# Total Segmentation error

**URL:** <https://discourse.slicer.org/t/total-segmentation-error/28211>\
**Category:** Support\
**Created:** [March 7, 2023, 10:50am UTC](https://discourse.slicer.org/t/total-segmentation-error/28211 "2023-03-07T10:50:27Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![Ackta](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ackta/32/18306_2.png) [@Ackta](https://discourse.slicer.org/u/Ackta)\
**Post date:** [March 7, 2023, 10:50am UTC](https://discourse.slicer.org/t/total-segmentation-error/28211/1 "2023-03-07T10:50:27Z")

</div>

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

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<div class="post-metadata">

**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [March 7, 2023, 2:48pm UTC](https://discourse.slicer.org/t/total-segmentation-error/28211/2 "2023-03-07T14:48:16Z")

</div>

Have you installed PyTorch first with the SlicerPyTorch extension? Restarted?  
And have you selected an input volume?

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [March 8, 2023, 3:47am UTC](https://discourse.slicer.org/t/total-segmentation-error/28211/3 "2023-03-08T03:47:50Z")

</div>

Let us know what additional details you see in the application log (menu: Help / Report a bug).

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<div class="post-metadata">

**Author:** ![Ackta](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ackta/32/18306_2.png) [@Ackta](https://discourse.slicer.org/u/Ackta)\
**Post date:** [March 8, 2023, 9:27am UTC](https://discourse.slicer.org/t/total-segmentation-error/28211/4 "2023-03-08T09:27:39Z")

</div>

[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: “”