Hello,
I am a radiologist and I use total segmentator a lot.
I have a problem with my total segmentator.
When I run it on a CT scan of the abdomen, it displays an error message.
Can anyone help me please.
I have version 5.6.2 of 3D slicer and the latest update of total segmentator.
Total segmentator has always worked very well so far.
Thanks for your help,
Mike
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).
DEBUG][Qt] 08.09.2024 15:32:53 [] (unknown:0) - Session start time .......: 20240908_153253
[DEBUG][Qt] 08.09.2024 15:32:53 [] (unknown:0) - Slicer version ...........: 5.6.2 (revision 32448 / f10cd8c) win-amd64 - installed release
[DEBUG][Qt] 08.09.2024 15:32:53 [] (unknown:0) - Operating system .........: Windows / Personal / (Build 22631, Code Page 65001) - 64-bit
[DEBUG][Qt] 08.09.2024 15:32:53 [] (unknown:0) - Memory ...................: 65369 MB physical, 75097 MB virtual
[DEBUG][Qt] 08.09.2024 15:32:53 [] (unknown:0) - CPU ......................: GenuineIntel , 32 cores, 32 logical processors
[DEBUG][Qt] 08.09.2024 15:32:53 [] (unknown:0) - VTK configuration ........: OpenGL2 rendering, TBB threading
[DEBUG][Qt] 08.09.2024 15:32:53 [] (unknown:0) - Qt configuration .........: version 5.15.2, with SSL, requested OpenGL 3.2 (compatibility profile)
[DEBUG][Qt] 08.09.2024 15:32:53 [] (unknown:0) - Internationalization .....: disabled, language=
[DEBUG][Qt] 08.09.2024 15:32:53 [] (unknown:0) - Developer mode ...........: disabled
[DEBUG][Qt] 08.09.2024 15:32:53 [] (unknown:0) - Application path .........: C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/bin
[DEBUG][Qt] 08.09.2024 15:32:53 [] (unknown:0) - Additional module paths ..: slicer.org/Extensions-32448/PyTorch/lib/Slicer-5.6/qt-scripted-modules, slicer.org/Extensions-32448/MONAILabel/lib/Slicer-5.6/qt-scripted-modules, slicer.org/Extensions-32448/NvidiaAIAssistedAnnotation/lib/Slicer-5.6/qt-scripted-modules, slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules
[DEBUG][Python] 08.09.2024 15:32:54 [Python] (C:\Users\salav\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] 08.09.2024 15:32:54 [Python] (C:\Users\salav\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] 08.09.2024 15:32:54 [] (unknown:0) - Switch to module: "Welcome"
[INFO][Python] 08.09.2024 15:32:54 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/NvidiaAIAssistedAnnotation/lib/Slicer-5.6/qt-scripted-modules/SegmentEditorNvidiaAIAA.py:32) - This plugin dir: C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/NvidiaAIAssistedAnnotation/lib/Slicer-5.6/qt-scripted-modules
[DEBUG][Qt] 08.09.2024 15:32:56 [] (unknown:0) - Switch to module: "DICOM"
[INFO][Python] 08.09.2024 15:33:00 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/bin/../lib/Slicer-5.6/qt-scripted-modules/DICOMScalarVolumePlugin.py:446) - Loading with imageIOName: GDCM
[INFO][Python] 08.09.2024 15:33:03 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/bin/../lib/Slicer-5.6/qt-scripted-modules/DICOMScalarVolumePlugin.py:525) - Window/level found in DICOM tags (center=40.0, width=400.0) has been applied to volume 3: Abdomen Veneus
[DEBUG][Qt] 08.09.2024 15:33:07 [] (unknown:0) - Switch to module: "TotalSegmentator"
[INFO][Stream] 08.09.2024 15:33:15 [] (unknown:0) - Requirement already satisfied: pillow<10.1 in c:\users\salav\appdata\local\slicer.org\slicer 5.6.2\lib\python\lib\site-packages (10.0.1)
[INFO][Python] 08.09.2024 15:33:17 [Python] (C:/Users/salav/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] 08.09.2024 15:33:17 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/PyTorch/lib/Slicer-5.6/qt-scripted-modules/PyTorchUtils.py:190) - PyTorch 2.3.1+cu118 imported successfully
[INFO][Python] 08.09.2024 15:33:17 [Python] (C:/Users/salav/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] 08.09.2024 15:33:17 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - Processing started
[INFO][Python] 08.09.2024 15:33:17 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - Writing input file to C:/Users/salav/AppData/Local/Temp/Slicer/__SlicerTemp__2024-09-08_15+33+17.326/total-segmentator-input.nii
[INFO][Python] 08.09.2024 15:33:17 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - Creating segmentations with TotalSegmentator AI...
[INFO][Python] 08.09.2024 15:33:17 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - Total Segmentator arguments: ['-i', 'C:/Users/salav/AppData/Local/Temp/Slicer/__SlicerTemp__2024-09-08_15+33+17.326/total-segmentator-input.nii', '-o', 'C:/Users/salav/AppData/Local/Temp/Slicer/__SlicerTemp__2024-09-08_15+33+17.326/segmentation', '--ml', '--task', 'total']
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - Traceback (most recent call last):
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - File "C:\Users\salav\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\runpy.py", line 197, in _run_module_as_main
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - return _run_code(code, main_globals, None,
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - File "C:\Users\salav\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\runpy.py", line 87, in _run_code
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - exec(code, run_globals)
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - File "C:\Users\salav\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Scripts\TotalSegmentator.exe\__main__.py", line 7, in <module>
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - File "C:\Users\salav\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\totalsegmentator\bin\TotalSegmentator.py", line 141, in main
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - totalsegmentator(args.input, args.output, args.ml, args.nr_thr_resamp, args.nr_thr_saving,
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - File "C:\Users\salav\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\totalsegmentator\python_api.py", line 119, in totalsegmentator
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - setup_totalseg()
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - File "C:\Users\salav\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\totalsegmentator\config.py", line 60, in setup_totalseg
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - config = json.load(f)
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - File "C:\Users\salav\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\json\__init__.py", line 293, in load
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - return loads(fp.read(),
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - File "C:\Users\salav\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\json\__init__.py", line 346, in loads
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - return _default_decoder.decode(s)
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - File "C:\Users\salav\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\json\decoder.py", line 337, in decode
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - obj, end = self.raw_decode(s, idx=_w(s, 0).end())
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - File "C:\Users\salav\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\json\decoder.py", line 355, in raw_decode
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - raise JSONDecodeError("Expecting value", s, err.value) from None
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) -
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) - If you use this tool please cite: https://pubs.rsna.org/doi/10.1148/ryai.230024
[INFO][Python] 08.09.2024 15:33:19 [Python] (C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py:595) -
[ERROR][Python] 08.09.2024 15:33:19 [Python] (C:\Users\salav\AppData\Local\slicer.org\Slicer 5.6.2\bin\Python\slicer\util.py:3009) - Failed to compute results.
Command '['C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/bin/../bin\\PythonSlicer.EXE', 'C:\\Users\\salav\\AppData\\Local\\slicer.org\\Slicer 5.6.2\\lib\\Python\\Scripts\\TotalSegmentator.exe', '-i', 'C:/Users/salav/AppData/Local/Temp/Slicer/__SlicerTemp__2024-09-08_15+33+17.326/total-segmentator-input.nii', '-o', 'C:/Users/salav/AppData/Local/Temp/Slicer/__SlicerTemp__2024-09-08_15+33+17.326/segmentation', '--ml', '--task', 'total']' returned non-zero exit status 1.
[CRITICAL][Stream] 08.09.2024 15:33:24 [] (unknown:0) - Traceback (most recent call last):
[CRITICAL][Stream] 08.09.2024 15:33:24 [] (unknown:0) - File "C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 307, in onApplyButton
[CRITICAL][Stream] 08.09.2024 15:33:24 [] (unknown:0) - self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),
[CRITICAL][Stream] 08.09.2024 15:33:24 [] (unknown:0) - File "C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 1001, in process
[CRITICAL][Stream] 08.09.2024 15:33:24 [] (unknown:0) - self.processVolume(inputFile, inputVolume,
[CRITICAL][Stream] 08.09.2024 15:33:24 [] (unknown:0) - File "C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 1075, in processVolume
[CRITICAL][Stream] 08.09.2024 15:33:24 [] (unknown:0) - self.logProcessOutput(proc)
[CRITICAL][Stream] 08.09.2024 15:33:24 [] (unknown:0) - File "C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/TotalSegmentator/lib/Slicer-5.6/qt-scripted-modules/TotalSegmentator.py", line 847, in logProcessOutput
[CRITICAL][Stream] 08.09.2024 15:33:24 [] (unknown:0) - raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
[CRITICAL][Stream] 08.09.2024 15:33:24 [] (unknown:0) - subprocess.CalledProcessError: Command '['C:/Users/salav/AppData/Local/slicer.org/Slicer 5.6.2/bin/../bin\\PythonSlicer.EXE', 'C:\\Users\\salav\\AppData\\Local\\slicer.org\\Slicer 5.6.2\\lib\\Python\\Scripts\\TotalSegmentator.exe', '-i', 'C:/Users/salav/AppData/Local/Temp/Slicer/__SlicerTemp__2024-09-08_15+33+17.326/total-segmentator-input.nii', '-o', 'C:/Users/salav/AppData/Local/Temp/Slicer/__SlicerTemp__2024-09-08_15+33+17.326/segmentation', '--ml', '--task', 'total']' returned non-zero exit status 1.
How can I get the total segmentator to work again, I really don’t understand. While MonaiAuto3DSeg.
Only there is no head and neck model on Monai Auto 3DSeg. If you could help me thank you.
Maybe you are seeing this issue: I broke my totalsegmentator - #5 by lassoan
Hello,
Have you tried to force reinstall/manually downlaod the weight in the advanced section of the module ?
That’s what fixed it for me last time
According to the log, an error occurs when TotalSegmentator attempts to read its configuration C:\Users\salav\.totalsegmentator\config.json file. Its content seems to be invalid. Probably the easiest fix is to delete this file.
Thank you all, that’s what I did and it’s working now.
…Thank you.
Mike