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
[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.