Problem report for Slicer 4.11.20200930 win-amd64: [please describe expected and actual behavior]
Segment disapears when using segment margin-> grow. This happens repeatedly on some segmentations of some CTs. I can’t find a pattern so far, but the problem has occured > 10 times.
Log:
[DEBUG][Qt] 07.11.2020 19:39:43 [] (unknown:0) - Session start time …: 2020-11-07 19:39:43
[DEBUG][Qt] 07.11.2020 19:39:43 [] (unknown:0) - Slicer version …: 4.11.20200930 (revision 29402 / 002be18) win-amd64 - installed release
[DEBUG][Qt] 07.11.2020 19:39:43 [] (unknown:0) - Operating system …: Windows / Professional / (Build 19041, Code Page 65001) - 64-bit
[DEBUG][Qt] 07.11.2020 19:39:43 [] (unknown:0) - Memory …: 32711 MB physical, 37575 MB virtual
[DEBUG][Qt] 07.11.2020 19:39:43 [] (unknown:0) - CPU …: AuthenticAMD AMD Ryzen 9 3900X 12-Core Processor , 24 cores, 24 logical processors
[DEBUG][Qt] 07.11.2020 19:39:43 [] (unknown:0) - VTK configuration …: OpenGL2 rendering, TBB threading
[DEBUG][Qt] 07.11.2020 19:39:43 [] (unknown:0) - Qt configuration …: version 5.15.1, with SSL, requested OpenGL 3.2 (compatibility profile)
[DEBUG][Qt] 07.11.2020 19:39:43 [] (unknown:0) - Developer mode enabled …: no
[DEBUG][Qt] 07.11.2020 19:39:43 [] (unknown:0) - Prefer executable CLI …: yes
[DEBUG][Qt] 07.11.2020 19:39:43 [] (unknown:0) - Application path …: C:/Users/eendo/AppData/Local/NA-MIC/Slicer 4.11.20200930/bin
[DEBUG][Qt] 07.11.2020 19:39:43 [] (unknown:0) - Additional module paths …: C:/Users/eendo/AppData/Roaming/NA-MIC/Extensions-29402/SegmentEditorExtraEffects/lib/Slicer-4.11/qt-scripted-modules, C:/Users/eendo/AppData/Roaming/NA-MIC/Extensions-29402/MarkupsToModel/lib/Slicer-4.11/qt-loadable-modules, C:/Users/eendo/AppData/Roaming/NA-MIC/Extensions-29402/SlicerVMTK/lib/Slicer-4.11/qt-loadable-modules, C:/Users/eendo/AppData/Roaming/NA-MIC/Extensions-29402/SlicerVMTK/lib/Slicer-4.11/qt-scripted-modules, C:/Users/eendo/AppData/Roaming/NA-MIC/Extensions-29402/SlicerRT/lib/Slicer-4.11/cli-modules, C:/Users/eendo/AppData/Roaming/NA-MIC/Extensions-29402/SlicerRT/lib/Slicer-4.11/qt-loadable-modules, C:/Users/eendo/AppData/Roaming/NA-MIC/Extensions-29402/SlicerRT/lib/Slicer-4.11/qt-scripted-modules, C:/Users/eendo/AppData/Roaming/NA-MIC/Extensions-29402/QuantitativeReporting/lib/Slicer-4.11/qt-scripted-modules, C:/Users/eendo/AppData/Roaming/NA-MIC/Extensions-29402/DCMQI/lib/Slicer-4.11/cli-modules, C:/Users/eendo/AppData/Roaming/NA-MIC/Extensions-29402/PETDICOMExtension/lib/Slicer-4.11/cli-modules, C:/Users/eendo/AppData/Roaming/NA-MIC/Extensions-29402/PETDICOMExtension/lib/Slicer-4.11/qt-scripted-modules, C:/Users/eendo/AppData/Roaming/NA-MIC/Extensions-29402/SlicerDevelopmentToolbox/lib/Slicer-4.11/qt-scripted-modules, C:/Users/eendo/AppData/Roaming/NA-MIC/Extensions-29402/ChangeTracker/lib/Slicer-4.11/cli-modules, C:/Users/eendo/AppData/Roaming/NA-MIC/Extensions-29402/ChangeTracker/lib/Slicer-4.11/qt-scripted-modules, C:/Users/eendo/Documents/aortaai_slicer/Aorta.AI, C:/Users/eendo/AppData/Roaming/NA-MIC/Extensions-29402/SlicerElastix/lib/Slicer-4.11/qt-scripted-modules
[DEBUG][Python] 07.11.2020 19:39:47 [Python] (C:\Users\eendo\AppData\Local\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][Stream] 07.11.2020 19:39:46 [] (unknown:0) - Traceback (most recent call last):
[CRITICAL][Stream] 07.11.2020 19:39:46 [] (unknown:0) - File “”, line 1, in
[CRITICAL][Stream] 07.11.2020 19:39:46 [] (unknown:0) - File “C:\Users\eendo\AppData\Local\NA-MIC\Slicer 4.11.20200930\lib\Python\Lib\imp.py”, line 170, in load_source
[CRITICAL][Stream] 07.11.2020 19:39:46 [] (unknown:0) - module = _exec(spec, sys.modules[name])
[CRITICAL][Stream] 07.11.2020 19:39:46 [] (unknown:0) - File “”, line 618, in _exec
[CRITICAL][Stream] 07.11.2020 19:39:46 [] (unknown:0) - File “”, line 678, in exec_module
[CRITICAL][Stream] 07.11.2020 19:39:46 [] (unknown:0) - File “”, line 219, in call_with_frames_removed
[CRITICAL][Stream] 07.11.2020 19:39:46 [] (unknown:0) - File “C:/Users/eendo/AppData/Roaming/NA-MIC/Extensions-29402/ChangeTracker/lib/Slicer-4.11/qt-scripted-modules/ChangeTracker.py”, line 4, in
[CRITICAL][Stream] 07.11.2020 19:39:46 [] (unknown:0) - import ChangeTrackerWizard
[CRITICAL][Stream] 07.11.2020 19:39:46 [] (unknown:0) - File "C:\Users\eendo\AppData\Roaming\NA-MIC\Extensions-29402\ChangeTracker\lib\Slicer-4.11\qt-scripted-modules\ChangeTrackerWizard_init.py", line 2, in
[CRITICAL][Stream] 07.11.2020 19:39:46 [] (unknown:0) - from ChangeTrackerStep import *
[CRITICAL][Stream] 07.11.2020 19:39:46 [] (unknown:0) - ModuleNotFoundError: No module named ‘ChangeTrackerStep’
[CRITICAL][Qt] 07.11.2020 19:39:46 [] (unknown:0) - loadSourceAsModule - Failed to load file “C:/Users/eendo/AppData/Roaming/NA-MIC/Extensions-29402/ChangeTracker/lib/Slicer-4.11/qt-scripted-modules/ChangeTracker.py” as module “ChangeTracker” !
[CRITICAL][Qt] 07.11.2020 19:39:46 [] (unknown:0) - Fail to instantiate module “ChangeTracker”
[CRITICAL][Qt] 07.11.2020 19:39:48 [] (unknown:0) - Error(s):
CLI executable: C:/Users/eendo/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] 07.11.2020 19:39:48 [] (unknown:0) - Fail to instantiate module “vtkvmtk”
[CRITICAL][Qt] 07.11.2020 19:39:48 [] (unknown:0) - The following modules failed to be instantiated:
[CRITICAL][Qt] 07.11.2020 19:39:48 [] (unknown:0) - ChangeTracker
[CRITICAL][Qt] 07.11.2020 19:39:48 [] (unknown:0) - vtkvmtk
[DEBUG][Python] 07.11.2020 19:39:50 [Python] (C:\Users\eendo\AppData\Local\NA-MIC\Slicer 4.11.20200930\lib\Slicer-4.11\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: Annotations
[WARNING][Qt] 07.11.2020 19:39:51 [] (unknown:0) - When loading module “ChangeTrackerSelfTest” , the dependency “ChangeTracker” failed to be loaded.
[DEBUG][Python] 07.11.2020 19:39:51 [Python] (C:\Users\eendo\AppData\Local\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] 07.11.2020 19:39:51 [Python] (C:\Users\eendo\AppData\Local\NA-MIC\Slicer 4.11.20200930\lib\Slicer-4.11\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:36) - Scripted subject hierarchy plugin registered: SegmentStatistics
[INFO][Python] 07.11.2020 19:39:52 [Python] (C:/Users/eendo/Documents/aortaai_slicer/Aorta.AI/SegmentEditorNvidiaAIAA.py:32) - This plugin dir: C:/Users/eendo/Documents/aortaai_slicer/Aorta.AI
[DEBUG][Python] 07.11.2020 19:39:52 [Python] (C:\Users\eendo\AppData\Local\NA-MIC\Slicer 4.11.20200930\lib\Slicer-4.11\qt-scripted-modules\DICOMLib\DICOMProcesses.py:171) - Starting storescp process
[DEBUG][Python] 07.11.2020 19:39:52 [Python] (C:\Users\eendo\AppData\Local\NA-MIC\Slicer 4.11.20200930\lib\Slicer-4.11\qt-scripted-modules\DICOMLib\DICOMProcesses.py:68) - ('Starting C:/Users/eendo/AppData/Local/NA-MIC/Slicer 4.11.20200930/bin/…/bin\storescp.exe with ', [‘11112’, ‘–accept-all’, ‘–output-directory’, ‘C:/slicerDB/AAA/incoming’, ‘–exec-sync’, ‘–exec-on-reception’, ‘C:/Users/eendo/AppData/Local/NA-MIC/Slicer 4.11.20200930/bin/…/bin\dcmdump.exe --load-short --print-short --print-filename --search PatientName “C:/slicerDB/AAA/incoming/#f”’])
[DEBUG][Python] 07.11.2020 19:39:52 [Python] (C:\Users\eendo\AppData\Local\NA-MIC\Slicer 4.11.20200930\lib\Slicer-4.11\qt-scripted-modules\DICOMLib\DICOMProcesses.py:72) - Process C:/Users/eendo/AppData/Local/NA-MIC/Slicer 4.11.20200930/bin/…/bin\storescp.exe now in state Starting
[DEBUG][Python] 07.11.2020 19:39:52 [Python] (C:\Users\eendo\AppData\Local\NA-MIC\Slicer 4.11.20200930\lib\Slicer-4.11\qt-scripted-modules\DICOMLib\DICOMProcesses.py:72) - Process C:/Users/eendo/AppData/Local/NA-MIC/Slicer 4.11.20200930/bin/…/bin\storescp.exe now in state Running
[INFO][Python] 07.11.2020 19:39:52 [Python] (C:/Users/eendo/AppData/Local/NA-MIC/Slicer 4.11.20200930/bin/…/lib/Slicer-4.11/qt-scripted-modules/DICOM.py:200) - DICOM C-Store SCP service started at port 11112
[DEBUG][Qt] 07.11.2020 19:39:51 [] (unknown:0) - Switch to module: “Welcome”
[INFO][Stream] 07.11.2020 19:39:52 [] (unknown:0) - This plugin dir: C:/Users/eendo/Documents/aortaai_slicer/Aorta.AI
[INFO][VTK] 07.11.2020 19:39:52 [vtkMRMLScene (000001EB5294DD30)] (D:\D\S\Slicer-0\Libs\MRML\Core\vtkMRMLScene.cxx:316) - vtkMRMLScene::Clear
[INFO][VTK] 07.11.2020 19:39:52 [vtkMRMLScene (000001EB5294DD30)] (D:\D\S\Slicer-0\Libs\MRML\Core\vtkMRMLScene.cxx:762) - vtkMRMLScene::Import
[INFO][VTK] 07.11.2020 19:39:52 [vtkMRMLVolumeArchetypeStorageNode (000001EB52960DC0)] (D:\D\S\Slicer-0\Libs\MRML\Core\vtkMRMLVolumeArchetypeStorageNode.cxx:473) - Loaded volume from file: C:/Users/eendo/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] 07.11.2020 19:39:52 [vtkMRMLScene (000001EB52AC0080)] (D:\D\S\Slicer-0\Libs\MRML\Core\vtkMRMLScene.cxx:316) - vtkMRMLScene::Clear
[INFO][VTK] 07.11.2020 19:39:52 [vtkMRMLScene (000001EB52AC0080)] (D:\D\S\Slicer-0\Libs\MRML\Core\vtkMRMLScene.cxx:762) - vtkMRMLScene::Import
[INFO][VTK] 07.11.2020 19:39:52 [vtkMRMLScene (000001EB5294DD30)] (D:\D\S\Slicer-0\Libs\MRML\Core\vtkMRMLScene.cxx:316) - vtkMRMLScene::Clear
[INFO][Stream] 07.11.2020 19:39:52 [] (unknown:0) - DICOM C-Store SCP service started at port 11112
[INFO][VTK] 07.11.2020 19:40:23 [vtkMRMLVolumeArchetypeStorageNode (000001EB52961770)] (D:\D\S\Slicer-0\Libs\MRML\Core\vtkMRMLVolumeArchetypeStorageNode.cxx:473) - Loaded volume from file: X:/badania/66_TODO/66.nii.gz. Dimensions: 512x512x395. Number of components: 1. Pixel type: short.
[INFO][VTK] 07.11.2020 19:40:23 [vtkMRMLScene (000001EB4C8C7030)] (D:\D\S\Slicer-0\Libs\MRML\Core\vtkMRMLScene.cxx:316) - vtkMRMLScene::Clear
[DEBUG][Qt] 07.11.2020 19:40:23 [] (unknown:0) - “Volume” Reader has successfully read the file “X:/badania/66_TODO/66.nii.gz” “[1.80s]”
[DEBUG][Qt] 07.11.2020 19:40:25 [] (unknown:0) - “Segmentation” Reader has successfully read the file “X:/badania/66_TODO/66_AI.seg.nrrd” “[1.52s]”
[DEBUG][Qt] 07.11.2020 19:40:29 [] (unknown:0) - “Segmentation” Reader has successfully read the file “X:/badania/66_TODO/66_kontrast.seg.nrrd” “[3.61s]”
[DEBUG][Qt] 07.11.2020 19:41:42 [] (unknown:0) - Switch to module: “SegmentEditor”
[WARNING][Qt] 07.11.2020 19:41:43 [] (unknown:0) - QLayout::addChildLayout: layout “” already has a parent
[WARNING][Qt] 07.11.2020 19:41:43 [] (unknown:0) - ctkSliderWidget::setSingleStep() 0 is out of bounds. 0 100 1
[DEBUG][Qt] 07.11.2020 19:41:48 [] (unknown:0) - Switch to module: “Data”
[DEBUG][Qt] 07.11.2020 19:42:02 [] (unknown:0) - Switch to module: “SegmentEditor”
[WARNING][Qt] 07.11.2020 19:42:08 [] (unknown:0) - ctkSliderWidget::setSingleStep() 0 is out of bounds. 0 100 1
[ERROR][VTK] 07.11.2020 19:42:18 [vtkITKImageMargin (000001EB76A2BD90)] (D:\D\S\Slicer-0\Libs\vtkITK\vtkITKImageMargin.cxx:198) - Incompatible data type for this version of ITK.
[CRITICAL][Qt] 07.11.2020 19:42:24 [] (unknown:0) - The VTKEvent( 17000 ) triggered by vtkObject( vtkMRMLSegmentationNode ) doesn’t return data of type vtkObject.
The slot ( “1onDisplayNodeModified(vtkObject*, vtkObject*)” ) owned by QObject( “” ) may be incorrect.
[CRITICAL][Qt] 07.11.2020 19:42:24 [] (unknown:0) - void __cdecl qSlicerSubjectHierarchyPluginLogic::onDisplayNodeModified(class vtkObject ,class vtkObject ) : Invalid object type calling display node modified event
[CRITICAL][Qt] 07.11.2020 19:42:32 [] (unknown:0) - The VTKEvent( 17000 ) triggered by vtkObject( vtkMRMLSegmentationNode ) doesn’t return data of type vtkObject.
The slot ( "1onDisplayNodeModified(vtkObject, vtkObject)" ) owned by QObject( “” ) may be incorrect.
[CRITICAL][Qt] 07.11.2020 19:42:32 [] (unknown:0) - void __cdecl qSlicerSubjectHierarchyPluginLogic::onDisplayNodeModified(class vtkObject *,class vtkObject *) : Invalid object type calling display node modified event
[ERROR][VTK] 07.11.2020 19:42:45 [vtkITKImageMargin (000001EB76A31220)] (D:\D\S\Slicer-0\Libs\vtkITK\vtkITKImageMargin.cxx:198) - Incompatible data type for this version of ITK.
Your help will be much appreciated.
Regards,
Lukasz