# TotalSegmentator + Slicer 5.8.1 - "ModuleNotFoundError: No module named 'pydicom.pixels'"

**URL:** <https://discourse.slicer.org/t/totalsegmentator-slicer-5-8-1-modulenotfounderror-no-module-named-pydicom-pixels/42386>\
**Category:** Support\
**Tags:** totalsegmentator\
**Created:** [March 31, 2025, 7:55pm UTC](https://discourse.slicer.org/t/totalsegmentator-slicer-5-8-1-modulenotfounderror-no-module-named-pydicom-pixels/42386 "2025-03-31T19:55:08Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![jochoaTX](https://avatars.discourse-cdn.com/v4/letter/j/b3f665/32.png) [@jochoaTX](https://discourse.slicer.org/u/jochoaTX)\
**Post date:** [March 31, 2025, 7:55pm UTC](https://discourse.slicer.org/t/totalsegmentator-slicer-5-8-1-modulenotfounderror-no-module-named-pydicom-pixels/42386/1 "2025-03-31T19:55:08Z")

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Operating system: WinPro 11  
Slicer version: 5.8.1  
Expected behavior: TotalSegmentator to totally segment  
Actual behavior: Pukes

I’ve declared defeat. Cannot solve this myself. It seems that TotalSegmentator may be looking for an earlier version of pydicom? Any help/suggestions appreciated - for the sake of my sanity. Here’s some context:

Processing started  
Writing input file to C:/Users/jocho/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2025-03-31\_11+33+57.728/total-segmentator-input.nii  
Creating segmentations with TotalSegmentator AI…  
Total Segmentator arguments: [‘-i’, ‘C:/Users/jocho/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2025-03-31\_11+33+57.728/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/jocho/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2025-03-31\_11+33+57.728/segmentation’, ‘–ml’, ‘–task’, ‘total’]  
Traceback (most recent call last):  
File “C:\ProgramData\slicer.org\Slicer 5.8.1\lib\Python\Lib\runpy.py”, line 197, in \_run\_module\_as\_main  
return _run\_code(code, main\_globals, None,  
File “C:\ProgramData\slicer.org\Slicer 5.8.1\lib\Python\Lib\runpy.py”, line 87, in run\_code  
exec(code, run\_globals)  
File "C:\ProgramData\slicer.org\Slicer 5.8.1\lib\Python\Scripts\TotalSegmentator.exe\_main.py", line 7, in   
File “C:\ProgramData\slicer.org\Slicer 5.8.1\lib\Python\Lib\site-packages\totalsegmentator\bin\TotalSegmentator.py”, line 143, in main  
totalsegmentator(args.input, args.output, args.ml, args.nr\_thr\_resamp, args.nr\_thr\_saving,  
File “C:\ProgramData\slicer.org\Slicer 5.8.1\lib\Python\Lib\site-packages\totalsegmentator\python\_api.py”, line 137, in totalsegmentator  
from totalsegmentator.nnunet import nnUNet\_predict\_image # this has to be after setting new env vars  
File “C:\ProgramData\slicer.org\Slicer 5.8.1\lib\Python\Lib\site-packages\totalsegmentator\nnunet.py”, line 54, in   
from totalsegmentator.dicom\_io import dcm\_to\_nifti, save\_mask\_as\_rtstruct  
File “C:\ProgramData\slicer.org\Slicer 5.8.1\lib\Python\Lib\site-packages\totalsegmentator\dicom\_io.py”, line 13, in   
import dicom2nifti  
File "C:\ProgramData\slicer.org\Slicer 5.8.1\lib\Python\Lib\site-packages\dicom2nifti\_init_.py", line 19, in   
from dicom2nifti.convert\_dicom import dicom\_series\_to\_nifti  
File “C:\ProgramData\slicer.org\Slicer 5.8.1\lib\Python\Lib\site-packages\dicom2nifti\convert\_dicom.py”, line 17, in   
import dicom2nifti.common as common  
File “C:\ProgramData\slicer.org\Slicer 5.8.1\lib\Python\Lib\site-packages\dicom2nifti\common.py”, line 16, in   
from pydicom.pixels import apply\_modality\_lut  
ModuleNotFoundError: No module named ‘pydicom.pixels’

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)

++++++++++++++  
Traceback (most recent call last):  
File “C:\ProgramData\slicer.org\Slicer 5.8.1\bin\Python\slicer\util.py”, line 3303, in tryWithErrorDisplay  
yield  
File “C:/ProgramData/slicer.org/Slicer 5.8.1/slicer.org/Extensions-33241/TotalSegmentator/lib/Slicer-5.8/qt-scripted-modules/TotalSegmentator.py”, line 307, in onApplyButton  
self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),  
File “C:/ProgramData/slicer.org/Slicer 5.8.1/slicer.org/Extensions-33241/TotalSegmentator/lib/Slicer-5.8/qt-scripted-modules/TotalSegmentator.py”, line 1037, in process  
self.processVolume(inputFile, inputVolume,  
File “C:/ProgramData/slicer.org/Slicer 5.8.1/slicer.org/Extensions-33241/TotalSegmentator/lib/Slicer-5.8/qt-scripted-modules/TotalSegmentator.py”, line 1104, in processVolume  
self.logProcessOutput(proc)  
File “C:/ProgramData/slicer.org/Slicer 5.8.1/slicer.org/Extensions-33241/TotalSegmentator/lib/Slicer-5.8/qt-scripted-modules/TotalSegmentator.py”, line 883, in logProcessOutput  
raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)  
subprocess.CalledProcessError: Command ‘[‘C:/ProgramData/slicer.org/Slicer 5.8.1/bin/../bin\PythonSlicer.EXE’, ‘C:\ProgramData\slicer.org\Slicer 5.8.1\lib\Python\Scripts\TotalSegmentator.exe’, ‘-i’, ‘C:/Users/jocho/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2025-03-31\_11+52+39.591/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/jocho/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2025-03-31\_11+52+39.591/segmentation’, ‘–ml’, ‘–task’, ‘total’]’ returned non-zero exit status 1.

+++++

[Python] Failed to compute results.  
[Python] Command ‘[‘C:/ProgramData/slicer.org/Slicer 5.8.1/bin/../bin\PythonSlicer.EXE’, ‘C:\ProgramData\slicer.org\Slicer 5.8.1\lib\Python\Scripts\TotalSegmentator.exe’, ‘-i’, ‘C:/Users/jocho/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2025-03-31\_11+52+39.591/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/jocho/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2025-03-31\_11+52+39.591/segmentation’, ‘–ml’, ‘–task’, ‘total’]’ returned non-zero exit status 1.  
Traceback (most recent call last):  
File “C:/ProgramData/slicer.org/Slicer 5.8.1/slicer.org/Extensions-33241/TotalSegmentator/lib/Slicer-5.8/qt-scripted-modules/TotalSegmentator.py”, line 307, in onApplyButton  
self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),  
File “C:/ProgramData/slicer.org/Slicer 5.8.1/slicer.org/Extensions-33241/TotalSegmentator/lib/Slicer-5.8/qt-scripted-modules/TotalSegmentator.py”, line 1037, in process  
self.processVolume(inputFile, inputVolume,  
File “C:/ProgramData/slicer.org/Slicer 5.8.1/slicer.org/Extensions-33241/TotalSegmentator/lib/Slicer-5.8/qt-scripted-modules/TotalSegmentator.py”, line 1104, in processVolume  
self.logProcessOutput(proc)  
File “C:/ProgramData/slicer.org/Slicer 5.8.1/slicer.org/Extensions-33241/TotalSegmentator/lib/Slicer-5.8/qt-scripted-modules/TotalSegmentator.py”, line 883, in logProcessOutput  
raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)  
subprocess.CalledProcessError: Command ‘[‘C:/ProgramData/slicer.org/Slicer 5.8.1/bin/../bin\PythonSlicer.EXE’, ‘C:\ProgramData\slicer.org\Slicer 5.8.1\lib\Python\Scripts\TotalSegmentator.exe’, ‘-i’, ‘C:/Users/jocho/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2025-03-31\_11+52+39.591/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/jocho/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2025-03-31\_11+52+39.591/segmentation’, ‘–ml’, ‘–task’, ‘total’]’ returned non-zero exit status 1.  
[Qt] QTextCursor::setPosition: Position ‘-18456’ out of range  
[Qt] QTextCursor::setPosition: Position ‘-18456’ out of range  
[Qt] QTextCursor::setPosition: Position ‘-18456’ out of range  
[Qt] QTextCursor::setPosition: Position ‘-18456’ out of range  
[Qt] QTextCursor::setPosition: Position ‘-18456’ out of range

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [March 31, 2025, 8:01pm UTC](https://discourse.slicer.org/t/totalsegmentator-slicer-5-8-1-modulenotfounderror-no-module-named-pydicom-pixels/42386/2 "2025-03-31T20:01:25Z")

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Thanks for reporting. The issue is due to an unused Python package (dicom2nifti) released a corrupted version for Python-3.9 a few days ago. The [error is reported to dicom2nifti developers](https://github.com/icometrix/dicom2nifti/issues/155) and a [fix is already implemented in TotalSegmentator extension](https://github.com/lassoan/SlicerTotalSegmentator/issues/72).

The fix will be available in the Extensions Manager from tomorrow. If you use the latest Slicer Preview Release (currently Slicer-5.8.1), then tomorrow you can go to the Extensions Manager and click “Check for updates” and then “Update all” to get the fix.

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**Author:** ![jochoaTX](https://avatars.discourse-cdn.com/v4/letter/j/b3f665/32.png) [@jochoaTX](https://discourse.slicer.org/u/jochoaTX)\
**Post date:** [April 1, 2025, 12:05am UTC](https://discourse.slicer.org/t/totalsegmentator-slicer-5-8-1-modulenotfounderror-no-module-named-pydicom-pixels/42386/3 "2025-04-01T00:05:06Z")

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Dr. Lasso- thank you very much for your very prompt responses! It gives me some hope that I’ll be able to get this module running. At one point, a little bit Self doubt started creeping into my head.

I appreciate all the work that you do for this community, and I know many others do to.

I’ll report back tomorrow, hopefully with an affirmative that everything worked out OK. Regards!