# TotalSegmentator keeps returning non-zero exit status 1

**URL:** <https://discourse.slicer.org/t/totalsegmentator-keeps-returning-non-zero-exit-status-1/46820>\
**Category:** Support\
**Created:** [April 24, 2026, 1:24am UTC](https://discourse.slicer.org/t/totalsegmentator-keeps-returning-non-zero-exit-status-1/46820 "2026-04-24T01:24:49Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![its-charliem](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/its-charliem/32/82254_2.png) [@its-charliem](https://discourse.slicer.org/u/its-charliem)\
**Post date:** [April 24, 2026, 1:24am UTC](https://discourse.slicer.org/t/totalsegmentator-keeps-returning-non-zero-exit-status-1/46820/1 "2026-04-24T01:24:49Z")

</div>

Problem report for 3D Slicer 5.10.0 win-amd64: [please describe expected and actual behavior]

Command ‘[‘C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/bin/../bin\\PythonSlicer.EXE’, ‘-m’, ‘pip’, ‘install’, ‘monai[fire,pyyaml,nibabel,pynrrd,psutil,tensorboard,skimage,itk,tqdm]\>=1.3’, ‘–upgrade’]’ returned non-zero exit status 1.

[CRITICAL][Stream] 23.04.2026 09:04:48 [] (unknown:0) - Traceback (most recent call last):

[CRITICAL][Stream] 23.04.2026 09:04:48 [] (unknown:0) - File “C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/MONAIAuto3DSeg/lib/Slicer-5.10/qt-scripted-modules/MONAIAuto3DSeg.py”, line 775, in onPackageUpgrade

[CRITICAL][Stream] 23.04.2026 09:04:48 [] (unknown:0) - restartRequired = self.logic.setupPythonRequirements(upgrade=True)

[CRITICAL][Stream] 23.04.2026 09:04:48 [] (unknown:0) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

[CRITICAL][Stream] 23.04.2026 09:04:48 [] (unknown:0) - File “C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/MONAIAuto3DSeg/lib/Slicer-5.10/qt-scripted-modules/MONAIAuto3DSeg.py”, line 1099, in setupPythonRequirements

[CRITICAL][Stream] 23.04.2026 09:04:48 [] (unknown:0) - self.DEPENDENCY\_HANDLER.setupPythonRequirements(upgrade)

[CRITICAL][Stream] 23.04.2026 09:04:48 [] (unknown:0) - File “C:\Users\DiMO 3D 1\AppData\Local\slicer.org\3D Slicer 5.10.0\slicer.org\Extensions-34045\MONAIAuto3DSeg\lib\Slicer-5.10\qt-scripted-modules\MONAIAuto3DSegLib\dependency\_handler.py”, line 92, in setupPythonRequirements

[CRITICAL][Stream] 23.04.2026 09:04:48 [] (unknown:0) - slicer.util.pip\_install(monaiInstallString)

[CRITICAL][Stream] 23.04.2026 09:04:48 [] (unknown:0) - File “C:\Users\DiMO 3D 1\AppData\Local\slicer.org\3D Slicer 5.10.0\bin\Python\slicer\util.py”, line 4034, in pip\_install

[CRITICAL][Stream] 23.04.2026 09:04:48 [] (unknown:0) - \_executePythonModule(“pip”, args)

[CRITICAL][Stream] 23.04.2026 09:04:48 [] (unknown:0) - File “C:\Users\DiMO 3D 1\AppData\Local\slicer.org\3D Slicer 5.10.0\bin\Python\slicer\util.py”, line 3988, in \_executePythonModule

[CRITICAL][Stream] 23.04.2026 09:04:48 [] (unknown:0) - logProcessOutput(proc)

[CRITICAL][Stream] 23.04.2026 09:04:48 [] (unknown:0) - File “C:\Users\DiMO 3D 1\AppData\Local\slicer.org\3D Slicer 5.10.0\bin\Python\slicer\util.py”, line 3954, in logProcessOutput

[CRITICAL][Stream] 23.04.2026 09:04:48 [] (unknown:0) - raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)

[CRITICAL][Stream] 23.04.2026 09:04:48 [] (unknown:0) - subprocess.CalledProcessError: Command ‘[‘C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/bin/../bin\\PythonSlicer.EXE’, ‘-m’, ‘pip’, ‘install’, ‘monai[fire,pyyaml,nibabel,pynrrd,psutil,tensorboard,skimage,itk,tqdm]\>=1.3’, ‘–upgrade’]’ returned non-zero exit status 1.

[DEBUG][Qt] 23.04.2026 09:04:52 [] (unknown:0) - Switch to module: “TotalSegmentator”

[INFO][Python] 23.04.2026 09:05:02 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/PyTorch/lib/Slicer-5.10/qt-scripted-modules/PyTorchUtils.py:153) - Importing torch…

[INFO][Python] 23.04.2026 09:05:03 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/PyTorch/lib/Slicer-5.10/qt-scripted-modules/PyTorchUtils.py:190) - PyTorch 2.9.1+cu126 imported successfully

[INFO][Python] 23.04.2026 09:05:03 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/PyTorch/lib/Slicer-5.10/qt-scripted-modules/PyTorchUtils.py:191) - CUDA available: True

[INFO][Python] 23.04.2026 09:05:03 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:687) - Processing started

[INFO][Python] 23.04.2026 09:05:03 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:687) - Writing input file to C:/Users/DiMO 3D 1/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2026-04-23\_09+05+03.721/total-segmentator-input.nii

[INFO][Python] 23.04.2026 09:05:04 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:687) - Creating segmentations with TotalSegmentator AI…

[INFO][Python] 23.04.2026 09:05:04 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:687) - Total Segmentator arguments: [‘-i’, ‘C:/Users/DiMO 3D 1/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2026-04-23\_09+05+03.721/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/DiMO 3D 1/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2026-04-23\_09+05+03.721/segmentation’, ‘–device’, ‘gpu’, ‘–ml’, ‘–task’, ‘total’]

[INFO][Python] 23.04.2026 09:05:08 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:687) - Traceback (most recent call last):

[INFO][Python] 23.04.2026 09:05:08 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:687) - File “”, line 198, in \_run\_module\_as\_main

[INFO][Python] 23.04.2026 09:05:08 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:687) - File “”, line 88, in \_run\_code

[INFO][Python] 23.04.2026 09:05:08 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:687) - File “C:\Users\DiMO 3D 1\AppData\Local\slicer.org\3D Slicer 5.10.0\lib\Python\Scripts\TotalSegmentator.exe\__main_\_.py”, line 7, in

[INFO][Python] 23.04.2026 09:05:08 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:687) - File “C:\Users\DiMO 3D 1\AppData\Local\slicer.org\3D Slicer 5.10.0\lib\Python\Lib\site-packages\totalsegmentator\bin\TotalSegmentator.py”, line 201, in main

[INFO][Python] 23.04.2026 09:05:08 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:687) - totalsegmentator(args.input, args.output, args.ml, args.nr\_thr\_resamp, args.nr\_thr\_saving,

[INFO][Python] 23.04.2026 09:05:08 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:687) - File “C:\Users\DiMO 3D 1\AppData\Local\slicer.org\3D Slicer 5.10.0\lib\Python\Lib\site-packages\totalsegmentator\python\_api.py”, line 156, in totalsegmentator

[INFO][Python] 23.04.2026 09:05:08 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:687) - from totalsegmentator.nnunet import nnUNet\_predict\_image # this has to be after setting new env vars

[INFO][Python] 23.04.2026 09:05:08 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:687) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

[INFO][Python] 23.04.2026 09:05:08 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:687) - File “C:\Users\DiMO 3D 1\AppData\Local\slicer.org\3D Slicer 5.10.0\lib\Python\Lib\site-packages\totalsegmentator\nnunet.py”, line 28, in

[INFO][Python] 23.04.2026 09:05:09 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:687) - from nnunetv2.utilities.find\_class\_by\_name import recursive\_find\_python\_class

[INFO][Python] 23.04.2026 09:05:09 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:687) - File “C:\Users\DiMO 3D 1\AppData\Local\slicer.org\3D Slicer 5.10.0\lib\Python\Lib\site-packages\nnunetv2\utilities\find\_class\_by\_name.py”, line 4, in

[INFO][Python] 23.04.2026 09:05:09 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:687) - from batchgenerators.utilities.file\_and\_folder\_operations import \*

[INFO][Python] 23.04.2026 09:05:09 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:687) - ModuleNotFoundError: No module named ‘batchgenerators’

[INFO][Python] 23.04.2026 09:05:09 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:687) -

[INFO][Python] 23.04.2026 09:05:09 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:687) - If you use this tool please cite: [https://pubs.rsna.org/doi/10.1148/ryai.230024](https://pubs.rsna.org/doi/10.1148/ryai.230024)

[INFO][Python] 23.04.2026 09:05:09 [Python] (C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py:687) -

[ERROR][Python] 23.04.2026 09:05:09 [Python] (C:\Users\DiMO 3D 1\AppData\Local\slicer.org\3D Slicer 5.10.0\bin\Python\slicer\util.py:3146) - Failed to compute results.

Command ‘[‘C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/bin/../bin\\PythonSlicer.EXE’, ‘C:\\Users\\DiMO 3D 1\\AppData\\Local\\slicer.org\\3D Slicer 5.10.0\\lib\\Python\\Scripts\\TotalSegmentator.exe’, ‘-i’, ‘C:/Users/DiMO 3D 1/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2026-04-23\_09+05+03.721/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/DiMO 3D 1/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2026-04-23\_09+05+03.721/segmentation’, ‘–device’, ‘gpu’, ‘–ml’, ‘–task’, ‘total’]’ returned non-zero exit status 1.

[CRITICAL][Stream] 23.04.2026 09:05:27 [] (unknown:0) - Traceback (most recent call last):

[CRITICAL][Stream] 23.04.2026 09:05:27 [] (unknown:0) - File “C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py”, line 360, in onApplyButton

[CRITICAL][Stream] 23.04.2026 09:05:27 [] (unknown:0) - self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),

[CRITICAL][Stream] 23.04.2026 09:05:27 [] (unknown:0) - File “C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py”, line 1132, in process

[CRITICAL][Stream] 23.04.2026 09:05:27 [] (unknown:0) - self.processVolume(inputFile, inputVolume,

[CRITICAL][Stream] 23.04.2026 09:05:27 [] (unknown:0) - File “C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py”, line 1216, in processVolume

[CRITICAL][Stream] 23.04.2026 09:05:27 [] (unknown:0) - self.logProcessOutput(proc)

[CRITICAL][Stream] 23.04.2026 09:05:27 [] (unknown:0) - File “C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/slicer.org/Extensions-34045/TotalSegmentator/lib/Slicer-5.10/qt-scripted-modules/TotalSegmentator.py”, line 964, in logProcessOutput

[CRITICAL][Stream] 23.04.2026 09:05:27 [] (unknown:0) - raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)

[CRITICAL][Stream] 23.04.2026 09:05:27 [] (unknown:0) - subprocess.CalledProcessError: Command ‘[‘C:/Users/DiMO 3D 1/AppData/Local/slicer.org/3D Slicer 5.10.0/bin/../bin\\PythonSlicer.EXE’, ‘C:\\Users\\DiMO 3D 1\\AppData\\Local\\slicer.org\\3D Slicer 5.10.0\\lib\\Python\\Scripts\\TotalSegmentator.exe’, ‘-i’, ‘C:/Users/DiMO 3D 1/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2026-04-23\_09+05+03.721/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/DiMO 3D 1/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2026-04-23\_09+05+03.721/segmentation’, ‘–device’, ‘gpu’, ‘–ml’, ‘–task’, ‘total’]’ returned non-zero exit status 1.