method is to use the keyboard shortcut "Ctrl+N" to load input 1 and "Ctrl+Shift+N" to load
additional 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.

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File Formats
VivoQuant is capable of handling a variety of file formats. The default options include:

1. DICOM: *.dcm, *.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 43
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."

Function
Selection of the "Open raw data" option opens a navigation window from which the raw data may be selected.

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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 is
imported to VivoQuant by clicking Load

Function 45
Sessions

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

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Session Manager
The Session Manager allows users to load previously 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.

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.

If exporting the session, specify a location on the local where the compressed zipacs folder will be saved.

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To load the compressed zipacs folder later, go to File -> 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.

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.

Session Manager 48
Operators
VivoQuant offers several operators for performing a wide range of image processing tasks.

• Navigation
• 3D ROI Tool
• Quantification++
• Reorientation/Registration
• Time Series
• Distance/Annotation
• Checkerboard
• Cropping
• Arithmetics
• Filtering
• Modeling

Operators 49
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.

Several methods exist for operating the slice control Navigator. 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.

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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
icon located on the toolbar

MIP-Specific Function
The functions for controlling the MIP are slightly 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.

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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.

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This information is also found in the Viewer Control. For more on using the Viewer Control, see the Viewer
Control page.

Tooltip 53
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
3. ROI Loading, Saving, and Quantification Tools
1. Load an ROI from disk
2. Save an ROI to disk
3. Center View on ROI
4. Render ROIs in the MIP view
5. Reset the camera view
6. Reset all ROIs
7. Show the image histogram
8. Load an ROI from an iPACS
9. Save an ROI to an iPACS
10. Merge ROIs from an iPACS or disk
11. Set quantification table columns
12. Show the quantification table
13. Save the quantification table to disk
14. Perform a cut on an image using an ROI
15. Show/hide the MIP data with the rendered ROI
16. Show/hide the 3D ROI table
17. Perform a copy/paste of an ROI set
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

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 is used to describe a particular
area or volume within an image for which the user wishes to characterize some quantity or quality.

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Getting There
The 3D ROI tool can be accessed via the tool pull-down menu on the VQ front panel.

When the 3D ROI Tool is selected a 3D ROI Tool operator window is displayed.

Each panel of the 3D ROI Operator window provides a grouped set of functionalities. Use the tabs to move
between panels.

Tab Description
ROI Loading, Saving, and
Quantification Tools
Painting Tools
2D Drawing Tools
3D Segmentation Tools

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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.

Icon Description
Add an ROI
Edit an ROI
Delete an ROI
Reset an ROI
Hide an ROI
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, increase or decrease the alpha values (a lower percentage will increase the transparency of an
ROI). Check "Hidden" to turn the ROI off in all views. Check "Immutable" to prevent edits to an ROI.

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.

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Edit an ROI. 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.

This will edit whichever ROI is selected in the ROI dropdown menu.

Another option is to right click on any ROI in the operator and select Edit ROI.

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.

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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).

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.

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).

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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).

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All selected ROIs will become hidden.

ROI Loading, Saving, and Quantification Tools

The left-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, it is necessary
for this panel to be active.

The buttons at the top of the operator window perform various functions within the operator.

Load or save an ROI from disk or iPACS

Render ROIs in the MIP view
Reset the camera view
Reset all ROIs

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Show the image histogram

Show the quantification table
Save the quantification table to disk
Perform a cut on an image using an ROI
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, click 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.

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:

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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.

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.

Center view on ROI. To center the field of view on the center of mass of a particular ROI, double click the
ROI in the ROI Table.

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 the 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

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"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.

Set quantification table columns. To determine which quantitative fields will be displayed in the
quantification table, and stored to the iPACS if applicable, use the selection widget under Operator ->
Quantification Table List.

The available quantification values are described below:

Option Description
ROI Name of the ROI
Patient PatientsName from the header
Series SeriesDescription from the header
Modality Modality from the header
Color Color of the ROI
Voxels Number of voxels contained in the ROI
Volume Volume of the ROI in mm3
Arithmetic mean of values of voxels contained in
Mean
the ROI

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Standard Deviation of values of voxels contained in

StdDev
the ROI
Min Minimum value of all voxels contained in the ROI
Max Maximum value of all voxels contained in the ROI
Median Median value of all voxels contained in the ROI
Sum of all voxels contained in the ROI, sometimes
Sum
interchangeable with 'Uptake'
Unit Unit of voxels in the selected dataset
Concentration (mean/volume) of the 10th Percentile
Conc 10%
of voxels contained in the ROI
Concentration (mean/volume) of the 50th Percentile
Conc 50%
of voxels contained in the ROI
Concentration (mean/volume) of the 3x3x3 cube of
Conc voxels with the greatest mean of all 3x3x3 cubes of
Peakregion voxels contained within the ROI. Referred to below
as Highest-uptake region
Concentration (mean/volume) of the 3x3x3 cube of
Conc voxels that has at its center the maximum voxel of
Peakmax the voxels contained in the ROI. Referred to below
as SUVmax.
Concentration (mean/volume) of the maximum
Conc Max
voxel of the voxels contained in the ROI
Concentration (mean/volume) of all the voxels
Conc
contained in the ROI
Unit of voxels in the selected data set over volume
Conc Unit
(mm3)

"Impact of the Definition of Peak Standardized

Uptake Value on Quantification of Treatment Response". Vanderhoek, et al. J Nuclear Medicine, 2012. Link.

Show the quantification table. To display the quantification table including all existing ROIs, click the
"Show Table" button.

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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 ROI. 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
the 'H' column to hide ROIs. Check the boxes in the 'I' column to make ROIs immutable.

Copy/paste the 3D ROI. Click the "Copy or Paste ROI" button to copy and/or paste ROIs between instances
of VivoQuant.

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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.

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.

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Erode/Dilate. The Erode/Dilate tool can be used to remove or add up to 5 layers of voxels from the input
ROI. The erosion or dilation will be applied 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.

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2D Drawing Tools
The 2D drawing tools match the options available within the Quantification++ Tool.

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.

Spline tool
Bully tool
Freehand tool
2D Thresholding tool
Apply Spline Path to ROI and move to next slice
Apply Spline Path to ROI
Clear Spline Path
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

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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.

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 loaded 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.

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.

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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.)

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.

Setting the Thresholds. 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.

Requires Requires
Seed? Thresholds?
Global Thresholding No Yes
Connected Thresholding Yes Yes
Neighborhood
Yes Yes
Thresholding
Otsu Thresholding No Yes
Confidence Connected Yes No

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ROI Connected Yes No

Interpolate Slices No No
Connected Components No No
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.

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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 radius parameter. Smaller radii will
result in smoother ROIs.

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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.

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

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radius can be configured. This algorithm works best on NM images, but may also work on some CT images.

If there are any ROIs present prior to using this tool, they will be deleted.

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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.

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
'I' 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-rendered 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.

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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.

Dashed red lines will appear on the image, indicating the boundaries of the selected region.

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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.

Undo/Redo Functionality
To undo/redo operations performed in the 3D ROI tool go to View->Undo or View->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.

The undo/redo function is applicable to all functions performed on 3D ROI data itself, i.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:

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• The input ROI will be set to background whenever the undo function is applied.
• To undo/redo filling a contour in the Spline Tool the user must navigate away from the spine tool
window.

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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.

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 (ROI).

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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.

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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 below determines the bounds of the ROI in the transverse
plane.

By using the "View" pulldown menu, it is also possible to draw ROI boundaries in the sagittal plane:

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or coronal plane:

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Choosing the ROI type

Four ROI types (labeled as Modes) are available.

• 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.
• 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.
• 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 Options section. This mode provides
an efficient way to fine-tune an ROI made in Spline or Freehand mode.
• 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 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.

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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 ( ) 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.

Field Description
Field available for comments/ROI names. A
ROI L-click in the field will activate and allow
comments to be entered.
Patient 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
Modality
for that row were calculated.
Color The color of the ROI as drawn in the display.
Total number of voxels contained in the selected
Voxels
ROI.
Volume The volume of the selected ROI in units of cubic
[mm ]3 millimeters.
The total amount of attenuation/activity in the
Sum 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
Unit may be specified in the Data Panel of the
Configuration Tool. Options include MBq, kBq,
mCi, and µCi.
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

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volume.
Hounsfield units (HU/mm^3) are used for CT data.
The SPECT units used by the Quantification++
Unit panel may be specified in the Data Panel of the
Configuration Tool. Options include MBq/mm3,
kBq/mm3, mCi/mm3, and µCi/mm3.
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
StdDev ROI from voxel-to-voxel. The smaller this value,
the more uniform the distribution of
attenuation/activity in the ROI.
The minimum attenuation/activity value of the
Min
voxels in the selected ROI.
The maximum attenuation/activity value of the
Max
voxels in the selected ROI.
Specifies via slice numbers the distance spanned
ZRange
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:

Menu Item Description

Plot data Plots the selected data on a line graph.

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Data to Calculates the Quantification factor with the

Quanti Calc acquired data.
Data to
Calculates the specific activity with the acquired
SpecAct
data.
Calc
Data to SUV Calculates the standarized uptake value with the
Calc acquired data.
Submit ROI
Submits #* ROI (the selected ROI) to the iPACS.
#* to iPACS
Deletes the entire row of the corresponding selected
Remove line
cell.
Deletes all information from the table, but not
permanently. The table can be reopened by
Clear table
right-clicking and the data for the corresponding
selection will reappear.
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 (i.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.

Data to Quanti Calc

The calculator will automatically import the associated data.

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Data to SpectAct Calc

The calculator will automatically import the associated data.

Data to SUV Calc

The calculator will automatically import the associated data.

File Menu
The Quantification++ package also provides several options for saving quantification and ROI information.

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Menu
Description
Item
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.
Load ROI Loads a previously saved ROI.
Save ROI Saves the current ROI as a .roi file.
Copy Copies the data in the Quantification table to the
table clipboard.
Clear
Clears the current Quantification 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
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.

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Menu
Description
Item
Clears all voxels outside the ROI within the currently
Cut outside selected slices, and all voxels outside the currently
ALL 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
Cut
direction (inside/outside) is selected. Slices outside
the set axial range will not be affected.
Apply ROI
Applies the ROI to every slice in the image.
to all slices
Creates a new ROI entry representing the
Select field-of-view (the entire volume of the image). The
FOV quantification table will be populated with this entry,
and labelled as 'FOV.'

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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.

Using the Tool

When the Reorientation/Registration tool is selected a Reorientation/Registration operator window is
displayed.

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The Data Selector Widget is used to determine which inputs will be reoriented by the Operator.

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.

The buttons at the top of the operator window perform various functions within the operator.

Option Description
Force re-render of VTK Viewer
Reset VTK Viewer position
Toggle ability to perform reorientation in VTK Viewer
Resets current reorientation operation
Apply current reorientation operation

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The Interpolator drop down menu designates which interpolator will be used during the transformation. Linear
is 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.

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.
3. Flips can be performed about any of the three axes by selecting the check box for Head/Foot,
Left/Right, or Anterior/Posterior.
4. 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.

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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.

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 is 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

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To begin the registration, select either "Inp1 to Ref" or "All to Ref". "Inp1 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.

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.

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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.

Applies a pre-defined
Load
Ctrl+Shift+L transformation to the active data
Transformation...
set.
Saves the current transformation
Save
Ctrl+Shift+S settings (rotation, translation,
Transformation...
flips) into a .xml file.
Saves the current transformation
settings (rotation, translation,
flips) as default settings for
image data. If the "Apply
Default Shift" checkbox is
Save as default
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
Reset Ctrl+R settings (rotation, translation,
flips) back to the default values.
Apply Ctrl+Return Applies the current
transformation settings (rotation,
translation, flips) to the active

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data set.
Provides the option of flipping
the data in any of three
Flips directions, described as
Head/Feet, Left/Right, and
Anterior/Posterior.
Directs the user to the Resample
Data tool. The Resample Data
Resample tool allows rebinning of
reconstructed data into an
arbitrary voxel size.
Transformation which applies
T1 to the source, and then
Pre-compose
applies T2 to that result to obtain
the target.
Transformation which applies
T2 to the source, and then
Post-compose
applies T1 to that result to obtain
the target.
Sets reference point for
Reorient ROI
transformation as center of ROI
around center
instead of center of image.
Toggles appearance of Scaling
Enable 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 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:

• http://www.insight-journal.org/browse/publication/154

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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:

• http://www.insight-journal.org/browse/publication/154

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.

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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.

Load the data into the VQ.

Use the reorientation tool to shift and/or rotate the image data set (Input 1) so that the image 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

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Return to the Data Browser or go to the Tools Menu and re-check the "Apply Default Shift" box.

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Reload the image/CT phantom data that were just acquired. They -- and all other data sets -- will now be
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 100

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.

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.

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 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 windowing, which will apply to all loaded images.
The windowing format (either Min/Max or Level/Width) is determined by the Display Configuration. To set,
simply check the Global box and enter appropriate windowing values 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 -> Save Movie, or by the keyboard
shortcut Ctrl + M.

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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.

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Distance/Annotation Tool
The Distance/Annotation tool enables you to measure the distance between two points in any image. For
example, it 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 is 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.

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 is 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.

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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.

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.

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Landmark-based Co-Registration
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 (i.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.

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Click on the Landmark-based Co-registration icon, , to perform the registration. Once registration is
complete, the shifted input data set will appear in the Main Window as Input 2.

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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
The Checkerboard Tool can be accessed via the tool pull-down menu on the VQ front panel.

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

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Cropping tool
The Cropping Tool allows images to be made smaller by removing any unwanted areas. For example, if an
image has been cut, 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.

Using the tool

Upon selection of the Cropping tool, the standard view options disappear and red sliders are displayed in their
place.

Two red sliders appear for each view direction (i.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

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the arrow keys in the cropping dialog. Manipulation of the red sliders creates a three-dimensional
rectangangular cropping volume. The current voxel position 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

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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.

Using the tool

Upon selection of the Arithmetics operator, the Arithmetics operator window is displayed.

The drop-down menu under Options contains a selection of the available operators:

• Add, Subtract, Multiply, Divide, and Average each operate on two images selected via the Data
Selector Widget. These operations are performed voxel-wise.
• Scalar Multiplication and Scalar Addition can be applied to any of the loaded images, selected via
the Data Selector Widget. Set the factor or addend by increasing or decreasing the scalar value.
• Merge whole integer value phantoms to load into the 3D ROI tool. Can be applied to any of the
loaded images, selected via the Data Selector Widget. This is very useful for fixed-volume ROI
analysis.

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Click OK to perform the chosen operation. A dialog will appear to indicate successful application of the
chosen function.

For all arithmetic operations, the user has the option to append the resulting volume(s) or perform the function
in-place, thus replacing the existing data with the amended data.

Units are 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 and will allow the user the option to
halt the operation.

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Filtering Tool
The Filtering Tool offers a variety of smoothing filters with configurable input parameters and can be applied
to any of the loaded images.

Getting There
The Filtering Tool can be accessed via the tool pull-down menu on the VQ front panel.

Using the tool

Upon selection of the Filtering Tool, the Filtering Operator window is displayed.

Using this tool, any loaded data can be selected for smoothing via the Data Selector Widget.

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:

• Gaussian Smoothing
• Curvature Flow
• Gradient Anisotropic Diffusion
• Curvature Anisotropic Diffusion

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• Positivity Smoothing (to remove negativity from FBP reconstructions)

• Zero Crossing Edge Detection
• Bilateral Smoothing
• 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.

Default
Parameter Description Used by
Value
Full-width Gauss, Zero
FWHM half-maximum kernel Crossing Edge 1.00mm
size Detection
Gradient
Anisotropic
Parameter governing
Diffusion,
Conductance sensitivity to edge 1.00
Curvature
contrast
Anisotropic
Diffusion
Curvature Flow,
Gradient
Anisotropic
Diffusion,
Iter Number of iterations Curvature 5
Anisotropic
Diffusion,
Positivity
Smoothing
If the fraction of
voxels that are
negative falls below Positivity
CutOffFrac 0.005
this value, further Smoothing
iterations of the filter
will not be performed.
Curvature Flow,
Gradient
Stepsize, effectively Anisotropic
Time Step analogous to kernel Diffusion, 0.125
width Curvature
Anisotropic
Diffusion
Difference between
the area under the
discrete Gaussian Zero Crossing
Max Error 0.5
curve and the area Edge Detection
under the continuous
Gaussian

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The standard deviation

of the gaussian
Bilateral
Range Sigma blurring kernel in the 50.0
Smoothing
image range. Units are
intensity.
The standard deviation
of the gaussian
Domain blurring kernel in each Bilateral
4.00
Sigma 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 take 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
No Smoothing Gauss Curvature Flow 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

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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 2010) 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.

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Bias Field Correction 117

Modeling
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.

Function
Upon selection of the Modeling Tool, the Modeling operator window is display

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.

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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.

Note: Access to models is dependent on your specific VivoQuant license. For information regarding your
license, please contact your account manager or email [email protected].

Models
MR Models
MR models are included with every VivoQuant license. These models include T2, T1, ADC, Fat and GLM.

Pharmacokinetic Models
Pharmacokinetic models are available as a plug-in for the Modeling operator. These models include the
Two-Tissue Compartment Model (2TCM), One-Tissue Compartment Model (1TCM), Logan Graphical
Method, Simplified Reference Tissue Model 1 & 2 (SRTM/SRTM2), Logan Non-Invasive Graphical Method,
and Patlak Analysis. Detailed information for these models may be found on the Pharmacokinetic Modeling
page.

Note: Access to these models is dependent on your VivoQuant license. For information regarding your
license, please contact your account manager or email [email protected].

Function 119
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.

Menus
Five Menus are arrayed across the top of the Main Window. These include:

Menu Function
Used for file manipulation and includes options for
File
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
View
a variety of display options, including layout and
zoom.
Provides access to several VQ image processing
Tools tools, including data control, reconstruction,
calibration, and configuration features.
Advanced Provides access to more advanced VQ image
Modules processing tools, including data control,

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reconstruction, calibration, and configuration

features.
Help content, including registration information and
Help
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.

Thumbnail
Function
Icon
Opens the Data Browser
Opens a browser that will unload currently loaded
data and replace it with the data selected in the
browser.
Opens a browser that will append data to currently
loaded data.
Opens the Save Image window.
Opens the Save Movie window.
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%.
Zooms out 25%.
Auto-zooms to fit data to screen.
Opens RGB color options.
Opens the Viewer Control panel.
Opens the MIP Control panel.
Opens the Data Manager panel.
Opens the Min Max Tool panel.

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Opens the VivoScript Evaluation window.

Edits the VivoScript file selected in the 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.

View
Function
Mode
The Slice View (default) simultaneously displays
Slice
images of single slices for the MIP, sagittal, coronal, and
View
transversal views of the loaded data sets.
The Tile View displays an array of slices for either,
Tile
sagittal, coronal, or transversal view of the loaded data
View
sets.
The Multi View displays sagittal, coronal, or transversal
Multi
slices of each data set adjacent to one another
View
simultaneously.
The Multi Planar Reconstruction View simultaneously
MPR
displays sagittal, coronal, and transversal slices in a
View
single window.
Operators
The operators are available in a pull-down menu located next to the thumbnail icons.

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Operator Function
Enables manually scrolling through
Navigation the image slices and rotation of the
Maximum intensity Projection (MIP).
Provides advanced tools for drawing,
3D ROI Tool visualizing, 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
Reorientation/Registration
registration algorithms are available to
automatically register data from a
wide variety of modalities.
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.
Allows you to measure the distance
Distance/Annotation
between two points in any image.
In checkerboard mode, the reference
and input data set(s) are arrayed in a
Checkerboard
pattern of alternating squares,
resembling a checkerboard.
Allows images to be made smaller by
Cropping
removing any unwanted areas.
Allows voxel-wise arimethic
operations on two input images, or
Arithmetics
scalar operations on any number of
input images.
Uses a selection of built-in smoothing
Filtering
filters with configurable parameters.
Provides an integrated solution for
representing the loaded data set with
Modeling
one of several mathematical models to
allow for predictions and analysis.
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.

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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.

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.

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Projections vs. Reconstructions 125

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 (MIP) 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.

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.

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There are several options for the output images.

Option Description
File name Set name of image file.
Set type of image file. Images can be
saved as

1. .png
Files of type
2. .jpeg
3. .bmp
4. .gif
5. .tif
Set type of image. Image types can be

1. Maximum intensity projection

(MIP)
Image type 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

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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
Storage type 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
Magnification
of the viewports, only the
magnification of the image file being
generated.

Function 128
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.

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 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 movie.

Function
Selection of the "Save Movie" option opens the Save Movie window.

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There are several options for the output movies.

Option Description
File name Set name of movie file
Set type of movie file. Movies can be
saved as
Files of
1. .gif
type
2. .mng
3. .mpg
4. .mpeg
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 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 color bars.
4. Smart labels - colorbars with
separate sets of gradations for each
color bar incremented with respect

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to the units of each color bar.

Set whether the image file will be stored as
Storage
a local image file or as a DICOM via
type
Secondary Capture.

Function 131
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 (i.e., reorientation, cropping, etc.) is opened into a dock upon use.

Any controller or operator 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).

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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.

Using docks 133

Displays
VivoQuant offers various display styles to enhance viewing and aid image analysis.

• Slice View: Showing orthogonal slices.

• Tile View: Showing a matrix of slices of one type.

• Multi View: Showing side by side slices of one type.

• MPR View: Showing side by side slices of one type.

Displays 134
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.

Using the Slice View Display

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 (i.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

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PageUp/PageDn keys while scrolling of the other two views is controlled by the arrow keys.

Scrolling Example

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 towards 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.

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Scrolling Shortcuts Table

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.

Active
← → ↑ ↓ PageUp PageDn
View
Previous Next Previous Next Previous Next
Coronal sagittal sagittal transversal transversal coronal coronal
slice slice slice slice slice slice
Previous Next Previous Next Previous Next
Sagittal coronal coronal transversal transversal sagittal sagittal
slice slice slice slice slice slice
Previous Next Previous Next Previous Next
Transversal sagittal sagittal coronal coronal transversal transversal
slice slice slice slice slice slice

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Other Slice View Tools

Scrolling through slices is also possible through the Viewer Control panel using the sliders and their
associated spin boxes.

The Layout and Zoom options are also intended for manipulating the appearance of the Slice View.

Other Slice View Tools 138

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.

Using the Tile View Display

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

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tiles. To learn how these keys control scrolling in the Slice View, click here..

← Previous slice
→ Next slice
↑ Previous row
↓ Next row
PageUp Previous screen
PageDn Next screen
To switch between views (i.e., coronal, sagittal, transversal) in the Tile View, right-click on a tile and choose
the desired view.

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.

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Using the Tile View Display 141

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 is especially useful for users who work with data across multiple image modalities.

Getting There
The Multi View is available via a pull-down menu on the Main Window.

Setting Up the Multi View Display

Selecting Multi View brings up the Multi View display and activates the Multi View-specific Layout
operator.

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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.

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.

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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.

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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.

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Using the Multi View Display

Navigation
To use the Multi View as you would other Displays, simply close out 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.

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For more information on using the Viewer Control in Multi View, see the Viewer Control in Multi View
section of the Viewer Control page.

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MPR View
The MPR (Multi-Planar Reconstruction) View simultaneously displays a sagittal, coronal, and transversal
slice of the reconstruction. The Viewer Control is 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.

Using the MPR View Display

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

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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.

Resets the MPR View display to the default

Reset
settings
Rotates the MPR View around the (X,Y,Z)
(X,Y,Z) Sliders
axis.
Toggles the display of the MPR View
BB Checkbox
Bounding Box.
XY,XZ,YZ Toggles the display of the coronal, sagittal,
Checkboxes and transveral slices.

Using the MPR View Display 149

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.

Function
The Capture Viewer panel is split into four fields: Info, Convert, Edit, and Image.

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Info

The Info field includes many boxes and buttons that affect the output image.

Option Description
Pull-down menu to choose image. Image
Series
selected here will be reflected in the "Series
Description
Desc" field

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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
Capture Desc
entered by user.
Date and time at which the image/movie was
Content Data
loaded into the Capture Viewer.
Size of the original data referred to in the Series
Data Size
Description pull-down menu.
Image Size Size of image currently being displayed.
When pressed, displays the DICOM Header for
DICOM
the data
When pressed, closes the Capture Viewer
Close
without saving image
When checked, maintains, or returns to, the
orig
original image size.
and Increases or decreases image size, respectively
Convert

The Convert field includes several options that affect the output image.

Option Description
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 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

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The Edit field includes several buttons

Option Description
Annotate Creates a text box in the image space
Creates a circle in the image space that can be moved
Circle
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.

Edit 153
View Menu
The View Menu is useful for modifying the information about a data set that appears in the Main Window.

• Show Reference/Input 1/Input 2

• Slice Number
• Crosshairs
• Position Labels
• Patient Name
• Active Indicator
• Layout
• Zoom

View Menu 154

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.

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.

To conceal the slice number from view, unselect Slice number by left-clicking on it.

Slice Number 155

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.

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.

To conceal the cross hairs from view, unselect Cross hair by left-clicking on it.

Cross-hairs 156
Position Labels
The position labels are displayed on each image plane and MIP. They clearly indicate which side of the mouse
is being viewed.

Getting There
To display the position labels on the image go to view under the view menu and select position Labels.

Function
The labels indicate the plane of view, i.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
Sagittal 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
Coronal
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 157

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 View menu and select patient Labels.

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.

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Function 159
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
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.

Reference and Input 1 ON. Input 2 OFF.

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Reference and Input 2 ON. Input 1 OFF.

Function 161
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.

Alternatively you can click on the layout thumbnails in the Main Window.

Thumbnail Description
Grid 2x2
Grid 1x4
MIP only
Slices only
Transversal only

Layout Options
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 screen.

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Grid 1x4
In the Grid 1x4 layout the MIP and all three slices are laid out in a single row.

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MIP only
In the MIP only layout, only the MIP is visible; the slices are not in view.

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Slices only
In the Slices only layout, only the slices are visible; the MIP is not in view.

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Transverse only
In the Transverse only layout, only the transverse slice is in view.

Transverse only 166

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 is to go to View under the View menu and
select Zoom.

The second method to execute the different zoom options is to use keyboard shortcuts.

Function Shortcut
Zoom in (25%) Cntrl + +
Zoom out (25%) Cntrl + -
Normal size Cntrl + 0
Full screen Cntrl + F
Auto zoom Cntrl + Z
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

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Zoom Out

Function
Zoom In
The zoom in option allows you to zoom in by 25% increments.

Zoom Out
The zoom out option allows you to zoom out by 25% increments.

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Normal Size
This is the default angle, selecting this option will bring the images back to their original viewing angle.

Full Screen
This options displays VivoQuant in full screen mode. Re-highlighting the full screen option will revert
VivoQuant back to its original size.

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.

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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.

Auto Zoom 170

Tools
The Tools Menu contains a wide range of tools available for a variety of post-processing applications.

• VivoScript
• View Control
• MIP Control
• Data Manager
• Min/Max Tool
• Workflow Assistant
• Histogram
• Preprocessing
• Resample
• Image & Movie
♦ How To Make Dynamic Movies
♦ Split Movie into Frames
♦ Join Frames to Movie
♦ Change Delay
♦ Image to Poster
♦ Image to Capture
• DICOM
• Update Check
• Configuration
♦ Display Configuration
♦ Data Configuration
♦ DICOM Configuration
♦ Network Configuration
♦ Registration Configuration

Tools 171
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&lt;10; ++i) {
...
}

Function
function blub() { ... }
function bar(p1, p2, p3) { return p1+p2+p2; }
var res = bar(1,2,3);

Array
var array = new Array();
array[0] = 'foo';
array[1] = 'bar';
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:

• Go to 'Tools-&gt;Configuration' and click on the 'VivoScript' tab.

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• Select a script for which quick access is desired by clicking the button and navigating to the
directory where the script is saved.
• Add a nickname for the script in the dialog box that appears.
• The script will now appear in the configuration window as well as in the Quick Scripts menu on the
VQScript Toolbar.

• Quick Scripts can be edited directly from the VQScript Toolbar by clicking on the pencil button .A
window will appear in which the user can edit the script.

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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 command 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.

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 VQScript Example Scripts page.

Adding Script Shortcuts to the Toolbar 174

VQScript Objects and Object Methods
VQ Object

Function Description
setDebuggerEnabled(bool toShow)
Writes text to VQ's debug console (e.g. the Windows debugger, a Unix termin
The text looks like:
debug(text)
Script: 1234 text

with 1234 being the time (in ms) since the script started.
mainWin() Returns VQ's Main Window object (see below)
dataManager() Returns VQ's Data Manager object (see below)
dataList()
sliceViewer() Returns VQ's Slice Viewer object (see below)
multiViewer()
mipViewer() Returns VQ's MIP Viewer object (see below)
controler() Returns VQ's View Contoller object (see below)
mipControler() Returns VQ's MIP controler object (see below)
vtkController() Returns VQ's VTK controller object (see below)
vtkViewer() Returns VQ's VTK viewer object (see below)
eCRF()
waitForECRF(int timeout = 0)
Asks VQ to quit (in an interactive session, the user is asked for confirmation, wh
quit()
terminates without further ado.
Convenience function (e.g. used for fileNames) that returns a 0-padded counter
counter(c, s)
counter(3,5) would return 00003.
showMessage(text) Shows text to the user. Please note that the user has to confirm the message an
askYesNoQuestion(const QString
Shows QString to user in Yes/No dialog box. Returns a boolean value (1 = yes,
&msg)
Returns a progress dialog, which can be used to show the current state of a longe

var progress = VQ.progressDialog("Saving Images", "Cancel", 0,

progressDialog(label, cancel, min, for(var x=0; x&lt;dm.getDimX(); x++) { // set posit
max) progress.setValue(x);
...
}
progress.hide();
getDouble(title, label, value=0, Shows input window to ask for a floating point number, e.g.
min=-214748364, max=2147483647,
decimals=1) var radius = VQ.getDouble("Smoothing", "Radius", 3.141, 1.0, 5

Defaults are shown above, and these parameters are optional, e.g. this will also w

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VQ.getDouble("Some", "Value");
getInt(title, label, value=0,
min=2147483647, max=2147483647, See getDouble(...), however, returns an integer value.
step=1)
getItem(title, label, value, items, Lets a user pick an item out of a list, e.g.
current=0)
var item = VQ.getItem("Some", "Item", [ "item 1", ♜item two"
getText(title, label, text="",
Allows user to input a line of text, returned by this function.
mode=normal)
getLocalPath(caption, startdir=".") Allows the user to select a local directory after being presented with the message
getSavePath(const QString &caption
= QString
getLocalFiles(const QString &caption
= "Select files:", const QString
&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.
folderExists(const QString &path)
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.
isTestMode()
setTestMode(bool b = true)
lumiQuantMaster()
dicomBrowser(DicomRepository
*rep)
Creates and returns a DICOM repository object, e.g.:

var folderUnix = VQ.dcmRep("folder:///path/to/dir");

var folderWin = VQ.dcmRep("folder://c:/path/to/dir");
dcmRep(repURL) var ipacs = VQ.dcmRep("ipacs://username:[email protected]
var ipacss = VQ.dcmRep("ipacss://username:[email protected]
var dicom = VQ.dcmRep("dicom://calling:[email protected]:port"

See queryStudies(...) for more examples.

loadRepository(const QString
&name)
etListOfRepositories(const QString
&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
querySeries(rep, studyInstanceUID)

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Performs query of DICOM repository rep for series matching argument criterio
string
queryImages(rep, studyInstanceUID, Performs query of DICOM repository rep for images matching argument criter
seriesInstanceUID) seriesInstanceUID are strings
downloadImages(rep,
studyInstanceUID, Downloads a full series (sopInstanceUID empty) or individual image. Retu
seriesInstanceUID, DICOM cache).
sopInstanceUID="")
Returns the data point associated with rep, type, UID and formname. fo
queryDataPoints(rep, type, UID,
iPACS, such as quantification, metadata, SubjectInformation or tumor_analysis.
formname)
point, such as images or project.
submitDataPoint(DicomRepository
*rep, const QString &uid, const
QScriptValue &data)
dicomBrowserLoad(DicomRepository
*rep, const QString
&studyInstanceUID, const QString
&seriesInstanceUID, bool append =
false)
queryStudyPlan(DicomRepository
*rep, const QString &plan, const
QString &cohort, const QString
&group, const QString &animal,
const QString &modality, const
QString &date, const QString &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
availableItems(const QString &name)
availableItemsObj(QScriptValue obj)
setOption(const QString
&dropDownName,const QString Sets a dropdown to provided optionValue text.
&optionValue)
setOptionObj(QScriptValue
dropDown,const QString Sets a dropdown, given by VQ.getWidget, to value provided by optionValue tex
&optionValue)
stripCredentials(const QString
&url_string)
stringMatch(const QString &ret,
const QString &text)
stringMatchList(const QString &ret,
const QString &text)
setConfig(const QString &entry,
const QVariant &val)

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getConfig(const QString &entry,

const QString &defaultValue)
getHome() Returns VQ home directory
getCache() Returns cache directory
getTempFolder()
deleteFile(const QString &filepath) Delets file at filepath
rmDir(const QString &dirpath) Deletes directory at dirpath
Calls VQ menu, use | as separator
triggerAction(name)
OA VQ.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
Store data as DICOM file locally with filename fileName
&fileName, int i, int format = -1)
saveDataViaITK4D(const QString
&fileName)
writeFile(fileName, text)
Writes or appends text to a file with name fileName.
appendFile
appendFile(const QString &fileName,
const QString &text)
readFile(const QString &fn)
brukerImporter() Returns a BrukerImporter object. See examples/loadBruker.vqs for an e
imgInfImporter()
gelImporter()
rawImporter()
imgHdrImporter()
centerCursor() Centers the crosshair in the field of view.
webDisk(rep) Returns an IPACSWebDisk object for the repository specified by rep. (See bel
hexColorToList(hex)
saveScreenshot(fileName) Saves a .png of the loaded image to the path specified by fileName.
unloadData(int startIndex, int
Unloads data from num sequential indicies, starting at index from. Using num=
numberToUnload)
applicationName() Returns 'VivoQuant' + versionNumber
buildID() Returns VQ Build ID
zipTool() Returns a ZipArchive object (see below).
evalDialog(const QString &text =
QString
mergeROIs(const QString &out,
const QScriptValue &map)
splitROI2DICOM(int id)
lsDir(const QString &dir, const
QString &filter = QString
frand()
suspend()

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Suspends execution of current script and generates dialog box. User must select
script.
getHash(const QString &key, const
QString &def = QString
getHashKeys()
setHash(const QString &key, const
QString &val)
clearHash()
storeHash(const QString &fileName)
loadHash(const QString &fileName)
ipacs()
translateUnit(const QString &type,
float value, const QString &input,
const QString &output)
repairSlice(int dataset, int pos, int
off=0, int thick=1)
getEnv(const QString &key, const
QString &defaultValue = QString
startTool(const QString &tool, const
QString &baseDir = ".", QStringList
args = QStringList
bedRemoval(const QString
&bedName = QString
getROIStats(int datID, int roiID)
getROIStats(int datID, int roiID)
combineFrames(QStringList
pngFiles, const QString &outfile, int
delay = 40, bool deleteAfter = false)
getNMCTWidget(const QString
&name)
atlasPath()
openNMCT()
setNMCTQuietModeOn()
runNMCT()
getMPRWidget()
loadRGB(int i, QStringList imgFiles,
float voxX, float voxY, float voxZ, int
rgbRep=4 /* sum */, bool
forcePlanar=true)
sendSlack(const QString &webhook,
const QScriptValue &data)
resume(QAbstractButton *button)
eCRFDone()
eCRFError()

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MainWin Object

Function Description
Opens view and op, e.g.
setViewMode(view, op)
VQ.mainWin().setViewMode("Tile View", "Navigation");
VQ.mainWin().setViewMode("Slice View", "3D ROI Tool");
type
saveImage(fileName, type)
• Slice Viewer: 0=MIP, 1=S, 2=C, 3=T, 4=All, 5=Everything
• Tile Viewer: 0=S, 1=C, 2=T, 3=Screen, 4=All
saveMovie(fileName, type) See saveImage()
toggleMIP(bool toEnable)
scriptOpenECRF(DicomRepository
*rep, const QString &uid, int
dataIndex=0,QString type=QString()
setControlStatus(bool on)
dDataFromCommandLine(const
QStringList &arguments)
openZIPACS(fileName) Opens the ZIPACS file at filename
loadScript()
executeScript(const QString &file,
bool interactive = false)
stopScript() Terminates script
evalScript() Evaluates script
openReference() Open data for Reference via dialog box
openInput1() Open data for Input 1 via dialog box
appendData() Append data via dialog box
openRaw() Open raw images via dialog box
importBrukerMR(const QString
Open BrukerMR file via dialog box
&directory = QString
importMultiMHD() Open MultiMHD file via dialog box
openRGBSliceViewer()
openDICOM() Opens Data Browser to load data from DICOM repository
openDICOMLocal() Opens dialog box to load data from local DICOM repository
print() Print images
zoomIn() Instead of zoomIn(), please use
zoomOut VQ.currentView().setScaleFactor(x)
Instead of zoomOut(), please use
zoomOut()
VQ.currentView().setScaleFactor(x)
normalSize() Auto zooms to original size
toggleFullScreen() Toggles Full Screen mode
setGlobalMinMax(b)

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toggleShowRGB(bool b)
setRGBChannel()
about() Opens 'About VivoQuant'
showManual() Opens VivoQuant Manual
requestHelp() Opens 'Request Help' tool
registration() Opens Registration tab of Configuration menu
Saves image with fileName. types are listed below type
saveImage(fileName, type)
• Slice Viewer: 0=MIP, 1=S, 2=C, 3=T, 4=All, 5=Everything
• Tile Viewer: 0=S, 1=C, 2=T, 3=Screen, 4=All
saveMovie(fileName, type) See saveImage()
scaleImage(float f) Scales image by factor of f
enableOpt(int mod, bool b)
showImagePreview(int idx)
checkForUpdate(bool verbose =
Checks for available VivoQuant update
false)
forceCheckForUpdate() Forces check for available VivoQuant update
loadDicomFromBrowser()
artCTRecoFromBrowser()
crosstalkRemoval() Runs Crosstalk removal NanoSPECT module
showMinMaxTool() Opens Min/Max Tool
showWorklistTool() Shows worklist tool panel
showHistogram() Shows histogram from Min/Max Tool
bedRemoval() Runs Bed Removal module
bioDistVis()
updateWindowTitle()
unloadedData()
loadedData(int idx)
changedData()
setupIPACSConnect()
showHints()
showStartupDialogs()
setupLayout2x2() Sets Main Display to Grid 2x2 view
setupLayout1x4() Sets Main Display to Grid 1x4 view
setupLayoutMIP() Sets Main Display to MIP only view
setupLayoutTrans() Sets Main Display to Transversal only view
setupLayoutSlice() Sets Main Display to Slices only layout
toggleCrosshair() Toggles appearance of crosshairs
Opens view and op, e.g.

setViewMode(view, op) VQ.mainWin().setViewMode("Tile View

VQ.mainWin().setViewMode("Slice Vie

finishedCTReco()

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tartCTReconstruction(const
QStringList &files = QStringList)
startBatchCT()
startIPACSSync()
startAppHomepage()
startOrgHomepage()
showConfig() Opens Configuration window
showCalibCTGeometrical()
showCalibMMP()
saveCalibrationTxt()
showUserData()
showNFFUniformity()
showNFFEnergy()
switchPatientName(bool b)
switchSliceNumber(bool b)
switchCornerInfo(bool b)
switchPosLabels(bool b)
switchCrosshair(bool b)
switchShowActive(bool b)
switchAutoZoom(bool b)
autoZoom()
showDICOMDump()
renameDICOM()
relabelDICOMStudies()
anonymizeDICOM()
getDataName(int type)
operatorHasChanged()
updateViewPort()
updatePaletteHeight()
enableLogfile(bool b)
startDbgView()
imageToCapture()
Forgets all passwords in memory (does not change DICOM Rep
logout()
configuration)
saveSession() Opens Save Session dialog box
loadSession(name) Opens Load Session dialog box
exportSession() Opens Export Session dialog box
updateGUIFromOptions()
handleLockScreen()
toggleVCView()
Toggles Visual Control
toggleMCView
toggleMCView() Toggles MIP Control
toggleDMView() Toggles Data Manager

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toggleMinMaxTool() Toggles Min/Max Tool

toggleWorkflowWidget() Toggles Workflow Widget
minimizeFloatingDock(bool
topLevel)
DataManager Object

Function Description
openDat(id, [files]) Opens data id (0=Ref, 1=Inp1, ...) contained in list of files [files].
getMinMax(int i, float
&min, float &max)
getMin(int i) Returns minimum value of image at index i
getMax(int i) Returns maximum value of image at index i
getMinMaxCached(int i,
float &min, float &max)
getMinCached(int i) Returns cached minimum value of image at index i
getMaxCached(int i) Returns cached maximum value of image at index i
setMinMaxCache(id, min,
Sets cached minimum and maximum values of image at index i
max)
getLevelWidthCached(int i,
float &level, float &width)
getLevelCached(int i)
getWidthCached(int i)
setLevelWidthCache(int i,
float level, float width)
getDataTypeString(int i=0)
voxelSize(id=0)
voxelSizeXY
voxelSizeDim(int dim, int
i=0)
voxelSizeX(int i=0) Returns dimension of voxel along X axis
voxelSizeY(int i=0) Returns dimension of voxel along Y axis
voxelSizeXY(int i=0)
voxelSizeZ(int i=0) Returns dimension of voxel along Z axis
getDesc(id, key) Returns key meta-information for data at index id
Updates meta-information for data at index id, e.g.

setDesc(id, key, value) dm.setDesc(0, "__repository_url", dcmRepUR

dm.setDesc(0, "__project", projectName);

getDcmString(int i, const
QString &key)
fillDICOMFromDesc() Fills DICOM header with meta-information
getSOPUID(int i) Returns SOPInstanceUID string for image at index

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getSeriesUID(int i) Returns SeriesUID as string for image at index i

getStudyUID(int i) Returns StudyUID as string for image at index i
setUniqueStudyID(int i) Creates and sets StudyInstanceUID
setUniqueStudyID(int i,
Sets StudyInstanceUID according to QString
const QString &id)
setDataTypeAll(const
QString &type)
getDataDetailsString(int
i=0)
getHeaderSummary(int
i=0)
isEmpty() Returns boolean; true if Data Manager is empty
hasData(int i=0) Returns boolean; true if index i has data
unloadData(from, num) Unloads data from num sequential indicies, starting at index from. Using num= -1 unload
swapData(int a, int b) Swaps data at index a and b
moveData(QList&lt;int&gt;
list, int dst)
toggleDefaultShift(bool on)
signalDataChange(int i)
signalDataUpdated(int i)
signalOptEnabled(int i,
bool b)
nalDataAboutToChange(int
i)
updatePaletteType()
SliceViewer Object

Function Description
setMinMaxCache(id, min, cutOff)
setOperator(AbstractOperator *op)
updateDisplay()
forceUpdateDisplay()
updateDisplay()
changedData(int i)
updatedData(int i)
unloadedData()
hangeBeforeGUIUpdate()
changedActive()
setupLayout(int type=0)
resetLayout()
linkControls(bool on)
toggleShowReference() Toggles display of Reference

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toggleShowInput1() Toggles display of Input 1

toggleShowInput2() Toggles display of Input 2
newDataComing(int type)
newDataLoaded(int type)
iewerConcurrentTasks()
callQuantiCalc(int mod, float activity, QString actUnit)
callSpecActCalc(int mod, float activity, float volume, const Opens SPECT Act. Calculator module and
QString &actUnit) inputs activity, volume, and actUnit
callSUVCalc(int mod, float activity, const QString &actUnit, Opens SUV Calculator module and inputs
float volume) activity, actUnit and volume
resetViewTransforms(bool triggerRender=true)
renderVTK() Forces re-render of VTK Viewer
enableVTK(bool toEnable) Enables VTK Viewer
syncDataListToMIP()
syncMIPToDataList()
Controler Object

Function Description
getIntense(int a)
getAlpha() Get the intensity value of the image at Input 1.
getDim() Get the intensity value of the Input 1 image.
getBalance() Get the intensity value of the Input 2 image
getActive(int a)
getShowROIs()
getShowAnnotations()
setIntense(int a1, float a2)
setAlpha(float a) Set the intensity of the image at Input 1 to f, a value between 0 and 1.
setDim(float a) Set the intensity of the Input 1 image to f, a value between 0 and 1.
setBalance(float a) Set the intensity of the Input 2 image to f, a value between 0 and 1.
getIntensity(i) 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
setIntensity(i,f)
value between 0 and 1.
If on is true, makes the image at the ith position active; otherwise makes
setActive(int a1, bool a2)
the image inactive.
setShowROIs(bool a)
setShowAnnotations(bool a)
setCropStyle(CropView a)
setPos(i, val) Sets slice number in i view to val ; For i, 0 = X, 1 = Y, 2 = Z
Set the lower and upper bounds on the color palette range for the image at
setRange(i, from, to) the ith position to the specified from and to values, respectively, where
from and to are values between 0 and 1.
setPal(i, palname)

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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").
getRange(int dataID, bool
isFrom /* otw to */)
Set the lower bound on the color palette range for the image at the ith
setFrom(i, f)
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
setTo(i, f)
position to f, where f is a value between 0 and 1.
Get the current lower bound on the color palette range for the image at the
getFrom(i)
ith position.
Get the current upper bound on the color palette range for the image at the
getTo(i)
ith position.
setPal(int dataID, const QString
&name)
getPal(int dataID)
invertPalette(int dataID)
getLinkedState()
updateImage()
adjustActiveState() Better to use setActive (see above)
emitResetViewport()
setViewPosX(int x)
setViewPosY(int y)
setViewPosZ(int z)
setIntensityRef(int val)
setIntensityInp1(int val)
setIntensityInp2(int val)
setActiveRef(bool active)
setActiveInp1(bool active)
setActiveInp2(bool active)
setCurrentViewport(int index)
setCurrentID(int id)
setCropStyle(CropView a)
setShowROIs(bool a)
setShowAnnotations(bool a)
syncStates()
setLinkedState(bool toLink)
MinMaxTool Object

Function Description
clipMin0() Sets all values below minimum to 0
clipMax0() Sets all values above maximum to 0

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clipMinMin() Sets all values below minimum to minimum

clipMaxMax() Sets all values above maximum to maximum
applyValues() Applies current values
resetValues() Restores values from cache
recalcValues() Recalculates actual minimum and maximum values
PercentileToImageVal()
centileButtonEnabled(int imageIdx)
copyToMax()
aveNewPercentilesCSV() Opens dialog box that allows user to save percentiles to .csv file
Opens dialog box that allows user to append percentiles to existing
appendPercentilesCSV()
.csv file
showTable(bool)
appendRow()
removeRow()
updateMode()
updateEnabledImages(int imgIdx)
show()
updateMIP() Updates MIP
updateDisplay() Updates Main Display
updateAll() Updates MIP, Main Display, etc.
showHistogram() Opens Histogram Tool
showPctileTool(bool)
updateROIList() Updates ROI List
updatePalette()
updateFromPalette()
MultiViewer Object

Function Description
setPlane(int id, int p)
setData(int row, int col, int viewIndex, int dataIndex)
getEnabled(int row, int col)
setEnabled(int id, bool e)
setEnabled(int id, bool e)
setPlane(int id, int p)
activateView()
deactivateView()
updateDisplay(int id)
updateDisplay(int id)
newDataLoaded(int type)
eViewportDataChanged(int id=-1)
handleResetViewport(int id=-1)

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IPACSWebDisk Object

Function Description
lsDir(path) Returns a list of files/directories.
Saves a file from the local path specified by src and stores it on the
put(src, dest)
WebDisk at the path specified by dest
Saves a file from the local path specified by src and stores it on the
put(src, dest)
WebDisk at the path specified by dest
mkdir(path) Creates a WebDisk directory
rm(path, recursive=false) Deletes a WebDisk directory
Retrieves the file specified by the path in src and places it locally in the
get(src, dest)
path specified by dest
getPublicLink(const QString
&file)
setExtraTimeout(int t)
execReport(const QString
&path)
openInBrowser(const QString
&path)
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)
setPaletteFromTo(int dataIndex, float pctFrom, float pctTo)
setPaletteFrom(int dataIndex, float percent)
getPaletteFrom(int dataIndex)
setPaletteTo(int dataIndex, float percent)
getPaletteTo(int dataIndex)
getPaletteLevel(int dataIndex)
getPaletteWidth(int dataIndex)

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setDataPalette(int dataIndex, const QString &name)

getDataPalette(int dataIndex)
pdatePaletteContrast(int i, float value1, float value2)
showForm()
toggleForm()
MIPViewer Object

Function Description
loadedSlice(int i)
updateDisplay()
scaleImage(float factor)
updateCacheStat()
setActive(QList<int> a)
setSync(bool s)
isSync()
parameterChanged()
invalidateImageCache()
MIPController Object

Function Description
setNumber(int val) Sets number of frames in MIP; default = 60
sliderPos(int i) Sets View Angle slider to value i
Returns the intensity of the image at Input 1; Better to use getAlpha(),
getAlpha()
setAlpha() in VQ.controler() object
Returns the intensity of the image at Reference; Better to use getDim(),
getDim()
setDim() in VQ.controler() object
Returns the intensity of the image at Input 2; Better to use getBalance(),
getBalance()
setBalance() in VQ.controler() object
getIntensity(int i) Returns Intensity of image at ndex i
setPal(int i, QString
Sets color palette of index i to name
name)
playMovie(bool
Plays MIP movie
checked)
saveMovie() Use saveMovie() in VQ.mainWin() object
saveImage() Use saveImage() in VQ.mainWin() object
speedChanged(int val) Changes speed of MIP movie
setEnabled(bool)

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VTKController Object

Function Description
getMIPEnabled()
getMPREnabled()
getAnnotationEnabled()
setAnnotationEnabled(bool toEnable)
getOrientEnabled()
setOrientEnabled(bool toEnable)
getRenderSpeed()
setInteractiveDelay(int msec)
setUseRenderDelay(bool toEnable)
getUseRenderDelay()
orceVolumeMapperMode(int mode)
setStillUpdateRate(double factor)
getAutoUpdate()
tSmoothingIterations(int iter)
setFeatureAngle(double angle)
setPassBand(double passBand)
disableAxes(bool b = true)
setPatientsName(const QString &text)
setMPRPlanes(int planes)
tScalarOpacityPoints(int imgIdx, QList<QVariant> imgRange, QList<QVariant>
opacityRange)
radientOpacityPoints(int imgIdx, QList<QVariant> imgRange, QList<QVariant>
opacityRange)
tOpacityPointsScalar(int imgIdx, QList<QVariant> imgRange, QList<QVariant>
opacityRange)
changeRenderSpeed(QString speed)
renderSpeedUpdated(QAction *action)
handleModified()
handleEnabledChanged()
Forces
updateVTK() re-rendering of
VTK
forceRender()
resetCamera()
setMPRImage(int i, double offset, QImage *image, int min=0)
updateMIPPointers()
imageLoaded(int i)
imageUnloaded()
imageUpdated(int i)

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updateVolumeColors()
interactive()
startInteractive()
endInteractive()
transform(const vtkMatrix4x4 *mat)
VTKViewer Object

Function Description
setEnableGradient(bool toEnable)
getGradientEnabled()
setBackgroundColor(const QString &fg, const QString &bg = QString()
setBackgroundColor(const QString &fg, const QString &bg = QString()
renderingProgress(vtkObject *obj)
setAzimuthAngle(int ang)
renderUpdate()
resetCamera()
resetPosition()
vtkUserEventsHandler(vtkObject *obj)
DicomRepository Object

Function Description
get(const QString &key)
set(const QString &key, const QString &val)
setUsername(const QString &u)
setPassword(const QString &p)
username()
password()
wasCanceled()
project()
stop()
3D ROI Operator Object

Function Description
addROI(const QString &name, const
QString &colorName, bool Appends a new ROI to the table using provided parameters, with
immutable=false, bool hidden=false, int default arguments as needed.
alphaSlice=127, int alphaSurface=255)
editROI(int index, const QString &name, Edits ROI at provided index (zero is background) using provided
const QString &colorName, bool parameters
immutable=false, bool hidden=false, int

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alphaSlice=127, int alphaSurface=255)

Delete ROI at provided index. If the index provided is less than
zero (default), the currently selected ROI will be deleted. Its voxels
deleteROI(int index=-1, int target=-1) will be reassigned to the ROI defined by "target" (can be zero for
background). If target is less than zero, the user will be prompted to
provide an ROI as a target.
Reassign voxels from ROI at "index" to ROI at "target". "index"
clearROI(int index=-1, int target=-1) and "target" are defined exactly as they are in the aforementioned
deleteROI function.
clearAllROIs() Deletes all ROIs and reassigns them to background.
Save quantification table to CSV formatted spreadsheet at file
exportTable(const QString &filename)
provided by filename
Set all voxels in an ROI to the minimum intensity value of that
image. Only affects visible images, or if Inp2 is selected, all images
cutROI(bool bg, bool quiet = false) after Inp2. If bg is true, the cut ROI will be background. If false,
the cut ROI will be the current ROI. The quiet option indicates
whether VivoQuant will ask the user for confirmation or not.
Cropping Operator Object

Function Description
executeCropping(bool
Run cropping with currently set parameters
forceClassicMIPCompatibility=false)
Set cropping boundaries to estimated border of images,
autoCrop()
exactly as the Cropping tool's autocrop button functions.
reset() Reset cropping boundaries to boundaries of the image
Embed image into user-provided bounds in the operator
embed()
GUI.
Reorientation/Registration Object

Function Description
saveTransformationToFile(const QString
Save current transform to a file provided by fileName
&fileName)
loadTransformationFromFile(const Load transformation from provided fileName. Returns an error
QString &fileName) message if the file could not be loaded succesfully.
Returns an array of transform parameters for the mode provided
getTransformParameters(int mode, int
(0=3D Manual, 1=2D Manual, 2=3D Auto, 3=2D Auto, 4=3D
slice = 0)
Deform, 5=2D Deform). If 2D, the slice may be provided.
getFixedTransformParameters(int mode, Returns an array of fixed parameters for the transform in the mode
int slice = 0) provided.
applyTransformation() Applies the currently visualized transform to the selected images.

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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 thumbnail in the Main Window.

The second method is to go to "Slice Control" under the Tools menu.

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.

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Sliders
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.

Color Controls
The Color Controls display information about the datasets loaded at the Reference, Input 1 and Input 2
positions.

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: if 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.

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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 from 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.

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.

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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 is important to note that "Link Views" only affects the slice-by-slice navigation between viewports.
Regardless of whether "Link Views" is checked, zooming and panning within each viewport will remain
independent.

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 button on the toolbar.

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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 detailed 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.

The second method is to go to "MIP Control" under the Tools menu.

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.

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Playing a MIP Movie

The MIP movie is automatically generated upon the loading of a data set. 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.

VTK Viewer
Each operator will have default VTK 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.

The following options are availabe for adjusting the VTK viewer:

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Icon Description
Force re-rendering of the VTK viewer. Hold this
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.
Toggle the classic MIP in the VTK viewer.
Toggle orientation cube in the VTK viewer.
Toggle visible annotations in the VTK viewer.
Change performance of VTK viewer by
optionally downsampling the VTK image. Hold
this button down to specify the resolution of the
image.

VTK Viewer 199

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.

The Data Manager may also be reached via the Tools Menu.

Finally, the Data Manager is also available by using the keyboard shortcut F7.

Using the Data Manager

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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 is the Palette Window the data is subject to in the Display. These can be adjusted
based on the windowing setting as determined by the Display Configuration. Note that this does not affect the
minimum and maximum values stored in the Min/Max Tool. For more on changing the minimum and
maximum values, see the Min/Max Tool page.

If the windowing is using the Min/Max option, the palette can be adjusted by clicking on the black bars at the
far left or right of the palette to adjust the window min or max, respectively. If the windowing is using the
Level/Width option, the width of the window is adjusted by clicking and dragging the ends, while the center is
adjusted by clicking and dragging the middle of the palette display. Furthermore, the Level/Width palette can
be adjusted similarly to the Min/Max by holding the Shift key while dragging the ends.

The windowing can be adjusted within the image as well, by holding a right-click and dragging the mouse. In
the Min/Max setting, dragging left/right will adjust the min while up/down will adjust the max. In the
Level/Width setting, dragging left/right will adjust the level, while up/down will adjust the width. This
function works within any of the operators and does not require that the Data Manager is active.

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

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palettes of multiple frames at once.

Ordering Data
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. Alternatively, data can be moved in the Reference, Input 1 or Input
2 location simply by right-clicking and selecting "Move to Reference/Input 1/Input 2".

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/Input 2 to perform a swap (see image below).

Options
Right clicking on a dataset brings up a menu, with several data manipulation options.

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Option Description
Use as If one data set has been selected in the Data
Reference/Input Manager, it may be moved to either the
1/Input 2 Reference/Input 1/Input 2.
Allows an annotation to be added to the
Annotate
data details
Copes data set details to the clipboard from
Copy Details where they may be pasted into other files
(i.e. Word documents).
Opens the DICOM header information for
DICOM Dump
the selected data sets
Allows data to be saved as DICOM,
Save Data as
TRaster, Raw, 4D or ITK image file.
Unload Data Unloads data from VivoQuant.
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 203
Min/Max Tool
The Min/Max Tool allows the user to adjust the windowing of visible voxels for the first three Inputs.

Getting There
The Min/Max Tool is available via the Tools menu.

The Min/Max Tool can also be accessed by clicking on the Min/Max Tool thumbnail in the Main Window.

Function
The Min/Max Tool displays the windowing values with units for the Reference, Input 1 and Input 2. Whether
the windowing is displayed based on Minimum/Maximum or Level/Width is determined by the Display
Configuration.

The windowing 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

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advantage to this is it enables users working with multiple datasets to, if they wish, keep the color scale
consistent across multiple datasets.

Option Description
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.
Stores min/max values in cache and applies values to the
Apply
datasets.
From Copies the current palette window as set in the Data
Pal Manager to the Min/Max Tool fields.
Copies the current Min/Max Tool fields to the palette
To Pal
window settings in the Data Manager.

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.

Option Description
(Min) Sets all values below the minimum to 0.

(Max) Sets all values above the maximum to 0.

Sets all values below the minimum to the
minimum.
Sets all values above the maximum to the
maximum.

Histogram
The Histogram button 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 Xth percentile from the histogram of the image.

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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
Max
Show 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

Percentile Tool 206

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 VQ Keyboard Shortcuts for a complete list.

Function
The Histogram Tool is operated via two control panels: Data Controls and File Controls.

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Data Controls
Option Description
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
Min displayed. The Set button, , automatically loads this
field with the minimum value in the object.
Sets the maximum value for which data will be
Max displayed. The Set button, , automatically loads this
field with the maximum value in the object.

File Controls
Option Description
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.
Exits the Histogram Tool.

Data Controls 208

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 -> Pre-processing.

Function

The Preprocessing Tool is divided into three sections. The first section is the Preprocessing Options section,
which includes the preprocessing operations that may be included in the protocol

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Automatically detects the bed position within the

CT Bed
image and removes the CT voxels which constitute
Removal
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
Co-register
checked, then 'Standard' and 'Translation' are used
respectively.
Performs automatic cropping. Search for
boundaries starts at the end slices of the image and
Autocrop
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
Calibration
factors per modality [comma separated] in format -
Factor
"Mod=1.0 Unit". Example: PT=13456.7 BQML.
The case of the unit should match what is listed in
the 'Information window'.
Up/Downsamples voxels to the specified pixel
Resample
dimensions.
Convert supported units to/from uptake and/or
concentration units. If converting to/from SUV,
NM/PT
please provide Weight and Injected Dose
Convert unit
information (note: units must be specified, defaults
are [g] and [kBq] respectively).
Series Appends text to end of series description for all
Description datasets.
Quality Generates and stores quality control image of
Control preprocessed image. Results stored in the project
Image webdisk of the repository specified below.
Save image data being preprocessed to specified
Store Data
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,
Format 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 is Storage Options, where users may designate the iPACS 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.

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Consult the DICOM settings page in the help guide

for more information.
Specify the sub-project (iPACS) or sub-folder (local
Project
path) to which data will be saved.
Copy and paste preprocessing protocol settings to be
Protocol 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.

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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 ->
Resample or by navigating to Tools -> Resample data.

Using the tool

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.

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DICOM
The DICOM Tools Submenu contains features to aid in the management of DICOM data.

• DICOM Dump
• Anonymizer
• Rename DICOM
• 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.

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".

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The fourth method is via the Data Manager. Right click on a dataset and click "DICOM Dump".

Function
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.

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In the upper right portion of the DICOM dump window is a Find option. A search string may be entered in the
"Find" 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 [12\18] # 4,2 VQ DICOM Example

• (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.
• 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".
• The actual data values for the data entry (12,18) are displayed next in the Value Field (VF). The
values are shown inside square brackets.
• 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.
• 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
two subsets -- 12 and 18.
• 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 (i.e., VQ DICOM
Example). For private tags, this field will display, "Unknown Tag and Data."

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Anonymizer
The Anonymizer anonymizes the data to the user.

Getting There
Go to the Tools Menu in the Main Window then DICOM.

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).

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 manually 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.

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.

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Getting There
DICOM files can be renamed by selecting "Rename DICOM" under the Tools -> DICOM menu

Function

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 if 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).

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Getting There
Go to the Tools Menu in the Main Window then DICOM.

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).

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 218

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

Function
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 if illegal characters (e.g., backwards or forwards slashes) are used. To
execute renaming, click "OK."

Rename DICOM Files 219

Keyboard Shortcuts
A list of the keyboard shortcuts which are available for many basic operations.

Windows / Linux Mac

Shortcut Function
Shortcut Shortcut
Ctrl + O ⌘+O Open Reference
Ctrl + N ⌘+N Open input 1
⌘ + Shift +
Ctrl + Shift + N Open input 2
N
Ctrl + D ⌘+D Open DICOM Data
Ctrl + I ⌘+I Save Image
Ctrl + M ⌘+M Save Movie
Ctrl + S ⌘+S Save Data (DICOM format)
Ctrl + P ⌘+P Print
F1 fn + F1 Manual
F2 fn + F2 Show Reference
F3 fn + F3 Show input 1
F4 fn + F4 Show input 2
F5 fn + F5 Slice Control
F6 fn + F6 MIP Control
F7 fn + F7 Data Manager
Ctrl + + ⌘++ zoom in
Ctrl + - ⌘+- zoom out
Ctrl + 0 ⌘+0 Normal Size
Ctrl + F ⌘+F Full Screen
Ctrl + U ⌘+U Auto Zoom
Ctrl + Z ⌘+Z Undo Operation
⌘ + Shift +
Ctrl + Shift + Z Redo Operation
Z
Ctrl + I ⌘+I Save Image
⌘ + Shift +
Ctrl + Shift + D DICOM Dump
D
⌘ + Shift +
Ctrl + Shift + H Histogram
H
⌘ + Shift +
Ctrl + Shift + U Update Check
U
Ctrl + Shift + C ⌘+, Configuration Panel
⌘+H Hide VivoQuant
Base NanoSPECT
Ctrl + B ⌘+B
Configuration
Ctrl + Q ⌘+Q Quit MMP Calibration Tool
Ctrl + T ⌘+T

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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 + ↑, fn + Scroll through slices in either
PageUp,PageDn
↓ the Slice View or Tile View.
3D ROI Tool
Specific Keyboard
Shortcuts
Naviagate to the Navigation
N N
tab in the 3D ROI Operator
Naviagate to the Manual
P P Painting tab in the 3D ROI
Operator
Naviagate to the Spline Tool
S S
tab in the 3D ROI Operator
Naviagate to the Magic
M M Segmentation tab in the 3D
ROI Operator
Naviagate to the Expert tab in
X X
the 3D ROI Operator
Shift + = Shift + = Add a ROI
- - Reset the active ROI
E E Edit the active ROI
Toggle visibility of the active
v v
ROI
Rotate through the ROI list in
R R the active ROI drop down
menu
Rotate through the ROI list in
Right Click of Right Click
the active ROI drop down
Mouse of Mouse
menu
T T Display quantification table
Display 3D ROI Histogram
H H
Tool
Within the Spline tool, confirm
Return or
Enter classification of voxels within
Enter
contour to active ROI
Within the Spline tool, confirm
Shift +
classification of voxels within
Shift + Enter Return or
contour to active ROI and
Enter
move to next slice
Space Space Within the Spline tool, scroll
through Spline, Freehand,

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Bully and Thresholding tools

Within the Spline tool, clear
C C
the currently drawn contour

Keyboard Shortcuts 222

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 [email protected].

Getting There
To access the tool, go to the 3D ROI Tool, then Operator -> Autoradiography Calibration.

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.

The second prompt asks if there will be a background ROI used. This influences the calibration curve. In most
cases a background ROI is recommended.

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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.

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Image Calibration 225

Image Magick
The Image Magick suite is 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
The Image Magick options available in VQ provide an excellent tool for generating informative movies for
dynamic and gated 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).

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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.

Image 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 DICOM/iPACS
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.

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Adjust the Zoom and Color Palettes to your liking.

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Use the Cropping Tool to select only the region of interest.

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If desired, now is a good time to employ the Filtering Operator. Note that if 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.

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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.

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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.

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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 (if
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.

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Ensure again that the minimum and maximum values are consistent across datasets.

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The newly loaded data sets are now properly prepared. Save the images and data as in Steps 9-11.

After saving all desired images, generate the dynamic movie using the Image Magick "Join Frames to Movie"
option.

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.

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16) Type in a name for the movie file. The default file format is .gif.

17) Use the Image Magick "Change Movie Delay" option to speed up or slow down the movie frame rate.

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18) Congratulations! Just double-click to open and watch the new movie.

How to make a dynamic movie 237

Update Check
VQ is frequently updated to provide users with more and better tools for all of their post-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.

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.

Update Check 238

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:

• Display
• Data
• DICOM Settings
• Network
• Registration
• 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.

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 239

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
Option Description
Several font styles are available for display in the
Font Style
Main Window.
Controls the size of the displayed text in the Main
Font Size
Window
Cross-hair A variety of cross-hair styles are available for use in
style the Main Window.
Cross-hair Cross-hair color options include red, yellow,
color magenta, white, green, and blue.
Pal files hold the color map information for the
Pal Path
different Color Palettes available in the VQ.
Preview Displays a preview of the font and cross-hair
Panel 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.

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Maximum Intensity Projection

Option Description
Frame
Sets the amount of time for which each MIP
Time -
projection image is displayed in a saved movie.
Display
Frame
Sets the delay time between MIP frames in a saved
Delay -
movie.
Movie
With sync mode enabled, only completed MIP frames
will be displayed. With sync mode disabled, the MIP
Sync mode
will freely rotate at all times but will display a
message in place of the MIP for uncompleted frames.
Color Palettes
Option Description
Sets the method for determining the range of the color
Type palette. Options are to set the Window Min/Max or the
Window Level/Width
The default Color Palettes for the first three loaded
Palette volumes of each Modality are set. Inputs beyond the third
of a particular modality follow the palette of third.

Maximum Intensity Projection 241

Data
The Data panel contains options for data handling, including data loading and quantification.

Data Loading
Use the &apos;Data Loading&apos; panel to set loading options.

Option Description
Check the box to disable the MIP viewer upon
Disable MIP
loading. For large datasets, this can improve the
viewer
loading speed.
Check the box to enable VivoQuant to ask for
Ask Disable your permission to initialize the MIP viewer upon
MIP loading. For large datasets, this can improve the
loading speed.
Choose &apos;yes&apos; to allow the addition of
zero-padding to a reference image to match the
volume of an input image, or &apos;no&apos; to
Grow keep the reference image size static (and
reference to potentially crop the input image, if it is larger
input volume than the reference). Choose &apos;ask&apos; to
allow a window to appear upon loading in an
input 1 data set that is larger than the image in the
reference position.
Max voxsize Specify the maximum pixel ratio (largest pixel
ratio for vol. dimension / smallest pixel dimension) by which a

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data set is interpolated as a volume image file.

Specify the minumum allowed voxel width. Data
will be resampled upon loading if their voxel
MinVoxSize 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
Anchor input
be anchored at the following options: center,
data
head, or foot.

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, i.e. MaxVoxSizeRatio < 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.

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If the pixel ratio of the loaded image is less than the given threshold, i.e. MaxVoxSizeRatio > 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,

• If the &apos;Force Planar&apos; check box is checked in the Data Browser, then the image will
load in planar mode regardless of the value set for MaxVoxSizeRatio.
• If the &apos;Force Planar&apos; check box is unchecked in the Data Browser, then the image will
load in the appropriate mode according to the value set for MaxVoxSizeRatio.

Quantification Options
Use the &apos;Quantification Options&apos; panel to set options used by the Quantification++ Operator and
the 3D ROI Operator.

Option Description
Select the unit to be used for quantifying SPECT
data. Options include MBq, kBq, mCi, and µCi. Note:
Concentration units (e.g. nCi/cc) will not be
Units of
converted to the unit of activity specified. The Tumor
Activity
Segmentation and NM/CT Brain analysis plugin
modules do support converting from concentration
units to units of µCi.
CSV Choose the CSV file delimiter of their choice, applied
Separator when saving Quantification data.

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Data Manager
In the "Data Manager" panel, there is a checkbox to enable or disable a confirmation message when moving
data.

Option Description
confirm Check to enable a confirmation message when
moving rearranging data in the Data Manager
Show Check to display the seconds in the study date
seconds in column in the DICOM browser. VQ has to be
Browser restarted to configure this change.
Check to apply a default reorientation to data being
Apply
loaded into VQ. The default shift can be defined in
default
the Reorientation/Registration operator. For more on
shift
this, please see the Reorientation/Registration page

Data Manager 245

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.

The second method is to select the Configuration option in the Tools menu and to then click on the DICOM
panel.

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.

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DICOM Settings

Option Description
Location of local DICOM database.
Allows optimized internal access to the
DB path
Mediso DICOM database. See
Optimized local access for details.
List of available repositories. The bank
of buttons immediately beneath the
Repositories
pulldown menu operate on the selected
repository in this field
Check connection to DICOM
repository. Local folders are verified to
exist and a C-ECHO is sent to DICOM
servers.
Add a new repository
Delete selected repository
Open the DICOM Editor
Shows list of additional dictionaries used
by the DICOM library. Please set
Dictionary environment variable DCMDICTPATH to
set this value. For more on the DICOM
dictionary, see DICOM Dump
Port over which the DICOM peer sends
Rcv Port
data.
When this box is checked, the palette
window will be loaded in accordance
load palette with the image data. When this box is
% not checked, the palette window will be
set to whatever the window was set to
last.
Checking this box enables support for
DICOMDIR
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:

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DICOM Cache

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.

Option Description
Size in Mb of the data currently stored in the
Current DICOM Cache. The percentage to the right
Size of the field indicates how close the cache is
to capacity.
Maximum amount of memory that can be
Max
made available for the DICOM Cache
size
(default = 1000.0 MB).
Length of time over which data will be
Life
stored in the DICOM Cache (default = 14
Time
days).
Clear Empties the DICOM Cache
Captures

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.

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Option Description
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.
edit: Open the DICOM Editor.
Opens a Windows Browser that can be
used to select a local folder as a
repository.
Fetch all DICOM meta data.
Remove repository from list.
DICOM Editor
The DICOM Editor is used to add repositories, including DICOM Servers, PACS Servers, or local folders.

Option Description
Name as shown in the repository selection
Displayed
box. Can contain any alphanumeric
Name
character.

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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
is superior.
Such DICOM servers are network
services on the local or a remote
computer. They provide a database to
efficiently browser study data. An iPACS
server is an online PACS server, a
regularly used picture archiving and
retrieval system for medical images.
Local Select a local directory. All sub-folders
DICOM will be displayed as projects in the second
folder repository drop-down window.
DICOM
server
Username and password are specific to
the user for their site's iPACS system.
iPACS Hostname will be the site of the server for
server the iPACS 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.

iPACS server

An iPACS 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).

iPACS Projects
The iPACS 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

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this example, an iPACS repository for "bioscan/demo" is being configured. The "bioscan/demo" repository
contains three projects.

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.

Select any project to view only data associated with that project.

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.

To simultaneously view all data belonging to a repository AND its projects, place a * at the end of the

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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.

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:

Option Description
Displayed NSxxWS_DCMSRV (or customer's
Name preference)
Type DICOM Server
Calling AET INVIVOSCOPE
Called AET NSxxWS_DCMSRV

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Hostname localhost
Port 104

where xx is replaced with the NanoSPECT number, typically no leading 0 for numbers < 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 VQ 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.

Options Description
Displayed ACQ_NSxx_DCMSRV (or customer's
Name preference)
Type DICOM Server
Calling AET INVIVOSCOPE
Called AET NSxx_DCMSRV
Hostname nanospectxx
Port 104

where xx is replaced with the NanoSPECT number, typically no leading 0 for numbers < 10.

In place of hostname (i.e., nanospectxx), it is also possible to use IP addresses (i.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.

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Adding VQ as a DICOM Client

Start C:\Program Files\Mediso\DICOM Server\DICOMServerMgr.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.

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

Host Port
(AET)
HiSPECT LOCALHOST 3104
HiSPECT_BATCH LOCALHOST 3105
INTERVIEWXP LOCALHOST 11112
INVIVOSCOPE 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.

Example
Computer Calling AET Hostname Port
Number
Example NS5 ACQ
INVIVOSCOPE NANOSPECT5WS 23104
#1 Computer
Example NS13 WS
INVIVOSCOPE LOCALHOST 23104
#2 Computer
NS13 2nd IP Address or 2nd
Example
WS VQ-WS2 WS Computer 23104
#3
Computer Name

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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.

Option Description
Displayed NS13WS_DCMSRV (or customer's
Name preference)
Type DICOM Server
Calling AET VQ-WS2
Called AET NS13WS_DCMSRV
Hostname nanospect13ws (or IP)
Port 104

Troubleshooting
• 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).
• 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 (i.e., nanospect13ws) to the computer's IP address.
• Check the DICOM Server logfiles (on the computer that you want to access), located in C:\Program
Files\Mediso\DICOM Server\logs.

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• Enable debugging in the VQ and collect output while trying to access the DICOM Server.

Troubleshooting 256
Network

The Network panel consists of two sections: Network Settings and Auto Import.

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-AutoImport directly will be automatically imported into the NS00WS_DCMSRV repository upon the
next restart of the VivoQuant.

Network 257
Registration
Getting There
The registration panel may be reached from the Configuration Panel or it may be reached directly via the Help
menu.

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.

Registration 258
AdvancedModules
The Advanced Modules Menu contains a wide range of tools available for a variety of post-processing
applications.

• SPECT Tools
♦ QuantiCalc
♦ Specific Activity Calculator
♦ NanoSPECT
◊ MMP SPECT Calibration
◊ Near-Field Uniformity QC
◊ Reconstruction
◊ Batch Mode
◊ BatchTool Generator
◊ PSF Manager
◊ Quantification Tables
◊ ECG Split
◊ Save Calibration.txt
◊ Crosstalk Removal
• CT Tools
♦ CT Reconstruction
◊ BatchCT
◊ Hounsfield Calibration
◊ CT Geometrical Calibration
• Bed Removal
• Plug-In Modules
♦ Whole Body Atlas Tool
♦ NM/CT Brain Atlas Segmentation Tool>
♦ fMRI Brain Atlas Segmentation Tool
♦ Tumor Segmentation Tool
♦ LumiQuant 3D BLI Reconstruction Tool
• TumorPK Model
• Dosimetry Calc

AdvancedModules 259
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.

• Whole Body Atlas Tool

• 3D Brain Atlas Tool>
• fMRI Tool
• Tumor Segmentation Tool
• LumiQuant 3D BLI Reconstruction Tool

For more information on the inviCRO's Advanced Segmentation Tool Kit, please contact your inviCRO
representative or email [email protected]. You can also access a helpful 'How To' illustrating the main
features of the 3D Brain Atlas Tool by going to Tools -> Workflow and selecting the '3D Brain Atlas Analysis
Tool' workflow.

Plug-In Modules 260

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

Overview
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.

Getting There
The Whole Body Atlas Tool is accessed by navigating to Tools -> Advanced Analysis -> Whole Body Atlas.
Here there are three options: Whole Body Segmentation Tool, Add to Library, and Download Sample Library.

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Adding to Reference Library

The Reference Library 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, if 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.

The GUI offers four editable fields:

Image to This option allows you to select which of the loaded

Submit images to submit to the Reference Library.
The Patient ID can be anything that is unique and will
Patient
help you identify this data set when selecting which
ID
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.
Protocol
This will be used as a filter to determine which scans
from the Reference Library will be used by the tool..
Species

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The Species dropdown list contains frequently imaged

species. If you wish to have additions made to the
options provided please contact your Account Manager
or [email protected].

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.

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.

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Reference List Selection

Selecting the proper Reference scan is imperitive to the proper functionality of the tool. The settings selected
by the users that factor into the images used are outlined in the table below:

This the the image in the Data Manager that will be the
Image
basis of the ROIs generated.
The species of the animal being segmented. This is
Species 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
Voxel
loaded. It is not recommended to use Reference Data
Size
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
Protocols 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
ROIs 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 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.

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Downloading Sample Library

A sample Reference Library is available depending on the user's VivoQuant license. This is to be used for
testing and learning how to operate the tool. It can be downloaded from Tools->Advanced Analysis->Whole
Body Atlas->Download Sample Library.

Downloading Sample Library 265

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.

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 Brain Atlas Tool 266

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 ->
Advanced Analysis -> Install Atlas -> Mouse & Rat. To change where the atlases are automatically stored, go
to Tools-> Advanced Analysis -> Install Atlas -> Change Atlas directory and re-install the atlases to this
location.

Getting There
The fMRI Tool is accessed by navigating to Tools -> Advanced Analysis -> fMRI Tool.

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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.

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.
Number of The number of time points will automatically
Time Points update upon loading a data set.
Import from Click on this button to import data into the fMRI
DM Tool that has already been loaded into VQ.
Click on this button to unload data from the tool
Reset
and reset the pipeline settings back to the default
Settings
settings.

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Select 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.

Output The output folder location will be displayed in this

Folder window once a local folder is selected by the user.
Click on the ellipsis button to open a window from
which the user can select a local output folder.
Provide a prefix (optional) to be added to all output
file names. Adding a prefix is useful when
prefix
performing multiple analyses that are being saved
to the same output folder.
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,
Save QC
brain mask, and/or atlas registration QC movies and
images.

Customize Analysis Pipeline

The pipeline section of the fMRI tool allows the user to fully customize their data analysis workflow.

The user can choose to enable or disable any of the following processing modules:

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• Motion Correction
• Smoothing
• Anatomical Registration
• Brain Mask
• Atlas Registration
• General Linear Modeling

Depending on which processes 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.

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.

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

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QC images will be stored to the output directory as well as displayed under the smoothing 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.

The user can choose from the following references:

• 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 is 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.
• Mean Functional: Register to the mean of the functional time series.
• Time Point: Register to a single time point. Either type a specific time point in the box or use the up
and down 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.

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The user can choose from the following masking options:

• None: Does not perform any brain masking.

• Manual: Pauses the processing and prompts the user to manually segment the brain in the 3D ROI
tool using automatic spline tool thresholding.
• Provided: The user must provide brain segmentation (RMHA file).
• 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 suffix '-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.

The user can customize the atlas registration by adjusting the following settings:

• Data to Atlas/Atlas to Data: Choose to register the atlas to the data or vice versa.

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• Atlas: This should populate with the correct provided atlas based on the header information from the
loaded data set.
• 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.
• H/F Flip: Check this box to flip the data (or atlas) in the head/foot direction before registration.
• Affine: Check this box to allow the tool to scale and shear the data (or atlas) during registration, if
necessary.
• Allow Inter-Slice Interp: Check this box to allow the tool to interpolate the data (or atlas) between
slices.
• Cutsom Atlas:: Check this box to provide custom atlas RMHA and anatomical 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.

Customize the analysis and output materials with the following settings:

• Save Residuals: Check this box to save a map of the residuals to the output folder. The name of the
map will be 'residuals'.
• Voxel Maps: Check this box to save parameter maps for the chosen regressors. These files will be
stores with suffix '-paramMap'.
• ROI Plots: Check this box to store all ROI plots in a folder within the specified output folder. The
name of this folder will be 'plots'.
• 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).

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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).

• Remove Last: Click on this button to remove the last regressor column of the design matrix.
• Import Design: Click on this button to load in a custom design matrix that is stored locally in CSV
format.

Run the Tool

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 Continue 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 274

Tumor Segmentation Tool
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 275

Pharmacokinetic Modeling
1. Getting There
2. Function
3. Input/Reference Function Pre-processing
1. Parent/Plasma Fractions
2. Arterial Input Functions
3. Reference Tissue Compartments
4. Saving/Loading Temporal Data
4. Models
1. Two-Tissue Compartment Model (2TCM)
2. One-Tissue Compartment Model (1TCM)
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

Pharmacokinetic modeling is available in VivoQuant as a plug-in for the Modeling operator. Access to the
plug-in depends on your VivoQuant license. For information on your license, please contact your account
manager or email [email protected].

Getting There
The Modeling operator can be accessed via the tool pull-down menu on the VQ front panel.

Function
For more on the function of the Modeling operator, see the Modeling operator page.

Input/Reference Function
Every tissue model requires the input of an additional temporal curve, either as an arterial input function or
concentration of a reference tissue. These temporal data may be derived from image data directly or from
acquired samples. The operator supports input and computation of parent fraction samples, plasma fraction
samples, whole blood concentration, and plasma concentration. In addition, these data can be stored and
retreived from disk and from an iPACS.

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Parent/Plasma Fraction
The experimentalist may have acquired blood samples throughout the subject's scanning session. From these
samples, the ratio of unmetabolized tracer to the sum of unmetabolized tracer and its derivative metabolites
can be measured and used to account for the dynamic nature of "available" tracer. This is also known as the
parent fraction or plasma free fraction. Without it, the tissue model must assume that metabolism of the tracer
is negligible. Whether measured, simulated, or estimated, the parent fraction can play an important role in
accurate estimation of tissue kinetics downstream. Similarly, the fraction of plasma to whole blood (including
red blood cells) has been shown to be an important factor in the estimation of an appropriate arterial input
function [1]. The fraction modeling can be selected from the dropdown of models or from the "Operator"
menu.

Both plasma and parent fraction data can be input using the same tool. Towards the bottom of the operator,
space is provided for a table of fraction data. There are 3 columns. The first can be used to exclude specific
time points from the table. The second column contains the time of each sample in units of minutes. The last
column contains "free fraction" values, assumed to have a value between zero and one. The user can choose to
use a linear interpolation of the points or fit a sum of exponentials to the provided points. The "Save Interp"
button can be used to save the points as is, at which point the tool will prompt the user for a name to give the
saved curve. If this option is chosen, the operator will prepend a value to time=zero, assuming that the fraction
is equal to one at that time. After the last provided time point, the value is assumed to remain constant equal to
the last fraction value.

The user may want to "smooth" the fraction points with a sum of exponentials. Up to 3 exponentials can be
used to fit the curve. If less exponentials are desired, the user can fix model parameters for one or more of the
exponentials (i.e. fix A3=0 and B3=0) [2]. To do so, use the "Run" button to estimate model parameters under
the input conditions provided by the user. Important: use the Estimate t0 button to estimate the start point
for the model. Once you are satisfied with the model estimates, click on "Save Fit" while the estimate plots
are open to save the current model-estimated fraction curve to the list.

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Model Assumptions

This model makes the following assumptions

• The exponential decay begins at user-provided t0

• Provided fraction measurments lie between zero and one

References

[1] "Red blood cells: a neglected compartment in pharmacokinetics and pharmacodynamics". Hinderling.
Pharmacol Rev, 1997. Link.

[2] "Optimal Metabolite Curve Fitting for Kinetic Modeling of 11C-WAY-100635". Wu, et al. JNM, 2007.
Link.

Arterial Input Function

An Arterial Input Function (AIF) is required for Logan, Patlak, 1- and 2-tissue compartment, and MA1
analysis. To add time points to an AIF, begin by selecting "Blood/Ref 3-Exp" from the list of models.

Similar to the parent fraction, the user can select to save a linear interpolation of points or a smooth model
estimate of AIF samples. Either way, samples should be input into the table of values as a first step. This may
be done with a copy/paste from an external spreadsheet program or by incrementing the "Time Points (table
rows)" number and manually editing the table. The table assumes a structure with the number of rows equal to
the number of samples. Each sample has three columns. The first column indicates whether that sample
should be excluded or not. The second column contains the time (in minutes) at which sample was measured.
Times should be consistently relative to the same reference start time as the final modeled time activity
curves. The third column contains the measured concentration value at that time. If parent or plasma fraction
data are available and applicable to the provided samples, select them from the dropdown. If none is selected,
the fraction is assumed to be one for the entirety of the time activity curve. If image dervied samples are
desired, the user may also compute the samples directly from the average concentration values with ROIs in
the loaded image. To do this, select the appropriate region from the dropdown and click on the "Compute IF"
button. For more information on segmenting regions of interest from an image, see the 3D ROI tool.

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Important: select a unit of concentration for the samples. By default, this dropdown will be set to the
unit of the loaded image data. If a sum of exponentials model for the samples is desired for "smoothing" the
data, click on "Run" to estimate exponential parameters for the data. Before doing so, it may be important to
select an appropriate t0 value. This is best estimated from the samples themselves with the "Estimate t0"
button, which will set t0 to the time point where the maximum concentration occurs in the samples. The
linearly interpolated samples or model fit may be saved for use in tissue modeling with the "Save Interp" or
"Save Fit" buttons, respectively.

Reference Tissue Compartment

The reference tissue compartment concentrations can be readily computed similar to the Arterial Input
Function (AIF). Like the AIF, you may input the concentrations from a spreadsheet or by manual input;
however, it is more likely you will want to derive the concentration values from a reference region segmented
on the loaded images. For more information on segmentation techniques in VivoQuant, see the 3D ROI tool.
Begin by navigating to the "Blood/Ref 3-Exp." model in the operator. Next select, the appropriate region of
interest in the dropdown next to "Img Derived" label.

The "Compute IF" button will compute the average concentration in the selected region and populate the
table, one row for each volume loaded. The time points are computed from the image acquisition times and
frame durations, set to the midpoint of each frame, and relative to the start of the dynamic scan. Should the
temporal information be missing from the image data, this can be added using the "Frame Time Editor", found
in the "Tools" menu. A sum of exponentials model can also be estimated from the table data. Ensure that the
parent/plasma fraction inputs are disabled by setting their respective dropdown setting to "1". To save a linear
interpolation of the concentrations, click on the "Save Interp" button. Should you want to fit a sum of
exponentials, begin by specifying an appropriate t0 parameter which can typically be estimated using the
"Estimate t0" button. Fitting the sum of exponentials model can be done with the "Run" button, at which point
you will be able to save the fit using the "Save Fit" button.

Saving and Loading of Fraction, AIF, and Reference Region Data

All temporal curves can be saved with the "Save Interp" or "Save Fit" buttons. When they are saved, their
user-provided name appears in the dropdown of "Saved Curves."

Controls next to the dropdown are available for saving, loading, and viewing the curves. The

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menu provides options for storing the temporal data to/from the iPACS or as a
spreadsheet on your local hard drive. This is particularly useful to avoid re-entry of the information should

you want to re-run analysis at a later date. The menu is an additional tool for the user to
store the current linearly interpolated samples or modeled data into the list of saved curves. The button

clears the currently selected temporal curve from the list. Lastly, the button opens a new
dialog window showing a plot of the temporal curve which can be saved as a local image for quality control.

Additional Resources
"Emission Tomography: The Fundamentals of PET and SPECT", Miles Wernick & John Aarsvold. Elsevier,
2004. Print.

"Fractions of unchanged tracer in plasma", Vesa Oikonen. Turku PET Center website. Link

"Converting blood TAC to plasma TAC", Vesa Oikonen. Turku PET Center website. Link

"Blood sampling in PET studies", Vesa Oikonen. Turku PET Center website. Link

"Arterial input function from PET image", Vesa Oikonen. Turku PET Center website. Link

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.

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Parameter Description
Concentration in F + NS compartment,
CND(t)
nodisplaceable tracer
Concentration in specifically bound (S)
CS(t)
compartment
CP(t) Concentration in plasma (P) compartment
Transfer of ligand from arterial plasma to
K1 (mL*cm3*min-1)
tissue
Transfer of ligand from tissue to arterial
k2 (min-1)
plasma
Transfer of ligand into specifically bound
k3 (min-1)
compartment
Transfer of ligand out of specifically bound
k4 (min-1)
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. K1, k2, k3 and k4). One such macroparameter that is
estimated by the 2TCM is the total volume of distribution, VT.

When the 2TCM is applied to image data with a reference region, the distribution volume ratio (DVR) can be
calculated: DVR = VT/VND, where VND 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 (BPND)
can then be calculated by BPND = DVR - 1.

Model Assumptions

This model makes the following assumptions

• The tracer binds reversibly.

• Nonspecifically bound ligand equilibrates rapidly with free tissue ligand.
• 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.
♦ 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,

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Required Inputs

This model requires the following inputs

• Metabolite-corrected arterial plasma input curve

• ROI(s) or voxels

Outputs

Region-level analysis:

• Plot of data from each ROI with 2TCM fit.

• VT, K1, k2, k3, k4, mean-squared error (MSE) of fit, Θ1, and Θ2 are shown when the cursor is hovered
over the model fit plot.
• VT, K1, k2, k3, k4, 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 function: general principle and application to [18F]fluorodeoxyglucose positron emission tomography".
Hong, et al. NeuroImage, 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].

Parameter Description
Concentration in F + NS compartment,
CND(t)
nondisplaceable tracer
CP(t) Concentration in plasma (P) compartment
Transfer of ligand from arterial plasma to
K1 (mL*cm3*min-1)
tissue
Transfer of ligand from tissue to arterial
k2 (min-1)
plasma

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VT = K1/k2 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.

In some cases, the exchange of tracer between the nondisplaceable and bound tissue is sufficiently fast that the
two cannot be distinguished kinetically. 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 k2a and VT = K1/k2a.

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 = VT/VND, where VND is the estimated
distribution volume in the reference region. Binding potential (BPND) can then be calculated by BPND = DVR -
1.

Model Assumptions

This model makes the following assumptions

• The tracer binds reversibly.

• Nonspecifically bound ligand equilibrates rapidly with free tissue ligand.
• 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.
♦ 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

• Metabolite-corrected arterial plasma input curve

• ROI(s) or voxels

Outputs

Region-level analysis

• Plot of data from each ROI with 1TCM fit.

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• VT, K1, k2, and mean-squared error (MSE) of fit are shown when the cursor is hovered over the model
fit plot
• VT, K1, k2, and mean-squared error (MSE) of fit, data, and 1TCM fit for each ROI can be saved out to
.csv.

Voxel-level analysis

• 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 it with the image viewer.
• VT, K1, k2, and mean-squared error (MSE) of fit are shown when the cursor is hovered over the model
fit plot.
• Parameter maps for VT, K1, k2, 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 clinical [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. NeuroImage, 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 based on the Patlak method for
irreversibly bound tracers [2]. The Logan method proposes that after some time t*, the plot of

vs.

where CT 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 total volume of distribution, VT.

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When the Logan Plot is applied to image data with a reference region, the distribution volume ratio (DVR) can
be calculated: DVR = VT/VND, where VND is the estimated disctribution volume in the reference region. BPND
is related to DVR by BPND = 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 CT(t), and this results in an underestimation of VT which
becomes more pronounced with larger true VT 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

• The tracer binds reversibly

• After some time t* the slope of the plot of vs. 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

• Metabolite-corrected arterial plasma input curve

• ROI(s) or voxels
• 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 t*
value is 0. This is likely not 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 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 plots to find the
point at which they become linear (t*), then re-run the model with the appropriate t* (in scan

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time) value.

Outputs

Region-level analysis

• 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.
• VT, fitted line intercept, and mean-squared error (MSE) of fit are shown when the cursor is hovered
over the Logan plot.
• Parameter maps for VT, fitted line intercept, and 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 clinical [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

Reference Region

Parameter Description
CT(t) Concentration in F + NS + S compartment

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Concentration in F + NS compartment,
CND(t)
nondisplaceable tracer
CP(t) Concentration in plasma (P) compartment
Transfer of ligand from arterial plasma to
K1 (mL*cm3*min-1)
tissue
Apparent transfer of ligand from tissue to
k2a (min-1)
arterial plasma
Transfer of ligand from arterial plasma to
K1' (mL*cm3*min-1)
reference tissue
Transfer of ligand from reference tissue to
k2' (min-1)
arterial plasma

Model Assumptions

This model makes the following assumptions

• The tracer binds reversibly

• 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
• 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 function method approach and unweighted fitting [3].

Required Inputs

This model requires the following inputs

• Reference tissue curve

• ROI(s) or voxels

Outputs

Region-level analysis

• Plot of data from each ROI with SRTM fit

• BPND, R1,k2,k2', and mean-squared error (MSE) of fit are shown when the cursor is hovered over the

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model fit plot.

• BPND, R1,k2,k2', and mean-squared error (MSE), data and SRTM fit for each ROI can be saved out to
.csv.

Voxel-level analysis

• Plot of data for each voxel with SRTM fit. Select the voxel for which you'd like to see the model fit
by clicking on it with the image viewer.
• BPND, R1,k2,k2', and mean-squared error (MSE) of fit are shown when the cursor is hovered over the
model fit plot.
• Parameter maps for BPND, R1,k2,k2' and MSE.

References

[1] "Simplified reference tissue model for PET receptor studies", Lammerstma and Hume. NeuroImage, 1996.
Link

[2] "The simplified reference tissue model: model assumption violations and their impact on binding
potential", Salinas, et al. JCBFM, 2015. Link

[3] "Parametric imaging of ligand-receptor binding in PET using a simplified reference region model". Gunn,
et al. NeuroImage, 1997. 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 k2' [1]. In practice, SRTM estimates k2' for every voxel or region, but since there is
only one reference region, in principle there is only one true k2' value [1]. Fixing k2' 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 bias [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

• The tracer binds reversibly

• 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
• 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)

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has the same concentration of tracer free in tissue and nonspecifically bound as the ROI
• There is only one true k2' value. k2' 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

• Reference tissue curve

• ROI(s) or voxels
• A fixed k2'
♦ Selection of a fixed k2': The value to which to fix k2' should be selected based on the tracer
and the experiment. For characterized tracers, we suggest reviewing the literature to see how
the fixed k2' has been selected in different studies and the effect of the method to fix k2' on
SRTM2 parameter estimates. Generally, k2' can be fixed to the median value estimated by a
first-pass of SRTM from all voxels with a BPND value > 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 k2' to the
population average value estimated from a 1-tissue compartment model fit to the reference
region [3] or estimated k2' for each subject by a simultaneous SRTM fit including all target
regions with coupled k2' [3,6]. SRTM fit with coupled k2' is not currently available in
VivoQuant.

Outputs

Region-level analysis

• Plot of data from each ROI with SRTM2 fit

• BPND, R1,k2a, and mean-squared error (MSE) of fit are shown when the cursor is hovered over the
model fit plot.
• BPND, R1,k2a, and mean-squared error (MSE), data and SRTM2 fit for each ROI can be saved out to
.csv.

Voxel-level analysis

• Plot of data for each voxel with SRTM2 fit. Select the voxel for which you'd like to see the model fit
by clicking on it with the image viewer.
• BPND, R1,k2a, and mean-squared error (MSE) of fit are shown when the cursor is hovered over the
model fit plot.
• Parameter maps for BPND, R1,k2a, and MSE.

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References

[1] "Noise reduction in the simplified reference tissue model for neuroreceptor functional imaging.", Wu and
Carson. JCBFM, 2002. Link

[2] "Parametric imaging of ligand-receptor binding in PET using a simplified reference region model". Gunn,
et al. NeuroImage, 1997. 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

[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 input 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

vs.

(where CT is the concentration of the tracer in the tissue and CR is the concentration of the tracer in the
reference region) becomes linear with slope equal to the distribution volume ratio (DVR). Binding potential
(BPND) is related to DVR by BPND = DVR - 1.

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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 CT(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

• The tracer binds reversibly

• 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
• After some time t* the slope of the plot of vs 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

• Reference tissue curve

• ROI(s) or voxels
• 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.

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Outputs

Region-level analysis

• Logan plot with line fit for each ROI.

• DVR, fitted line intercept, and mean-squared error (MSE) of fit are shown when the cursor is hovered
over the Logan plot.
• DVR, fitted line intercept, and transformed Logan space data for each ROI can be saved out to .csv

Voxel-level analysis

• 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.
• DVR, fitted line intercept, and MSE of fit are shown when the cursor is hovered over the Logan plot.
• 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

[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 analysis is rearrangement of tracer kinetic equations to yield a useful linear equation [1]. Patlak
analysis proposes that after some time t*, the plot of

vs.

where CT 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, Ki. The
rate constant Ki represents influx and trapping of the tracer into the tissue [1,2].

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In terms of a two-tissue compartment model where k4 = 0 because the tracer is irreversibly trapped, Ki =

Model Assumptions

This model makes the following assumptions

• The tracer binds irreversibly

• After some time t*, the slope of the plot of vs. 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

• Metabolite-corrected arterial plasma input curve

• ROI(s) or voxels
• t* (in scan time)
♦ Selection 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

• Patlak plot with line fit for each ROI.

• Ki, fitted line intercept (V), and mean-squared error (MSE) of fit are shown when the cursor is
hovered over the Patlak plot.
• Ki and transformed Patlak space data for each ROI can be saved out to .csv

Voxel-level analysis

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• Patlak plot with line fit for each voxel. Select the voxel for which you'd like to see the Patlak plot by
clicking on it within the image viewer.
• Ki, fitted line intercept (V), and mean-squared error (MSE) of fit are shown when the cursor is
hovered over the Patlak plot.
• Parameter maps for Ki, 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 Rate, (Ki)", Vesa Oikonen. Turku PET Center website. Link.

Additional Resources

"Multiple Time Graphical Analysis (MTGA)", Vesa Oikonen. Turku PET Center website. Link.

Patlak Analysis (Patlak Plot) 294

SPECT Tools
The SPECT Tools sub-menu contains features primarily associated with improving SPECT quantification.

• QuantiCalc
• Specific Activity Calculator
• SUV Calculator
• Crosstalk Removal
• Biodist. Visualization
• Split Projections

SPECT Tools 295

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 There
The QuantiCalc tool is available via the Tools Menu

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.

The procedure for collecting Quantification Factor data involves performing a highly-specified SPECT
measurement on a syringe filled with isotope. The fields of the QuantiCalc window may then be filled in
according to:

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• 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.
• NanoSPECT: Record the activity value measured by the NanoSPECT from reconstructed data.
Include the time of data collection.
• Isotope: Select the isotope present in the syringe. Isotopes offered include Ga-67, I-123, I-125,
Lu-177, Tc-99, Tl-201, In-111, and Xe-133. The half-life of the selected isotope will be entered
automatically in units of hours.
• 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.
• 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 Factors for the NanoSPECT/CT, please see this guide.

Function 297
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.

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.

Value Units Description

Activity MBq, kBq, mCi, Amount of isotope as measured in a
or µCi and dosimeter or with the NanoSPECT.
measurement

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time
Volume cm3, mm3, ml, µl The volume containing the activity.
The 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
Specific kBq/pmol and describes the number of excited
Activity measurement atoms out of the total atoms present
time in a given sample, i.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
pmol/ml,
Molarity concentration, of excited molecules in
nmol/ml
a sample of activity.

Function 299
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.

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 with the
activity concentration to calculate the SUV. Units for these entries are user-selectable.

Value Units Description

Amount of isotope as measured
MBq, kBq, mCi,
Activity in a dosimeter or with the
or µCi
NanoSPECT.
The volume containing the
Volume cm3, mm3, ml, µl
activity.
Concentration kBq/ml, The ratio of activity to volume.
MBq/ml,

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mCi/ml,
kBq/mm3,
MBq/mm3
Patient The weight of the animal or
g, kg
Weight object of interest.
The amount of isotope
MBq, kBq, mCi,
Injected Dose successfully injected into the
or µCi
subject.
The specific uptake value (SUV)
mg/ml, g/ml,
given the patient weight, activity
SUV kg/ml, g/l,
concentration, and injected dose
g/mm3, kg/mm3
specified in the other fields.

Function 301
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

Function
Please visit How To Guides on the VivoQuant website to download a stand-alone PDF guide for performing
Crosstalk Removal.

Crosstalk Removal 302

Biodist. Visualization
The Biodistribution Visualization tool creates an atlas representation of measured mouse biodistribution
values.

Getting There
Biodistribution Visualization is available in the Advanced Modules Menu in SPECT Tools.

Function
To use the Biodistribution Visualization function, enter the total measured activity for each region-of-interest
available in the atlas list.

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After entering the appropriate values, select one of the buttons at the end of the list.

Button Description
New Clears all fields
Load Load a previously saved biodistribution text file.
Save Save the current biodistribution data into a text file.
Cancel Closes the Biodist. Visualization window
Prepares the atlas with the entered biodistribution
OK
information.

Function 304
Split Projections
The Split Projections tool may be used to split a single 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.

One specialized application for the Split Projections tool is the splitting of gated data. In this case, the data
may be split directly from inside the Data Browser.

Function
Upon selection of the Split Projections tool, the Data Browser opens. Select an appropriate 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.

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Function 306
CT Tools
The CT Tools Submenu contains features to aid in the preparation of CT data for analysis and display.

• CT Reconstruction
• Bed Removal
• Resample Data

CT Window Presets can also be selected from within this window.

CT Tools 307
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

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.

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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.

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Reconstruction Parameters

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 µm, 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

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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 (i.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 (i.e., Fast instead of Ultra-Fine in Nucline).

The exact memory requirements are as such:

Algorithm Bytes per Voxel

Exact cone beam 2*4 per thread
Fast cone beam 4

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):

Setup Requirements
Fast cone beam: 6 bpv
bytes per voxel (bpv) Exact cone beam 1 thread: 10 bpv
Exact cone beam 2 threads: 18 bpv
Voxels = 9,720,000
Fast cone beam: 55 MB
Mouse, 36x36x60 mm, 200µm voxels
Exact cone beam 1 thread: 93 MB
Exact cone beam 2 threads: 167 MB
Mouse, 36x36x37 mm, 100µm voxels Voxels = 47,952,000

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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
Mouse, 36x36x20 mm, 50µm voxels
Exact cone beam 1 thread: 1977 MB
Exact cone beam 2 threads: 3560 MB
Voxels = 5,405,625
Fast cone beam: 31 MB
Rat, 62x62x90 mm, 400µm voxels
Exact cone beam 1 thread: 52 MB
Exact cone beam 2 threads: 92 MB
Voxels = 28,830,000
Fast cone beam: 164 MB
Rat, 62x62x60 mm, 200µm voxels
Exact cone beam 1 thread: 275 MB
Exact cone beam 2 threads: 495 MB
Voxels = 76,880,000
Fast cone beam: 440 MB
Rat, 62x62x20 mm, 100µm voxels
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

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The Preview panel displays the CT reconstruction as it is being calculated. The Color Panel provides several
color map options.

File Menu

Option Description
Identical to the function of &apos;Ctrl+D&apos;, this
Load option opens the Data Browser window from where a
DICOM set of CT projection data may be loaded. Note that the
Data... Browser opens with the &apos;CT Projection&apos;
data filter set.
Identical to the function of &apos;Ctrl+L&apos;, this
Load
option opens a Windows Explorer browser window.
Local
A properly chosen CT projection data set is then
Data...
loaded into the CT Reconstruction tool.

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Allows the user to save the data in DICOM format

Save...
both into the selected repository and a local folder.
The reconstruction is opened in the VQ. If the
Transfer to
reconstruction is allowed to finish, this transfer occurs
VQ
automatically.
Settings Menu

Option Description
Save Settings Saves the current CT Reconstruction Settings
The Hounsfield Calibration uses the linear
response of the detector at each of the x-ray
Hounsfield... 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.
Threads Note that it only makes sense to enable as many
threads as there are cores available in the
computer&apos;s processor.
Defines the priority given to the CT
Thread
Reconstruction with respect to other tasks being
Priority
performed by the CPU.
Allows the user to disable the use of normalization
in the reconstruction. Disabling normalization
Advanced prevents the use of Hounsfield Calibration, but
reduces the memory usage required for the
reconstruction.
For users imaging with the Minerve bed system,
Auto Bed
this option will automatically remove the Minerve
Removal
bed from the CT during reconstruction.
Help Menu

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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.

Option Description
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
the voxel size may slightly alter the voxel volume.
Allows the user to modify the reconstructed volume
Voxel 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
Z offset volume to better center features of interest, enabling
(disabled) more reasonable resolution times for high-resolution
images.
Sets the number of rays used by the Exact Cone
Sampling
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.

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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".

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.

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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.

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.

Option Description
Mod Provides information on the modality used i.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.
This is the name of the folder from which the X-ray
Patient
projection data was taken.
Parameter
Provides information on the status of the
reconstruction. If the status is Running then the
reconstruction is underway, if it is Waiting then the
Status 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.

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Status
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.

Option Description
Hides the Batch CT window from the desktop. Also
Hide
reached using the Ctrl+H keyboard shortcut.
Quits the Batch CT application. Also reached using
Quit
the Ctrl+Q keyboard shortcut.
Stop Stops the Batch CT application. Also reached using
Service the Ctrl+T keyboard shortcut.
Start
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.

Option Description
Pause Pauses the current reconstruction job.

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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
MoveDown
studies to be reconstructed.
EditJob Allows you to edit the reconstruction parameters.
Deletes the projection data from the reconstruction
DeleteJob
list.
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.

Option Description
Thread
Sets the number of threads used during reconstruction.
Number
The BatchCT tool may be given different priority
levels. Lower priority means that the tool will run only
Thread
when the computer is completely idle. A higher
Priority
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
Show
added, completed, etc. This switch controls whether or
bubbles
not these bubbles appear.

Jobs Menu 319

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

Reset the HU values in the panel so that each Slope = 1.0 and each Intercept = 0.0.

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Fill a large (>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.

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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 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.

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Hounsfield Calibration 323

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

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.

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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.

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Reconstruction Parameters

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 µm, 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

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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 (i.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 (i.e., Fast instead of Ultra-Fine in Nucline).

The exact memory requirements are as such:

Algorithm Bytes per Voxel

Exact cone beam 2*4 per thread
Fast cone beam 4

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):

Setup Requirements
Fast cone beam: 6 bpv
bytes per voxel (bpv) Exact cone beam 1 thread: 10 bpv
Exact cone beam 2 threads: 18 bpv
Voxels = 9,720,000
Fast cone beam: 55 MB
Mouse, 36x36x60 mm, 200µm voxels
Exact cone beam 1 thread: 93 MB
Exact cone beam 2 threads: 167 MB
Mouse, 36x36x37 mm, 100µm voxels Voxels = 47,952,000

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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
Mouse, 36x36x20 mm, 50µm voxels
Exact cone beam 1 thread: 1977 MB
Exact cone beam 2 threads: 3560 MB
Voxels = 5,405,625
Fast cone beam: 31 MB
Rat, 62x62x90 mm, 400µm voxels
Exact cone beam 1 thread: 52 MB
Exact cone beam 2 threads: 92 MB
Voxels = 28,830,000
Fast cone beam: 164 MB
Rat, 62x62x60 mm, 200µm voxels
Exact cone beam 1 thread: 275 MB
Exact cone beam 2 threads: 495 MB
Voxels = 76,880,000
Fast cone beam: 440 MB
Rat, 62x62x20 mm, 100µm voxels
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

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The Preview panel displays the CT reconstruction as it is being calculated. The Color Panel provides several
color map options.

File Menu

Option Description
Identical to the function of &apos;Ctrl+D&apos;, this
Load option opens the Data Browser window from where a
DICOM set of CT projection data may be loaded. Note that the
Data... Browser opens with the &apos;CT Projection&apos;
data filter set.
Identical to the function of &apos;Ctrl+L&apos;, this
Load
option opens a Windows Explorer browser window.
Local
A properly chosen CT projection data set is then
Data...
loaded into the CT Reconstruction tool.

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Allows the user to save the data in DICOM format

Save...
both into the selected repository and a local folder.
The reconstruction is opened in the VQ. If the
Transfer to
reconstruction is allowed to finish, this transfer occurs
VQ
automatically.
Settings Menu

Option Description
Save Settings Saves the current CT Reconstruction Settings
The Hounsfield Calibration uses the linear
response of the detector at each of the x-ray
Hounsfield... 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.
Threads Note that it only makes sense to enable as many
threads as there are cores available in the
computer&apos;s processor.
Defines the priority given to the CT
Thread
Reconstruction with respect to other tasks being
Priority
performed by the CPU.
Allows the user to disable the use of normalization
in the reconstruction. Disabling normalization
Advanced prevents the use of Hounsfield Calibration, but
reduces the memory usage required for the
reconstruction.
For users imaging with the Minerve bed system,
Auto Bed
this option will automatically remove the Minerve
Removal
bed from the CT during reconstruction.
Help Menu

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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.

Option Description
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
the voxel size may slightly alter the voxel volume.
Allows the user to modify the reconstructed volume
Voxel 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
Z offset volume to better center features of interest, enabling
(disabled) more reasonable resolution times for high-resolution
images.
Sets the number of rays used by the Exact Cone
Sampling
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.

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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".

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.

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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.

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.

Option Description
Mod Provides information on the modality used i.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.
This is the name of the folder from which the X-ray
Patient
projection data was taken.
Parameter
Provides information on the status of the
reconstruction. If the status is Running then the
reconstruction is underway, if it is Waiting then the
Status 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.

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Status
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.

Option Description
Hides the Batch CT window from the desktop. Also
Hide
reached using the Ctrl+H keyboard shortcut.
Quits the Batch CT application. Also reached using
Quit
the Ctrl+Q keyboard shortcut.
Stop Stops the Batch CT application. Also reached using
Service the Ctrl+T keyboard shortcut.
Start
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.

Option Description
Pause Pauses the current reconstruction job.

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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
MoveDown
studies to be reconstructed.
EditJob Allows you to edit the reconstruction parameters.
Deletes the projection data from the reconstruction
DeleteJob
list.
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.

Option Description
Thread
Sets the number of threads used during reconstruction.
Number
The BatchCT tool may be given different priority
levels. Lower priority means that the tool will run only
Thread
when the computer is completely idle. A higher
Priority
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
Show
added, completed, etc. This switch controls whether or
bubbles
not these bubbles appear.

Jobs Menu 335

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 VQ Calibration
application.

Getting There
The Calibration menu is available in the Tools Menu.

Function
Several calibration measurements are required to calibrate and maintain the NanoSPECT/CT imaging system.
The Calibration menu provides options for analyzing:

• CT Geometrical Calibrations
• Multi-Pinhole SPECT Calibrations
• Near Field Flood QC Measurements
• Access to the VQ Calibration Application

Calibration 336
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.

If running the VQ Calibration Application, enter the tool by pressing "CT Geometrical Calibration."

Function
The gantry of the NanoSPECT has a reproducible wobble 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.

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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.

The CT Geometrical calibration panel is divided into five sections -- Projections, Orbits, 2nd Order
Corrections, 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.

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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.

To zoom in on a particular orbit, draw a box by holding down the left mouse button and dragging.

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Upon release of the button, the display will show only the selected orbit. To return to the full view, just
right-click.

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 values be less than +/-0.5mm to enable
successful correction of the gantry motion in the CT reconstruction.

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).

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The Control panel houses four buttons, including

• Open -- Opens the Data Browser where a CT Geometrical data set may be selected for analysis.
• Close -- Closes the CT Geometrical panel.
• Save Calib -- Saves the existing calibration in the format used by the NanoSPECT/CT.
• Show Calib

Function 341
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.

If running the VQ Calibration Application, enter the tool by pressing "Multiplexing Multi-Pinhole SPECT
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, Output, 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

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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
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.

After successfully completing the analysis, the result CalibrationData_YYYYMMDD.txt file can be copied
into C:\Nucline\Calibrations\CalibrationData.txt to update the calibration information used by the
NanoSPECT.

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Templates

The Templates section controls the input and output files used/generated by the calibration analysis.

• 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 (i.e., only a 4-point measurement)
have been performed.
• Empty Template: As a default, an empty template, designed for use with the Nucline software, is used
to generate the CalibrationData.txt file.
• Output File: Any name may be specified for the Output file of the calibration analysis. The default
name is CalibrationData_YYYYMMDD.txt.
• 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.

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• Show Calib: Opens the current CalibrationData_YYYYMMDD.txt file for viewing.

• Open... : Opens a browser that is to be used for loading MMP Calibration data (DICOM format).
• Clear: Clears the Output panel of the MMP Calibration window
• 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 allows 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.

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.

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.

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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.

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.

Error
Calibration Interpretation Limits
Message
Intrinsic Intrinsic detector
Rx >2.4 mm
Resolution resolution
Intrinsic <0.97mm or
Px Pixel Size
Resolution >1.03mm
Intrinsic
Lx Quality of linearity >30 (A.U.)
Resolution
Collimator Detector plane to >130.1mm or
Hx
Depth aperture plane distance <134.1mm
Absolute distance
Collimated between aperture center
Hx >1.5mm
Beam and detector center (y or
z)
Absolute aperture offset
4-Point Ax >1.0mm
(transaxial or axial)
Absolute detector offset
4-Point Dx >1.5mm
(transaxial or axial)
>45.9mm or
4-Point Rx Radius of rotation
<43.9mm
Overall quality of the
4-Point Q >3.0 (A.U.)
calibration
4-Point B Horizontal bed offset >3.0mm

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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

Collimated Beam Preview

Four-Point Preview

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Output

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.

MMP Menus

Several useful fixes and features may be found in the MMP Menus of File, Tools, and Help.

MMP Keyboard
Item Function
Menu Shortcut
Identical to the "Open"
button in the Control panel,
File Open Data... this opens a browser to allow Ctrl-O
the loading of calibration
data files.
The ID of the NanoSPECT
Basic and # of heads (typically 2 or
File Ctrl-B
Configuration 4) are set in this panel,
pictured below.
File Enable By default, the collimator
ColDepth depth phantom is not used in
the MMP Calibration

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analysis. However, it may be

enabled with this checkbox.
Used to exit the MMP
File Exit Ctrl+Q
Calibration tool.
By default, the collimator
depth phantom is not used in
Enable
File the MMP Calibration
ColDepth
analysis. However, it may be
enabled with this checkbox.
In the presence of only one
single-pinhole aperture,
Merge 4-point 4-point data are collected one
Tools
files 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
Tools
File needed. This tool converts
the calibration file
accordingly.

Templates 349
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.

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.

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The data for each head will appear in the appropriate box. To run the analysis, press "Calculate".

As the data are analyzed, the screen is grayed out. Progress can be monitored in the "Results" panel shown on
the left.

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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.

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."

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Function 353
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 unit 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

Function
Getting Started
Start the tool by selecting 'Export Quantification'.

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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 another spreadsheet software.

Tip: It is likely easier to make changes in batch in a spreadsheet software.

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 -> AUC Calculation.

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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 'isotopes.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.

Next click "Update Plot" and enter in the initial percent injected doses assumed for each of the ROIs.

The Plot should now appear next to the table in the window

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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 357

Help
The Help Menu provides access to important information like registration and the manual.

• Registration
• Debug
• Manual
• About

Help 358
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.

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

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 359
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.

The keyboard shortcut of F1 can also be used to open the manual.

Function
Once the Manual is open the user can browse 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:

• Installation
• File Management
• View
• Post-Processing
• Tools
• Help
• Keyboard Shortcuts

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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 361
About
Getting There
To open the About section go to "About" under the Help menu.

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 362
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.

To install the software, double-click on the installer icon on the 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".

Initializing the VQ Help Reporter will save a copy of the session currently in-progress.

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Most reports will first request a written description of the problem to be included in a text file attached to the
report.

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.

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.

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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".

The "Add Comment" button opens a text dialogue that may be used to add additional written comments to the
report.

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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.

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 registry files (automatically gathered), example DICOM files, a
screenshot, a comment file, and a manually selected "User file".

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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 (i.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.

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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 the zip file to a local machine
and then, please email [email protected] with a link to your report.

NOTE: A contact email must be included to "Save" or "Send" the report.

Please contact [email protected] should you have any questions.

How to use the VQ Reporter Tool 368

iPACS Sync
The iPACS Sync application is designed for batch two-way data transfers between the WebDisk of a specific
iPACS project and a local storage location. Directories and files are synchronized between the source and
destination locations and data transfers are authorized by an iPACS user's account permissions.

Batch Transfer Data to and from the iPACS

Browse the following links to learn more about using iPACS Sync to batch transfer data.

• Download latest iPACS Sync Application

• Run a Sync Job
• Configure a Sync Job
• Sync Specific Files from an iPACS

iPACS Sync 369

Configure a Sync Job
This page contains information on the various steps and options available for configuring an iPACS Sync job:

• Create a Sync Job using the Wizard

• Configuring Additional Settings
• iPACS Setup
• Directory Setup
• Scheduler
• Notifications
• Advanced
• 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.

1. 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.

4. The wizard will attempt to download and install the sync key file for the specified 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.
5. Once the Sync Key is installed, click Next.
6. Specify the direction of the Sync.
7. Provide the complete path to the local directory to use in the Sync.
8. Select the project on the iPACS to use for the Sync.

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♦ The 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 WebDisk
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.

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.

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 iPACS 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.

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Select the job to configure from the Open drop-down, or enter a name and click Create to create a new
Sync job.

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 data transfer iteration.
Click the configuration button to automatically obtain the sync key file from the iPACS if necessary.

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 iPACS to use for the Sync; the button will retrieve a list of projects on the iPACS, and
the Filter field can be used to limit the projects that are displayed in the drop-down to those that match the
filter. The WebDisk folder for the selected project will automatically be entered into the WebDisk field.
Subfolders can be selected by clicking the arrow to the right of the text field.

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Setting Description
Files that have been successfully transferred to the
Delete local files server are deleted locally. This feature is potentialy
after transfer dangerous and could lead to LOSS OF DATA if not
used properly.
Schedule when files are removed from source
Delete after
location.
Scheduler
Create a schedule for when a Sync job will run.

Setting Description
Specify how often a Sync job runs while the
Scan interval
application is open.
A Sync job will automatically start whenever a new
Autosync changes
folder is added to the top level folder.
Only during scheduled A Sync job will automatically start at the time
scan interval specified on the days selected.
Notifications

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Setting Description
Message Turn 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.
Username Username used associate with your email account.
Password Authorization to access your email account.
From Email account from which the notification will be sent.
Recipients Notifcaitons will be sent to the provided email addressess.
Advanced
Include or exclude files by specifying their extension. (e.g. *.dcm *.img *.hdr *.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:
-*

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.

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Setting Description
Verbose Print more detailed log messages.
Compression Data is compressed before sending.
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
Sync deleted files
could lead to LOSS OF DATA if not used
properly.
Modified files at destination end will not be
Keep newer files
overwritten.
Ignore all version control hidden files (.svn folder)
CVS Exclude
when resotring files via iPACS sync.
Always Prompt for User will be asked to specify download destination
download destination for each file downloaded via iPACS sync from the
(global setting) iPACS.
Store Job
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 375
iPACS Sync GUI
The following sections describe how to run an iPACS Sync job:

• Run a Sync Job

• Icon Descriptions
• 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.

Icon Descriptions
Icon Description
Pause a Sync Job
Run all active Sync Jobs
Stop a Sync Job
Open the configuration page
Open the help guide
Quick Sync
This feature is a simple way to quickly download files from a WebDisk folder, or it can facilitate the transfer
of large amounts of data from the iPACS to a local location.

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
Sync.
2. A 'browser.irsync' file will be downloaded.

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3. In the iPACS Sync client, open the 'browser.irsync' file by going to Jobs -> Quick Sync File, then
selecting the file.
4. If a saved job has not been configured for this iPACS, the client will require login credentials for the
iPACS.
5. Select a folder where the iPACS files will be saved.
6. The iPACS Sync client will run a job to transfer the selected files to the specified location.

Quick Sync 377

Troubleshooting
Should you run into any issues with VivoQuant, please contact us at <[email protected]>, consider
using our Service Reporter, and check out the list of trouble shooting categories below:

Trouble shooting categories

• Service Reporter: Gather information (automatically and manually selected) to send a service/support
report.
• Memory: Solve memory issues on Windows 32-bit systems
• Debugging: View VQ debug messages and/or activate log file
• Saving images/movies: Solve issues saving images or movies
• Logfile: Where to find the VQ logfile
• 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 378
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)\WINDOWS="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 your 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
Edit
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 is
only limited by the physically available RAM in your Mac.

Memory configuration 379

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.

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

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 380
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 381

VQ Keywords
/23ABCDEFGHIJKLMNOPQRSTUVWZ

• Function
• Getting There
• Patlak Analysis (Patlak Plot)

/
• /3GB

2
• 2D Drawing Tools
• 2nd Capture

3
• 3D and 2D Automatic Options
• 3D and 2D Manual Options
• 3D Segmentation Tools
• 3DROITool Object

A
• About
• ACQ_NSxx_DCMSRV
• Adding to Reference Library
• Adding VQ as a DICOM Client
• Alpha version
• Anonymizer
• Append
• Append Projections
• Apply default shift
• Arterial Input Function
• Automatic Non-Linear Registration
• Automatic Slice-by-Slice Non-Linear Registration
• Axial Sliders

B
• Batch Mode Reconstruction

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• BatchCT Tool
• BatchTool Generator
• Beta version
• Bias Field Correction
• boot.ini

C
• Cache
• Calibration failures!
• Calibration failures!
• Capture Viewer
• Captures
• Change Delay
• Choosing the ROI type
• Choosing the View Direction
• Color Controls
• Color Maps
• Configuration
• Confirm Configuration
• Control
• Control
• Controls
• Convert
• Coronal
• Cropping object
• Cross-hairs
• CT Geometrical
• Customize Analysis Pipeline
• Cutting and Quantification Table Control

D
• Data
• Data
• Data Browser
• Data Browser Repository Panel
• Data Formats
• Data Loading
• Data Manager
• Data to Quanti Calc
• Data to SpectAct Calc
• Data to SUV Calc
• DataList Object
• DataManager Object
• DB path
• DCMDICTPATH

B 383
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• Debug
• Delete an ROI.
• DICOM
• DICOM
• DICOM
• DICOM Cache
• DICOM Dump
• DICOM Editor
• DICOM Peers
• DICOM Repository
• DICOM Repository
• DICOM Secondary Capture
• DICOM server
• DICOM server
• DICOM Settings
• DICOM Settings
• DicomRepository Object
• Dictionary
• Display
• Displayed Name
• Displays
• Downloading Sample Library

E
• ECG Split
• ECMAScript
• Edit
• Edit an ROI.
• Enable Logfile
• Expert Settings

F
• File Formats
• File Drop Down Menu
• File Formats
• File Menu
• Filter
• Find
• Folder Filter
• Function
• Function

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G
• Getting There
• Getting There
• Getting There
• Getting There
• Getting There

H
• Help Menu
• Hide an ROI.
• HiSPECT
• HiSPECT
• HiSPECT Reconstruction
• HiSPECT_BATCH
• How to configure the NanoSPECT's DICOM Servers
• How to make a dynamic movie
• How to Set a Default Image Shift

I
• Image to Capture
• Image to Poster
• Image View
• Info
• Input/Reference Function
• Install Atlas
• INTERVIEWXP
• INVIVOSCOPE
• iPACS Projects
• iPACS server
• iPACS server
• iPACS Servers
• IPACSWebDisk Object

J
• JavaScript
• Join Frames to Movie

K
• Known issues with graphics card

G 385
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L
• Landmark-based Co-Registration
• Load Data into the Tool
• Local DICOM folder
• Logan Graphical Method (Logan Plot)
• Logan Non-Invasive Graphical Method (Logan reference plot)

M
• Mac OS X
• MainWin Object
• Memory configuration
• MinMaxTool Object
• MIP Rotation Speed
• MIPController Object
• MIPViewer Object
• MMP Menus
• MMP Menus
• Models
• MPR View
• MPR View
• Multi View
• Multi View
• Multi-Pinhole SPECT
• Multi-Planar Reconstruction
• MultiViewer Object

N
• Network
• nih_fire color map
• Noise Suppression
• NSxxWS_DCMSRV

O
• One-Tissue Compartment Model (1TCM)
• Open
• Optimized local access
• Output
• Output
• Overview

L 386
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P
• Painting Tools
• Parent/Plasma Fraction
• Placeholders
• Playing a MIP Movie
• Plot data
• Preprocessing Tool
• Preview
• Preview
• prism color map
• Profile
• Projects
• PSF Manager

Q
• Quantification Database
• Quantification Options
• Quantification Table Options
• Quantification Tables

R
• Raw
• Reconstruction Parameters
• Reference Tissue Compartment
• Registration
• Relabel Study
• Release candidate
• Rename DICOM Files
• Reorientation Object
• Repositories
• Repository
• Repository Type
• Reset an ROI.
• Right-Click function
• ROI Creation and Deletion
• ROI Loading, Saving, and Quantification Tools
• Run DicomProxy
• Run the Tool
• Run Tool and View Log
• Running a Batch Job

P 387
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S
• Sagittal
• Save as default
• Save Calibration.txt
• Saving
• Saving 3D ROI Images/Movies
• Saving and Loading of Fraction, AIF, and Reference Region Data
• Secondary Capture
• Segmenting With The Tool
• Select an Output Repository
• Select Images
• Server Options
• Settings
• Settings Menu
• Show data type:
• Simplified Reference Tissue Model (SRTM)
• Simplified Reference Tissue Model 2 (SRTM2)
• Slice View
• Slice View
• SliceViewer Object
• sliceViewer Object
• sliceViewer Object
• sliceViewer Object
• sliceViewer Object
• sliceViewer Object
• sliceViewer Object
• sliceViewer Object
• sliceViewer Object
• Sliders
• SPECT
• SPECT reconstruction
• Split Movie Into Frames
• Stable version
• Study Browser
• Sum Projections
• Sync Pos.

T
• Templates
• Templates
• The Calibrations
• The Calibrations
• The Quantification Table
• The VQScript Toolbar
• Tile View

S 388
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• Transversal
• TRaster
• Troubleshoot
• Troubleshooting
• Troubleshooting
• Two-Tissue Compartment Model (2TCM)

U
• Undo/Redo Functionality
• Using the Tool

V
• Versions (alpha, beta, rc, stable, patch)
• Via ITK
• ViewControl Object
• Volume Rendered Image
• Volume Rendering Controls
• Volume Rendering Parameters
• VQ Object
• VQScript
• VQScript Example Scripts
• VTK Viewer
• VTKController Object
• VTKViewer Object

W
• Windows 32-bit
• Windows 64-bit
• Windows XP

Z
• ZipArchive Object

Last updated: Mon Nov 28 16:52:01 2016

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