Operating system: Win10
Slicer version: 4.11
Expected behavior: Centerline computation
Actual behavior: Centerline computation is not in Vascular Modeling Toolkit modular
Hi, I am using 3D_Slicer 4.11 to extract the centerline and reconstruct 3D model of blood vessel. I have installed the SlicerVMTK, SegmentEditorExtraEffects. But I have a problem, that is, there is no “centerline conputation” in Vascular Modeling Toolkit modular. Please help me, thank you.
Could you copy here the application log (menu: Help / Report a bug)?
ok, i have pasted the log.
[DEBUG][Qt] 21.03.2021 09:25:41 [] (unknown:0) - Session start time …: 2021-03-21 09:25:41
[DEBUG][Qt] 21.03.2021 09:25:41 [] (unknown:0) - Slicer version …: 4.11.20200930 (revision 29402 / 002be18) win-amd64 - installed release
[DEBUG][Qt] 21.03.2021 09:25:41 [] (unknown:0) - Operating system …: Windows / Professional / (Build 19042, Code Page 65001) - 64-bit
[DEBUG][Qt] 21.03.2021 09:25:41 [] (unknown:0) - Memory …: 8078 MB physical, 9358 MB virtual
[DEBUG][Qt] 21.03.2021 09:25:41 [] (unknown:0) - CPU …: GenuineIntel , 4 cores, 4 logical processors
[DEBUG][Qt] 21.03.2021 09:25:41 [] (unknown:0) - VTK configuration …: OpenGL2 rendering, TBB threading
[DEBUG][Qt] 21.03.2021 09:25:41 [] (unknown:0) - Qt configuration …: version 5.15.1, with SSL, requested OpenGL 3.2 (compatibility profile)
[DEBUG][Qt] 21.03.2021 09:25:41 [] (unknown:0) - Developer mode enabled …: no
[DEBUG][Qt] 21.03.2021 09:25:41 [] (unknown:0) - Prefer executable CLI …: yes
[DEBUG][Qt] 21.03.2021 09:25:41 [] (unknown:0) - Application path …: D:/ProgramData/NA-MIC/Slicer 4.11.20200930/bin
[DEBUG][Qt] 21.03.2021 09:25:41 [] (unknown:0) - Additional module paths …: C:/Users/pc/AppData/Roaming/NA-MIC/Extensions-29402/DCMQI/lib/Slicer-4.11/cli-modules, C:/Users/pc/AppData/Roaming/NA-MIC/Extensions-29402/DebuggingTools/lib/Slicer-4.11/qt-scripted-modules, C:/Users/pc/AppData/Roaming/NA-MIC/Extensions-29402/MatlabBridge/lib/Slicer-4.11/cli-modules, C:/Users/pc/AppData/Roaming/NA-MIC/Extensions-29402/MatlabBridge/lib/Slicer-4.11/qt-loadable-modules, C:/Users/pc/AppData/Roaming/NA-MIC/Extensions-29402/SlicerOpenIGTLink/lib/Slicer-4.11/qt-loadable-modules, C:/Users/pc/AppData/Roaming/NA-MIC/Extensions-29402/SlicerOpenIGTLink/lib/Slicer-4.11/qt-scripted-modules, C:/Users/pc/AppData/Roaming/NA-MIC/Extensions-29402/SegmentEditorExtraEffects/lib/Slicer-4.11/qt-scripted-modules, C:/Users/pc/AppData/Roaming/NA-MIC/Extensions-29402/MarkupsToModel/lib/Slicer-4.11/qt-loadable-modules, C:/Users/pc/AppData/Roaming/NA-MIC/Extensions-29402/SlicerVMTK/lib/Slicer-4.11/qt-loadable-modules, C:/Users/pc/AppData/Roaming/NA-MIC/Extensions-29402/SlicerVMTK/lib/Slicer-4.11/qt-scripted-modules, C:/Users/pc/AppData/Roaming/NA-MIC/Extensions-29402/MatlabModules
[DEBUG][Python] 21.03.2021 09:25:48 [Python] (D:\ProgramData\NA-MIC\Slicer 4.11.20200930\lib\Python\Lib\site-packages\pydicom\datadict.py:432) - Reversing DICOM dictionary so can look up tag from a keyword…
[CRITICAL][Qt] 21.03.2021 09:25:50 [] (unknown:0) - Error(s):
CLI executable: C:/Users/pc/AppData/Roaming/NA-MIC/Extensions-29402/SlicerVMTK/lib/Slicer-4.11/qt-loadable-modules/vtkvmtk.py
The process failed to start. Either the invoked program is missing, or you may have insufficient permissions to invoke the program.
[CRITICAL][Qt] 21.03.2021 09:25:50 [] (unknown:0) - Fail to instantiate module “vtkvmtk”
[CRITICAL][Qt] 21.03.2021 09:25:50 [] (unknown:0) - The following modules failed to be instantiated:
[CRITICAL][Qt] 21.03.2021 09:25:50 [] (unknown:0) - vtkvmtk
[DEBUG][Python] 21.03.2021 09:25:51 [Python] (D:\ProgramData\NA-MIC\Slicer 4.11.20200930\lib\Slicer-4.11\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: Annotations
[DEBUG][Qt] 21.03.2021 09:25:52 [] (unknown:0) - Matlab executable found on system at 0
[DEBUG][Python] 21.03.2021 09:25:53 [Python] (D:\ProgramData\NA-MIC\Slicer 4.11.20200930\lib\Slicer-4.11\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: SegmentEditor
[DEBUG][Python] 21.03.2021 09:25:53 [Python] (D:\ProgramData\NA-MIC\Slicer 4.11.20200930\lib\Slicer-4.11\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: SegmentStatistics
[DEBUG][Qt] 21.03.2021 09:25:54 [] (unknown:0) - Switch to module: “Welcome”
[INFO][VTK] 21.03.2021 09:25:59 [vtkMRMLScene (000002419E6C61D0)] (D:\D\S\Slicer-0\Libs\MRML\Core\vtkMRMLScene.cxx:316) - vtkMRMLScene::Clear
[INFO][VTK] 21.03.2021 09:25:59 [vtkMRMLScene (000002419E6C61D0)] (D:\D\S\Slicer-0\Libs\MRML\Core\vtkMRMLScene.cxx:762) - vtkMRMLScene::Import
[INFO][VTK] 21.03.2021 09:25:59 [vtkMRMLVolumeArchetypeStorageNode (00000241AE6F1150)] (D:\D\S\Slicer-0\Libs\MRML\Core\vtkMRMLVolumeArchetypeStorageNode.cxx:473) - Loaded volume from file: C:/Users/pc/AppData/Roaming/NA-MIC/Extensions-29402/SlicerVMTK/lib/Slicer-4.11/qt-scripted-modules/Resources/Vesselness.png. Dimensions: 65x50x1. Number of components: 3. Pixel type: unsigned char.
[INFO][VTK] 21.03.2021 09:25:59 [vtkMRMLScene (00000241AE25A020)] (D:\D\S\Slicer-0\Libs\MRML\Core\vtkMRMLScene.cxx:316) - vtkMRMLScene::Clear
[INFO][VTK] 21.03.2021 09:25:59 [vtkMRMLScene (00000241AE25A020)] (D:\D\S\Slicer-0\Libs\MRML\Core\vtkMRMLScene.cxx:762) - vtkMRMLScene::Import
[INFO][VTK] 21.03.2021 09:25:59 [vtkMRMLScene (000002419E6C61D0)] (D:\D\S\Slicer-0\Libs\MRML\Core\vtkMRMLScene.cxx:316) - vtkMRMLScene::Clear
[INFO][Stream] 21.03.2021 09:25:59 [] (unknown:0) - Loading Slicer RC file [C:/Users/pc/.slicerrc.py]
[DEBUG][Python] 21.03.2021 09:28:33 [Python] (D:/ProgramData/NA-MIC/Slicer 4.11.20200930/bin/…/lib/Slicer-4.11/qt-scripted-modules/SampleData.py:373) -
Status: Idle
[DEBUG][Qt] 21.03.2021 09:28:33 [] (unknown:0) - Switch to module: “SampleData”
[DEBUG][Python] 21.03.2021 09:28:36 [Python] (D:/ProgramData/NA-MIC/Slicer 4.11.20200930/bin/…/lib/Slicer-4.11/qt-scripted-modules/SampleData.py:373) - Requesting download Panoramix-cropped.nrrd from https://github.com/Slicer/SlicerTestingData/releases/download/SHA256/146af87511520c500a3706b7b2bfb545f40d5d04dd180be3a7a2c6940e447433 …
[DEBUG][Python] 21.03.2021 09:28:40 [Python] (D:/ProgramData/NA-MIC/Slicer 4.11.20200930/bin/…/lib/Slicer-4.11/qt-scripted-modules/SampleData.py:373) - Downloaded 3.5 MB (10% of 35.4 MB)…
[DEBUG][Python] 21.03.2021 09:28:50 [Python] (D:/ProgramData/NA-MIC/Slicer 4.11.20200930/bin/…/lib/Slicer-4.11/qt-scripted-modules/SampleData.py:373) - Downloaded 7.1 MB (20% of 35.4 MB)…
[DEBUG][Python] 21.03.2021 09:28:59 [Python] (D:/ProgramData/NA-MIC/Slicer 4.11.20200930/bin/…/lib/Slicer-4.11/qt-scripted-modules/SampleData.py:373) - Downloaded 10.6 MB (30% of 35.4 MB)…
[DEBUG][Python] 21.03.2021 09:29:09 [Python] (D:/ProgramData/NA-MIC/Slicer 4.11.20200930/bin/…/lib/Slicer-4.11/qt-scripted-modules/SampleData.py:373) - Downloaded 14.2 MB (40% of 35.4 MB)…
[DEBUG][Python] 21.03.2021 09:29:20 [Python] (D:/ProgramData/NA-MIC/Slicer 4.11.20200930/bin/…/lib/Slicer-4.11/qt-scripted-modules/SampleData.py:373) - Downloaded 17.7 MB (50% of 35.4 MB)…
[DEBUG][Python] 21.03.2021 09:29:32 [Python] (D:/ProgramData/NA-MIC/Slicer 4.11.20200930/bin/…/lib/Slicer-4.11/qt-scripted-modules/SampleData.py:373) - Downloaded 21.2 MB (60% of 35.4 MB)…
[DEBUG][Python] 21.03.2021 09:29:39 [Python] (D:/ProgramData/NA-MIC/Slicer 4.11.20200930/bin/…/lib/Slicer-4.11/qt-scripted-modules/SampleData.py:373) - Downloaded 24.8 MB (70% of 35.4 MB)…
[DEBUG][Python] 21.03.2021 09:29:46 [Python] (D:/ProgramData/NA-MIC/Slicer 4.11.20200930/bin/…/lib/Slicer-4.11/qt-scripted-modules/SampleData.py:373) - Downloaded 28.3 MB (80% of 35.4 MB)…
[DEBUG][Python] 21.03.2021 09:29:57 [Python] (D:/ProgramData/NA-MIC/Slicer 4.11.20200930/bin/…/lib/Slicer-4.11/qt-scripted-modules/SampleData.py:373) - Downloaded 31.8 MB (90% of 35.4 MB)…
[DEBUG][Python] 21.03.2021 09:30:07 [Python] (D:/ProgramData/NA-MIC/Slicer 4.11.20200930/bin/…/lib/Slicer-4.11/qt-scripted-modules/SampleData.py:373) - Downloaded 35.4 MB (100% of 35.4 MB)…
[DEBUG][Python] 21.03.2021 09:30:07 [Python] (D:/ProgramData/NA-MIC/Slicer 4.11.20200930/bin/…/lib/Slicer-4.11/qt-scripted-modules/SampleData.py:373) - Download finished
[DEBUG][Python] 21.03.2021 09:30:07 [Python] (D:/ProgramData/NA-MIC/Slicer 4.11.20200930/bin/…/lib/Slicer-4.11/qt-scripted-modules/SampleData.py:373) - Verifying checksum
[DEBUG][Python] 21.03.2021 09:30:07 [Python] (D:/ProgramData/NA-MIC/Slicer 4.11.20200930/bin/…/lib/Slicer-4.11/qt-scripted-modules/SampleData.py:373) - Checksum OK
[DEBUG][Python] 21.03.2021 09:30:07 [Python] (D:/ProgramData/NA-MIC/Slicer 4.11.20200930/bin/…/lib/Slicer-4.11/qt-scripted-modules/SampleData.py:373) - Requesting load Panoramix-cropped from C:/Users/pc/AppData/Local/Temp/Slicer/RemoteIO/Panoramix-cropped.nrrd …
[INFO][VTK] 21.03.2021 09:30:08 [vtkMRMLVolumeArchetypeStorageNode (00000241AE6F1910)] (D:\D\S\Slicer-0\Libs\MRML\Core\vtkMRMLVolumeArchetypeStorageNode.cxx:473) - Loaded volume from file: C:/Users/pc/AppData/Local/Temp/Slicer/RemoteIO/Panoramix-cropped.nrrd. Dimensions: 441x321x215. Number of components: 1. Pixel type: short.
[INFO][VTK] 21.03.2021 09:30:08 [vtkMRMLScene (00000241B0578260)] (D:\D\S\Slicer-0\Libs\MRML\Core\vtkMRMLScene.cxx:316) - vtkMRMLScene::Clear
[DEBUG][Qt] 21.03.2021 09:30:08 [] (unknown:0) - “Volume” Reader has successfully read the file “C:/Users/pc/AppData/Local/Temp/Slicer/RemoteIO/Panoramix-cropped.nrrd” “[1.00s]”
[DEBUG][Python] 21.03.2021 09:30:09 [Python] (D:/ProgramData/NA-MIC/Slicer 4.11.20200930/bin/…/lib/Slicer-4.11/qt-scripted-modules/SampleData.py:373) - Load finished
[DEBUG][Qt] 21.03.2021 09:31:47 [] (unknown:0) - Switch to module: “SegmentEditor”
[WARNING][Qt] 21.03.2021 09:31:48 [] (unknown:0) - QLayout::addChildLayout: layout “” already has a parent
[WARNING][Qt] 21.03.2021 09:31:48 [] (unknown:0) - ctkSliderWidget::setSingleStep() 0 is out of bounds. 0 100 1
[INFO][Python] 21.03.2021 09:36:32 [Python] (D:\ProgramData\NA-MIC\Slicer 4.11.20200930\lib\Slicer-4.11\qt-scripted-modules\SegmentEditorEffects\SegmentEditorIslandsEffect.py:155) - 1 islands created (3 ignored)
[INFO][Stream] 21.03.2021 09:36:32 [] (unknown:0) - 1 islands created (3 ignored)
[DEBUG][Qt] 21.03.2021 09:36:47 [] (unknown:0) - Switch to module: “Data”
[DEBUG][Qt] 21.03.2021 09:37:18 [] (unknown:0) - Switch to module: “SurfaceToolbox”
[INFO][Python] 21.03.2021 09:38:07 [Python] (D:/ProgramData/NA-MIC/Slicer 4.11.20200930/bin/…/lib/Slicer-4.11/qt-scripted-modules/SurfaceToolbox.py:378) - Processing started
[INFO][Python] 21.03.2021 09:38:07 [Python] (D:/ProgramData/NA-MIC/Slicer 4.11.20200930/bin/…/lib/Slicer-4.11/qt-scripted-modules/SurfaceToolbox.py:519) - Processing completed in 0.02 seconds
[INFO][Stream] 21.03.2021 09:38:07 [] (unknown:0) - Processing started
[INFO][Stream] 21.03.2021 09:38:07 [] (unknown:0) - Processing completed in 0.02 seconds
[DEBUG][Qt] 21.03.2021 09:38:24 [] (unknown:0) - Switch to module: “Data”
[DEBUG][Qt] 21.03.2021 09:39:18 [] (unknown:0) - Switch to module: “CenterlineMetrics”