Hi , i`ve update slicer to 5.2.2, and i receive this error from total segmentation.
“Traceback (most recent call last):
File “C:\Users\Administrator\AppData\Local\NA-MIC\Slicer 5.2.2\bin\Python\slicer\util.py”, line 2967, in tryWithErrorDisplay
yield
File “C:/Users/Administrator/AppData/Local/NA-MIC/Slicer 5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py”, line 264, in onApplyButton
self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),
File “C:/Users/Administrator/AppData/Local/NA-MIC/Slicer 5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py”, line 749, in process
self.logProcessOutput(proc)
File “C:/Users/Administrator/AppData/Local/NA-MIC/Slicer 5.2.2/NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules/TotalSegmentator.py”, line 656, in logProcessOutput
raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command ‘[‘C:/Users/Administrator/AppData/Local/NA-MIC/Slicer 5.2.2/bin/…/bin\PythonSlicer.EXE’, ‘C:\Users\Administrator\AppData\Local\NA-MIC\Slicer 5.2.2\lib\Python\Scripts\TotalSegmentator’, ‘-i’, ‘F:/3dSlicer TMP/__SlicerTemp__2023-03-07_11+42+36.788/total-segmentator-input.nii’, ‘-o’, ‘F:/3dSlicer TMP/__SlicerTemp__2023-03-07_11+42+36.788/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–fast’]’ returned non-zero exit status 1.”
Thanks
Have you installed PyTorch first with the SlicerPyTorch extension? Restarted?
And have you selected an input volume?
Let us know what additional details you see in the application log (menu: Help / Report a bug).
[DEBUG][Qt] 06.03.2023 17:17:28 (unknown:0) - Session start time …: 2023-03-06 17:17:28
[DEBUG][Qt] 06.03.2023 17:17:28 (unknown:0) - Slicer version …: 5.2.2 (revision 31382 / fb46bd1) win-amd64 - installed release
[DEBUG][Qt] 06.03.2023 17:17:28 (unknown:0) - Operating system …: Windows / Professional / (Build 19044, Code Page 65001) - 64-bit
[DEBUG][Qt] 06.03.2023 17:17:28 (unknown:0) - Memory …: 65203 MB physical, 130739 MB virtual
[DEBUG][Qt] 06.03.2023 17:17:28 (unknown:0) - CPU …: GenuineIntel , 24 cores, 24 logical processors
[DEBUG][Qt] 06.03.2023 17:17:28 (unknown:0) - VTK configuration …: OpenGL2 rendering, TBB threading
[DEBUG][Qt] 06.03.2023 17:17:28 (unknown:0) - Qt configuration …: version 5.15.2, with SSL, requested OpenGL 3.2 (compatibility profile)
[DEBUG][Qt] 06.03.2023 17:17:28 (unknown:0) - Internationalization …: disabled, language=
[DEBUG][Qt] 06.03.2023 17:17:28 (unknown:0) - Developer mode …: enabled
[DEBUG][Qt] 06.03.2023 17:17:28 (unknown:0) - Application path …: C:/Users/Administrator/AppData/Local/NA-MIC/Slicer 5.2.2/bin
[DEBUG][Qt] 06.03.2023 17:17:28 (unknown:0) - Additional module paths …: C:/Users/Administrator/AppData/Roaming/Blender Foundation/Blender/3.3/scripts/addons/linkSlicerBlender-socket/slicer_module, NA-MIC/Extensions-31382/AnglePlanesExtension/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/BoneTextureExtension/lib/Slicer-5.2/cli-modules, NA-MIC/Extensions-31382/BoneTextureExtension/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/DatabaseInteractor/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/CMFreg/lib/Slicer-5.2/cli-modules, NA-MIC/Extensions-31382/CMFreg/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/EasyClip/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/MeshStatisticsExtension/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/MeshToLabelMap/lib/Slicer-5.2/cli-modules, NA-MIC/Extensions-31382/MeshToLabelMap/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/ModelToModelDistance/lib/Slicer-5.2/cli-modules, NA-MIC/Extensions-31382/Q3DC/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/SPHARM-PDM/lib/Slicer-5.2/cli-modules, NA-MIC/Extensions-31382/SPHARM-PDM/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/ShapePopulationViewer/lib/Slicer-5.2/qt-loadable-modules, NA-MIC/Extensions-31382/SlicerCMF/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/SlicerMarkupConstraints/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/ShapeVariationAnalyzer/lib/Slicer-5.2/cli-modules, NA-MIC/Extensions-31382/ShapeVariationAnalyzer/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/CurveMaker/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/SegmentEditorExtraEffects/lib/Slicer-5.2/qt-loadable-modules, NA-MIC/Extensions-31382/SegmentEditorExtraEffects/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/MarkupsToModel/lib/Slicer-5.2/qt-loadable-modules, NA-MIC/Extensions-31382/PickAndPaintExtension/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/SlicerAutomatedDentalTools/lib/Slicer-5.2/cli-modules, NA-MIC/Extensions-31382/SlicerAutomatedDentalTools/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/SlicerDentalModelSeg/lib/Slicer-5.2/cli-modules, NA-MIC/Extensions-31382/SlicerDentalModelSeg/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/Sandbox/lib/Slicer-5.2/qt-loadable-modules, NA-MIC/Extensions-31382/Sandbox/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/NvidiaAIAssistedAnnotation/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/ModelCropper/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/OrthodonticAnalysis/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/SurfaceWrapSolidify/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/BoneReconstructionPlanner/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/SlicerRT/lib/Slicer-5.2/cli-modules, NA-MIC/Extensions-31382/SlicerRT/lib/Slicer-5.2/qt-loadable-modules, NA-MIC/Extensions-31382/SlicerRT/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/MONAILabel/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/IntensitySegmenter/lib/Slicer-5.2/cli-modules, NA-MIC/Extensions-31382/TotalSegmentator/lib/Slicer-5.2/qt-scripted-modules, NA-MIC/Extensions-31382/PyTorch/lib/Slicer-5.2/qt-scripted-modules
[CRITICAL][Stream] 06.03.2023 17:17:32 (unknown:0) - C:\Users\Administrator\AppData\Local\NA-MIC\Slicer 5.2.2\NA-MIC\Extensions-31382\ShapeVariationAnalyzer\lib\Slicer-5.2\qt-scripted-modules\cpns\cpns.py:57: SyntaxWarning: “is” with a literal. Did you mean “==”?
[CRITICAL][Stream] 06.03.2023 17:17:32 (unknown:0) - if len(self.fileList) is 0:
[WARNING][Qt] 06.03.2023 17:17:33 (unknown:0) - libpng warning: iCCP: known incorrect sRGB profile
[DEBUG][Python] 06.03.2023 17:17:33 [Python] (C:\Users\Administrator\AppData\Local\NA-MIC\Slicer 5.2.2\lib\Slicer-5.2\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:38) - Scripted subject hierarchy plugin registered: Annotations
[DEBUG][Python] 06.03.2023 17:17:35 [Python] (C:\Users\Administrator\AppData\Local\NA-MIC\Slicer 5.2.2\lib\Slicer-5.2\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:38) - Scripted subject hierarchy plugin registered: SegmentEditor
[DEBUG][Python] 06.03.2023 17:17:35 [Python] (C:\Users\Administrator\AppData\Local\NA-MIC\Slicer 5.2.2\lib\Slicer-5.2\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:38) - Scripted subject hierarchy plugin registered: SegmentStatistics
[DEBUG][Qt] 06.03.2023 17:17:35 (unknown:0) - Switch to module: “Welcome”
[INFO][Python] 06.03.2023 17:17:35 [Python] (C:/Users/Administrator/AppData/Local/NA-MIC/Slicer 5.2.2/NA-MIC/Extensions-31382/NvidiaAIAssistedAnnotation/lib/Slicer-5.2/qt-scripted-modules/SegmentEditorNvidiaAIAA.py:32) - This plugin dir: C:/Users/Administrator/AppData/Local/NA-MIC/Slicer 5.2.2/NA-MIC/Extensions-31382/NvidiaAIAssistedAnnotation/lib/Slicer-5.2/qt-scripted-modules
[DEBUG][Qt] 06.03.2023 17:17:49 (unknown:0) - Switch to module: “DICOM”
[INFO][Python] 06.03.2023 17:18:06 [Python] (C:/Users/Administrator/AppData/Local/NA-MIC/Slicer 5.2.2/bin/…/lib/Slicer-5.2/qt-scripted-modules/DICOMScalarVolumePlugin.py:393) - Loading with imageIOName: GDCM
[INFO][Python] 06.03.2023 17:18:12 [Python] (C:/Users/Administrator/AppData/Local/NA-MIC/Slicer 5.2.2/bin/…/lib/Slicer-5.2/qt-scripted-modules/DICOMScalarVolumePlugin.py:472) - Window/level found in DICOM tags (center=1048.0, width=4096.0) has been applied to volume 11: Assiale
[DEBUG][Qt] 06.03.2023 17:18:31 (unknown:0) - Switch to module: “SegmentEditor”
[WARNING][Qt] 06.03.2023 17:18:31 (unknown:0) - QLayout::addChildLayout: layout “” already has a parent
[WARNING][Qt] 06.03.2023 17:18:31 (unknown:0) - ctkSliderWidget::setSingleStep() 0 is out of bounds. 0 100 1
[DEBUG][Qt] 06.03.2023 18:31:35 (unknown:0) - Switch to module: “”