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

yk_Chen
Sat, 31 Aug 2024 14:13:27 +0000
Support

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.

11 posts - 7 participants