TotalSegmentator Failed to compute results....returned non-zero exit status 1

yk_Chen · August 31, 2024, 2:13pm

Operating system: Windows 10
Slicer version:5.6.2
Hi,
I have properly installed Pytorch and other python packages, and restarted and reinstalled Slicer several times. But when I hit Apply, I get this error. I suspect that I may have downloaded the relevant package in the wrong folder, but I am not sure how to solve it.

And here is the detail:

[Python] Failed to compute results.
[Python] Command '['C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/bin/../bin\\PythonSlicer.EXE', 'C:\\Users\\Administrator\\AppData\\Local\\slicer.org\\Slicer 5.6.2\\lib\\Python\\Scripts\\TotalSegmentator.exe', '-i', 'C:/Users/Administrator/AppData/Local/Temp/Slicer/__SlicerTemp__2024-08-31_22+00+02.786/total-segmentator-input.nii', '-o', 'C:/Users/Administrator/AppData/Local/Temp/Slicer/__SlicerTemp__2024-08-31_22+00+02.786/segmentation', '--ml', '--task', 'total']' returned non-zero exit status 1.
Traceback (most recent call last):
  File "C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 298, in onApplyButton
    self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),
  File "C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 971, in process
    self.processVolume(inputFile, inputVolume,
  File "C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 1045, in processVolume
    self.logProcessOutput(proc)
  File "C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 817, in logProcessOutput
    raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command '['C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/bin/../bin\\PythonSlicer.EXE', 'C:\\Users\\Administrator\\AppData\\Local\\slicer.org\\Slicer 5.6.2\\lib\\Python\\Scripts\\TotalSegmentator.exe', '-i', 'C:/Users/Administrator/AppData/Local/Temp/Slicer/__SlicerTemp__2024-08-31_22+00+02.786/total-segmentator-input.nii', '-o', 'C:/Users/Administrator/AppData/Local/Temp/Slicer/__SlicerTemp__2024-08-31_22+00+02.786/segmentation', '--ml', '--task', 'total']' returned non-zero exit status 1.

The following is more detailed info from “report a bug”

[DEBUG][Qt] 31.08.2024 21:59:46 [] (unknown:0) - Session start time .......: 20240831_215946
[DEBUG][Qt] 31.08.2024 21:59:46 [] (unknown:0) - Slicer version ...........: 5.6.2 (revision 32448 / f10cd8c) win-amd64 - installed release
[DEBUG][Qt] 31.08.2024 21:59:46 [] (unknown:0) - Operating system .........: Windows /  Professional / (Build 19041, Code Page 65001) - 64-bit
[DEBUG][Qt] 31.08.2024 21:59:46 [] (unknown:0) - Memory ...................: 64665 MB physical, 130201 MB virtual
[DEBUG][Qt] 31.08.2024 21:59:46 [] (unknown:0) - CPU ......................: AuthenticAMD AMD Ryzen 9 7900X 12-Core Processor            , 24 cores, 24 logical processors
[DEBUG][Qt] 31.08.2024 21:59:46 [] (unknown:0) - VTK configuration ........: OpenGL2 rendering, TBB threading
[DEBUG][Qt] 31.08.2024 21:59:46 [] (unknown:0) - Qt configuration .........: version 5.15.2, with SSL, requested OpenGL 3.2 (compatibility profile)
[DEBUG][Qt] 31.08.2024 21:59:46 [] (unknown:0) - Internationalization .....: disabled, language=
[DEBUG][Qt] 31.08.2024 21:59:46 [] (unknown:0) - Developer mode ...........: disabled
[DEBUG][Qt] 31.08.2024 21:59:46 [] (unknown:0) - Application path .........: C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/bin
[DEBUG][Qt] 31.08.2024 21:59:46 [] (unknown:0) - Additional module paths ..: 
[DEBUG][Python] 31.08.2024 21:59:47 [Python] (C:\Users\Administrator\AppData\Local\slicer.org\Slicer 5.6.2\lib\Slicer-5.6\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:39) - Scripted subject hierarchy plugin registered: SegmentEditor
[DEBUG][Python] 31.08.2024 21:59:47 [Python] (C:\Users\Administrator\AppData\Local\slicer.org\Slicer 5.6.2\lib\Slicer-5.6\qt-scripted-modules\SubjectHierarchyPlugins\AbstractScriptedSubjectHierarchyPlugin.py:39) - Scripted subject hierarchy plugin registered: SegmentStatistics
[DEBUG][Qt] 31.08.2024 21:59:47 [] (unknown:0) - Switch to module:  "Welcome"
[DEBUG][Qt] 31.08.2024 21:59:55 [] (unknown:0) - "Volume" Reader has successfully read the file "D:/DicomDate Dep1Astd/3-403193.nii.gz" "[0.17s]"
[DEBUG][Qt] 31.08.2024 21:59:59 [] (unknown:0) - Switch to module:  "TotalSegmentator"
[INFO][Stream] 31.08.2024 22:00:01 [] (unknown:0) - Looking in indexes: 
[INFO][Stream] 31.08.2024 22:00:01 [] (unknown:0) - Requirement already satisfied: pillow<10.1 in c:\users\administrator\appdata\local\slicer.org\slicer 5.6.2\lib\python\lib\site-packages (10.0.1)
[INFO][Python] 31.08.2024 22:00:02 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/PyTorch/lib/Slicer-5.6/qt-scripted-modules/PyTorchUtils.py:153) - Importing torch...
[INFO][Python] 31.08.2024 22:00:02 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/PyTorch/lib/Slicer-5.6/qt-scripted-modules/PyTorchUtils.py:190) - PyTorch 2.4.0+cu118 imported successfully
[INFO][Python] 31.08.2024 22:00:02 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/PyTorch/lib/Slicer-5.6/qt-scripted-modules/PyTorchUtils.py:191) - CUDA available: True
[INFO][Python] 31.08.2024 22:00:02 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) - Processing started
[INFO][Python] 31.08.2024 22:00:02 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) - Writing input file to C:/Users/Administrator/AppData/Local/Temp/Slicer/__SlicerTemp__2024-08-31_22+00+02.786/total-segmentator-input.nii
[INFO][Python] 31.08.2024 22:00:02 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) - Creating segmentations with TotalSegmentator AI...
[INFO][Python] 31.08.2024 22:00:02 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) - Total Segmentator arguments: ['-i', 'C:/Users/Administrator/AppData/Local/Temp/Slicer/__SlicerTemp__2024-08-31_22+00+02.786/total-segmentator-input.nii', '-o', 'C:/Users/Administrator/AppData/Local/Temp/Slicer/__SlicerTemp__2024-08-31_22+00+02.786/segmentation', '--ml', '--task', 'total']
[INFO][Python] 31.08.2024 22:00:04 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) - Traceback (most recent call last):
[INFO][Python] 31.08.2024 22:00:04 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -   File "C:\Users\Administrator\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\runpy.py", line 197, in _run_module_as_main
[INFO][Python] 31.08.2024 22:00:04 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -     return _run_code(code, main_globals, None,
[INFO][Python] 31.08.2024 22:00:04 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -   File "C:\Users\Administrator\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\runpy.py", line 87, in _run_code
[INFO][Python] 31.08.2024 22:00:04 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -     exec(code, run_globals)
[INFO][Python] 31.08.2024 22:00:04 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -   File "C:\Users\Administrator\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Scripts\TotalSegmentator.exe\__main__.py", line 7, in <module>
[INFO][Python] 31.08.2024 22:00:04 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -   File "C:\Users\Administrator\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\totalsegmentator\bin\TotalSegmentator.py", line 138, in main
[INFO][Python] 31.08.2024 22:00:04 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -     totalsegmentator(args.input, args.output, args.ml, args.nr_thr_resamp, args.nr_thr_saving,
[INFO][Python] 31.08.2024 22:00:04 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -   File "C:\Users\Administrator\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\totalsegmentator\python_api.py", line 126, in totalsegmentator
[INFO][Python] 31.08.2024 22:00:04 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -     from totalsegmentator.nnunet import nnUNet_predict_image  # this has to be after setting new env vars
[INFO][Python] 31.08.2024 22:00:04 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -   File "C:\Users\Administrator\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\totalsegmentator\nnunet.py", line 30, in <module>
[INFO][Python] 31.08.2024 22:00:04 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -     from nnunetv2.inference.predict_from_raw_data import nnUNetPredictor
[INFO][Python] 31.08.2024 22:00:04 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -   File "C:\Users\Administrator\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\nnunetv2\inference\predict_from_raw_data.py", line 11, in <module>
[INFO][Python] 31.08.2024 22:00:04 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -     from acvl_utils.cropping_and_padding.padding import pad_nd_image
[INFO][Python] 31.08.2024 22:00:04 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) - ModuleNotFoundError: No module named 'acvl_utils'
[INFO][Python] 31.08.2024 22:00:04 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -
[INFO][Python] 31.08.2024 22:00:04 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) - If you use this tool please cite: 
[INFO][Python] 31.08.2024 22:00:04 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -
[ERROR][Python] 31.08.2024 22:00:04 [Python] (C:\Users\Administrator\AppData\Local\slicer.org\Slicer 5.6.2\bin\Python\slicer\util.py:3009) - Failed to compute results.

Command '['C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/bin/../bin\\PythonSlicer.EXE', 'C:\\Users\\Administrator\\AppData\\Local\\slicer.org\\Slicer 5.6.2\\lib\\Python\\Scripts\\TotalSegmentator.exe', '-i', 'C:/Users/Administrator/AppData/Local/Temp/Slicer/__SlicerTemp__2024-08-31_22+00+02.786/total-segmentator-input.nii', '-o', 'C:/Users/Administrator/AppData/Local/Temp/Slicer/__SlicerTemp__2024-08-31_22+00+02.786/segmentation', '--ml', '--task', 'total']' returned non-zero exit status 1.
[CRITICAL][Stream] 31.08.2024 22:00:16 [] (unknown:0) - Traceback (most recent call last):
[CRITICAL][Stream] 31.08.2024 22:00:16 [] (unknown:0) -   File "C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 298, in onApplyButton
[CRITICAL][Stream] 31.08.2024 22:00:16 [] (unknown:0) -     self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),
[CRITICAL][Stream] 31.08.2024 22:00:16 [] (unknown:0) -   File "C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 971, in process
[CRITICAL][Stream] 31.08.2024 22:00:16 [] (unknown:0) -     self.processVolume(inputFile, inputVolume,
[CRITICAL][Stream] 31.08.2024 22:00:16 [] (unknown:0) -   File "C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 1045, in processVolume
[CRITICAL][Stream] 31.08.2024 22:00:16 [] (unknown:0) -     self.logProcessOutput(proc)
[CRITICAL][Stream] 31.08.2024 22:00:16 [] (unknown:0) -   File "C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 817, in logProcessOutput
[CRITICAL][Stream] 31.08.2024 22:00:16 [] (unknown:0) -     raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
[CRITICAL][Stream] 31.08.2024 22:00:16 [] (unknown:0) - subprocess.CalledProcessError: Command '['C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/bin/../bin\\PythonSlicer.EXE', 'C:\\Users\\Administrator\\AppData\\Local\\slicer.org\\Slicer 5.6.2\\lib\\Python\\Scripts\\TotalSegmentator.exe', '-i', 'C:/Users/Administrator/AppData/Local/Temp/Slicer/__SlicerTemp__2024-08-31_22+00+02.786/total-segmentator-input.nii', '-o', 'C:/Users/Administrator/AppData/Local/Temp/Slicer/__SlicerTemp__2024-08-31_22+00+02.786/segmentation', '--ml', '--task', 'total']' returned non-zero exit status 1.
[INFO][Python] 31.08.2024 22:09:03 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/PyTorch/lib/Slicer-5.6/qt-scripted-modules/PyTorchUtils.py:153) - Importing torch...
[INFO][Python] 31.08.2024 22:09:03 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/PyTorch/lib/Slicer-5.6/qt-scripted-modules/PyTorchUtils.py:190) - PyTorch 2.4.0+cu118 imported successfully
[INFO][Python] 31.08.2024 22:09:03 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/PyTorch/lib/Slicer-5.6/qt-scripted-modules/PyTorchUtils.py:191) - CUDA available: True
[INFO][Python] 31.08.2024 22:09:03 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) - Processing started
[INFO][Python] 31.08.2024 22:09:03 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) - Writing input file to C:/Users/Administrator/AppData/Local/Temp/Slicer/__SlicerTemp__2024-08-31_22+09+03.824/total-segmentator-input.nii
[INFO][Python] 31.08.2024 22:09:03 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) - Creating segmentations with TotalSegmentator AI...
[INFO][Python] 31.08.2024 22:09:03 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) - Total Segmentator arguments: ['-i', 'C:/Users/Administrator/AppData/Local/Temp/Slicer/__SlicerTemp__2024-08-31_22+09+03.824/total-segmentator-input.nii', '-o', 'C:/Users/Administrator/AppData/Local/Temp/Slicer/__SlicerTemp__2024-08-31_22+09+03.824/segmentation', '--ml', '--task', 'total']
[INFO][Python] 31.08.2024 22:09:05 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) - Traceback (most recent call last):
[INFO][Python] 31.08.2024 22:09:05 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -   File "C:\Users\Administrator\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\runpy.py", line 197, in _run_module_as_main
[INFO][Python] 31.08.2024 22:09:05 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -     return _run_code(code, main_globals, None,
[INFO][Python] 31.08.2024 22:09:05 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -   File "C:\Users\Administrator\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\runpy.py", line 87, in _run_code
[INFO][Python] 31.08.2024 22:09:05 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -     exec(code, run_globals)
[INFO][Python] 31.08.2024 22:09:05 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -   File "C:\Users\Administrator\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Scripts\TotalSegmentator.exe\__main__.py", line 7, in <module>
[INFO][Python] 31.08.2024 22:09:05 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -   File "C:\Users\Administrator\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\totalsegmentator\bin\TotalSegmentator.py", line 138, in main
[INFO][Python] 31.08.2024 22:09:05 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -     totalsegmentator(args.input, args.output, args.ml, args.nr_thr_resamp, args.nr_thr_saving,
[INFO][Python] 31.08.2024 22:09:05 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -   File "C:\Users\Administrator\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\totalsegmentator\python_api.py", line 126, in totalsegmentator
[INFO][Python] 31.08.2024 22:09:05 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -     from totalsegmentator.nnunet import nnUNet_predict_image  # this has to be after setting new env vars
[INFO][Python] 31.08.2024 22:09:05 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -   File "C:\Users\Administrator\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\totalsegmentator\nnunet.py", line 30, in <module>
[INFO][Python] 31.08.2024 22:09:05 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -     from nnunetv2.inference.predict_from_raw_data import nnUNetPredictor
[INFO][Python] 31.08.2024 22:09:05 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -   File "C:\Users\Administrator\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\nnunetv2\inference\predict_from_raw_data.py", line 11, in <module>
[INFO][Python] 31.08.2024 22:09:05 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -     from acvl_utils.cropping_and_padding.padding import pad_nd_image
[INFO][Python] 31.08.2024 22:09:05 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) - ModuleNotFoundError: No module named 'acvl_utils'
[INFO][Python] 31.08.2024 22:09:05 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -
[INFO][Python] 31.08.2024 22:09:05 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) 
[INFO][Python] 31.08.2024 22:09:05 [Python] (C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:565) -
[ERROR][Python] 31.08.2024 22:09:05 [Python] (C:\Users\Administrator\AppData\Local\slicer.org\Slicer 5.6.2\bin\Python\slicer\util.py:3009) - Failed to compute results.

Command '['C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/bin/../bin\\PythonSlicer.EXE', 'C:\\Users\\Administrator\\AppData\\Local\\slicer.org\\Slicer 5.6.2\\lib\\Python\\Scripts\\TotalSegmentator.exe', '-i', 'C:/Users/Administrator/AppData/Local/Temp/Slicer/__SlicerTemp__2024-08-31_22+09+03.824/total-segmentator-input.nii', '-o', 'C:/Users/Administrator/AppData/Local/Temp/Slicer/__SlicerTemp__2024-08-31_22+09+03.824/segmentation', '--ml', '--task', 'total']' returned non-zero exit status 1.
[CRITICAL][Stream] 31.08.2024 22:10:42 [] (unknown:0) - Traceback (most recent call last):
[CRITICAL][Stream] 31.08.2024 22:10:42 [] (unknown:0) -   File "C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 298, in onApplyButton
[CRITICAL][Stream] 31.08.2024 22:10:42 [] (unknown:0) -     self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),
[CRITICAL][Stream] 31.08.2024 22:10:42 [] (unknown:0) -   File "C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 971, in process
[CRITICAL][Stream] 31.08.2024 22:10:42 [] (unknown:0) -     self.processVolume(inputFile, inputVolume,
[CRITICAL][Stream] 31.08.2024 22:10:42 [] (unknown:0) -   File "C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 1045, in processVolume
[CRITICAL][Stream] 31.08.2024 22:10:42 [] (unknown:0) -     self.logProcessOutput(proc)
[CRITICAL][Stream] 31.08.2024 22:10:42 [] (unknown:0) -   File "C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 817, in logProcessOutput
[CRITICAL][Stream] 31.08.2024 22:10:42 [] (unknown:0) -     raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
[CRITICAL][Stream] 31.08.2024 22:10:42 [] (unknown:0) - subprocess.CalledProcessError: Command '['C:/Users/Administrator/AppData/Local/slicer.org/Slicer 5.6.2/bin/../bin\\PythonSlicer.EXE', 'C:\\Users\\Administrator\\AppData\\Local\\slicer.org\\Slicer 5.6.2\\lib\\Python\\Scripts\\TotalSegmentator.exe', '-i', 'C:/Users/Administrator/AppData/Local/Temp/Slicer/__SlicerTemp__2024-08-31_22+09+03.824/total-segmentator-input.nii', '-o', 'C:/Users/Administrator/AppData/Local/Temp/Slicer/__SlicerTemp__2024-08-31_22+09+03.824/segmentation', '--ml', '--task', 'total']' returned non-zero exit status 1.

pieper · August 31, 2024, 2:17pm

Use the “Help->Report a bug” menu to get the full log file for a failed run and look at it for more diagnostic info. If you still need help, post the log here (make sure it doesn’t have patient information in it).

yk_Chen · August 31, 2024, 2:28pm

I’ve updated it in the post. I need your help. Thank you very much!

lassoan · August 31, 2024, 2:47pm

The detailed log was helpful. Here is the error:

It means that some of the required Python packages were not installed. Did you see any error messages when you first started segmentation and Python dependencies were installed?

You can fix it by clicking Force reinstall button in Advanced section.

yk_Chen · September 4, 2024, 1:47pm

yeah, i have solved the problem, thank you very much!

Carlos_Arrieta · November 9, 2024, 4:20pm

I have a MacBook Pro M4 and I have the same error… I tried force reinstalling the python packages and still get the same error… I am running 5.7.0

Processing started
Writing input file to /private/var/folders/72/n0v1btkn7q5gdq7rg3_s_1s00000gn/T/Slicer-carlosarrieta/__SlicerTemp__2024-11-09_11+14+38.364/total-segmentator-input.nii
Creating segmentations with TotalSegmentator AI…
Total Segmentator arguments: [‘-i’, ‘/private/var/folders/72/n0v1btkn7q5gdq7rg3_s_1s00000gn/T/Slicer-carlosarrieta/__SlicerTemp__2024-11-09_11+14+38.364/total-segmentator-input.nii’, ‘-o’, ‘/private/var/folders/72/n0v1btkn7q5gdq7rg3_s_1s00000gn/T/Slicer-carlosarrieta/__SlicerTemp__2024-11-09_11+14+38.364/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–device’, ‘cpu’]

If you use this tool please cite: https://pubs.rsna.org/doi/10.1148/ryai.230024

Traceback (most recent call last):
File “/Applications/Slicer.app/Contents/lib/Python/bin/TotalSegmentator”, line 8, in
sys.exit(main())
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/totalsegmentator/bin/TotalSegmentator.py”, line 141, in main
totalsegmentator(args.input, args.output, args.ml, args.nr_thr_resamp, args.nr_thr_saving,
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/totalsegmentator/python_api.py”, line 127, in totalsegmentator
from totalsegmentator.nnunet import nnUNet_predict_image # this has to be after setting new env vars
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/totalsegmentator/nnunet.py”, line 30, in
from nnunetv2.inference.predict_from_raw_data import nnUNetPredictor
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/nnunetv2/inference/predict_from_raw_data.py”, line 22, in
from nnunetv2.inference.data_iterators import PreprocessAdapterFromNpy, preprocessing_iterator_fromfiles,
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/nnunetv2/inference/data_iterators.py”, line 12, in
from nnunetv2.preprocessing.preprocessors.default_preprocessor import DefaultPreprocessor
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/nnunetv2/preprocessing/preprocessors/default_preprocessor.py”, line 25, in
from nnunetv2.preprocessing.cropping.cropping import crop_to_nonzero
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/nnunetv2/preprocessing/cropping/cropping.py”, line 5, in
from acvl_utils.cropping_and_padding.bounding_boxes import get_bbox_from_mask, crop_to_bbox, bounding_box_to_slice
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/acvl_utils/cropping_and_padding/bounding_boxes.py”, line 5, in
import blosc2
ModuleNotFoundError: No module named ‘blosc2’

Traceback (most recent call last):
File “/Applications/Slicer.app/Contents/bin/Python/slicer/util.py”, line 3295, in tryWithErrorDisplay
yield
File “/Applications/Slicer.app/Contents/Extensions-33089/TotalSegmentator/lib/Slicer-5.7/qt-scripted-modules/TotalSegmentator.py”, line 307, in onApplyButton
self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),
File “/Applications/Slicer.app/Contents/Extensions-33089/TotalSegmentator/lib/Slicer-5.7/qt-scripted-modules/TotalSegmentator.py”, line 1002, in process
self.processVolume(inputFile, inputVolume,
File “/Applications/Slicer.app/Contents/Extensions-33089/TotalSegmentator/lib/Slicer-5.7/qt-scripted-modules/TotalSegmentator.py”, line 1076, in processVolume
self.logProcessOutput(proc)
File “/Applications/Slicer.app/Contents/Extensions-33089/TotalSegmentator/lib/Slicer-5.7/qt-scripted-modules/TotalSegmentator.py”, line 848, in logProcessOutput
raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command ‘[’/Applications/Slicer.app/Contents/bin/…/bin/PythonSlicer’, ‘/Applications/Slicer.app/Contents/lib/Python/bin/TotalSegmentator’, ‘-i’, ‘/private/var/folders/72/n0v1btkn7q5gdq7rg3_s_1s00000gn/T/Slicer-carlosarrieta/__SlicerTemp__2024-11-09_11+20+01.602/total-segmentator-input.nii’, ‘-o’, ‘/private/var/folders/72/n0v1btkn7q5gdq7rg3_s_1s00000gn/T/Slicer-carlosarrieta/__SlicerTemp__2024-11-09_11+20+01.602/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–fast’]’ returned non-zero exit status 1.

jamesobutler · November 9, 2024, 5:04pm

It appears MIC-DFZ has messed up their packages with a recent new dependency release. See the following link below for details:

github.com/MIC-DKFZ/acvl_utils

broken nnunetv2 import

opened 12:44PM - 07 Nov 24 UTC

jeandre-db

ImportError: cannot import name 'crop_to_bbox' from 'acvl_utils.cropping_and_pad…ding.bounding_boxes' (/local_disk0/.ephemeral_nfs/cluster_libraries/python/lib/python3.11/site-packages/acvl_utils/cropping_and_padding/bounding_boxes.py) File <command-1458388170907476>, line 7 5 import pyspark.sql.functions as f 6 from nnunetv2.imageio.simpleitk_reader_writer import SimpleITKIO ----> 7 from nnunetv2.inference.predict_from_raw_data import nnUNetPredictor 8 from nnunetv2.paths import nnUNet_results, nnUNet_raw 9 import torch It seems that the update to acvl broke nnunetv2 imports. locking the version to 0.2 fixes this issue.

github.com/MIC-DKFZ/nnUNet

`nnunetv2.inference` crashes on import (`No module named 'blosc2'`) due to buggy `acvl_utils` release

opened 05:31PM - 07 Nov 24 UTC

joshuacwnewton

Traceback: ``` File "/home/runner/sct_0.0/spinalcordtoolbox/deepseg/infere…nce.py", line 27, in <module> import spinalcordtoolbox.deepseg.nnunet as ds_nnunet File "/home/runner/sct_0.0/spinalcordtoolbox/deepseg/nnunet.py", line 13, in <module> from nnunetv2.inference.predict_from_raw_data import nnUNetPredictor # noqa: E402 File "/home/runner/sct_0.0/python/envs/venv_sct/lib/python3.9/site-packages/nnunetv2/inference/predict_from_raw_data.py", line 22, in <module> from nnunetv2.inference.data_iterators import PreprocessAdapterFromNpy, preprocessing_iterator_fromfiles, \ File "/home/runner/sct_0.0/python/envs/venv_sct/lib/python3.9/site-packages/nnunetv2/inference/data_iterators.py", line 12, in <module> from nnunetv2.preprocessing.preprocessors.default_preprocessor import DefaultPreprocessor File "/home/runner/sct_0.0/python/envs/venv_sct/lib/python3.9/site-packages/nnunetv2/preprocessing/preprocessors/default_preprocessor.py", line 23, in <module> from nnunetv2.preprocessing.cropping.cropping import crop_to_nonzero File "/home/runner/sct_0.0/python/envs/venv_sct/lib/python3.9/site-packages/nnunetv2/preprocessing/cropping/cropping.py", line 5, in <module> from acvl_utils.cropping_and_padding.bounding_boxes import get_bbox_from_mask, crop_to_bbox, bounding_box_to_slice File "/home/runner/sct_0.0/python/envs/venv_sct/lib/python3.9/site-packages/acvl_utils/cropping_and_padding/bounding_boxes.py", line 5, in <module> import blosc2 ModuleNotFoundError: No module named 'blosc2' ``` This is a duplicate of https://github.com/MIC-DKFZ/acvl_utils/issues/2, but I'm re-reporting here just in case anyone else runs into this bug and tries to find it by checking nnUNet's issues.

alireza-hokmabadi · November 9, 2024, 8:14pm

To resolve the issue temporarily, you can downgrade acvl_utils until the nnUNet team includes the missing crop_to_bbox function in a future update.

Run the following command to downgrade:
pip install acvl_utils==0.2

lassoan · November 11, 2024, 6:44pm

nnunet is still not fixed. If anyone comes across this issue, the current workaround is to open Slicer’s Python console (Ctrl+3) and type this command:

pip_install("acvl_utils==0.2")

I’ve pushed a fix (a temporary workaround) to the Slicer TotalSegmentator extension that automatically gets a working acvl_utils package version. This will fix the problem for all new Slicer installations from tomorrow.

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