# Having trouble with TotalSegmentator

**URL:** <https://discourse.slicer.org/t/having-trouble-with-totalsegmentator/43710>\
**Category:** Support\
**Tags:** segmentation, extensions-manager\
**Created:** [July 14, 2025, 1:48pm UTC](https://discourse.slicer.org/t/having-trouble-with-totalsegmentator/43710 "2025-07-14T13:48:41Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Celina\_Hallal](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/celina_hallal/32/12339_2.png) [@Celina\_Hallal](https://discourse.slicer.org/u/Celina_Hallal)\
**Post date:** [July 14, 2025, 1:48pm UTC](https://discourse.slicer.org/t/having-trouble-with-totalsegmentator/43710/1 "2025-07-14T13:48:41Z")

</div>

Operating system: MacOS Sequoia 15.5  
Slicer version: 5.9.0  
Expected behavior: Automated segmentation of organs, segmentation of liver segments  
Actual behavior: Extension fails to compute results

I am trying to use TotalSegmentator, but it keeps returning the same error even after reinstalling it

Failed to compute results.

Command ‘[’/Applications/Slicer.app/Contents/bin/../bin/PythonSlicer’, ‘/Applications/Slicer.app/Contents/lib/Python/bin/TotalSegmentator’, ‘-i’, ‘/private/var/folders/cy/jc\_jw\_l536l0p8\_ky67hg0sm0000gn/T/Slicer-celinahallal/\_\_SlicerTemp\_\_2025-07-14\_10+12+45.692/total-segmentator-input.nii’, ‘-o’, ‘/private/var/folders/cy/jc\_jw\_l536l0p8\_ky67hg0sm0000gn/T/Slicer-celinahallal/\_\_SlicerTemp\_\_2025-07-14\_10+12+45.692/segmentation’, ‘–fast’]’ returned non-zero exit status 1.

Processing started  
Writing input file to /private/var/folders/cy/jc\_jw\_l536l0p8\_ky67hg0sm0000gn/T/Slicer-celinahallal/\_\_SlicerTemp\_\_2025-07-14\_10+12+45.692/total-segmentator-input.nii  
Creating segmentations with TotalSegmentator AI (pre-run)…  
Total Segmentator arguments: [‘-i’, ‘/private/var/folders/cy/jc\_jw\_l536l0p8\_ky67hg0sm0000gn/T/Slicer-celinahallal/\_\_SlicerTemp\_\_2025-07-14\_10+12+45.692/total-segmentator-input.nii’, ‘-o’, ‘/private/var/folders/cy/jc\_jw\_l536l0p8\_ky67hg0sm0000gn/T/Slicer-celinahallal/\_\_SlicerTemp\_\_2025-07-14\_10+12+45.692/segmentation’, ‘–fast’]  
No GPU detected. Running on CPU. This can be very slow. The ‘–fast’ or the `--roi_subset` option can help to reduce runtime.

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 “/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 40, in   
from totalsegmentator.dicom\_io import dcm\_to\_nifti, save\_mask\_as\_rtstruct  
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/totalsegmentator/dicom\_io.py”, line 13, in   
import dicom2nifti  
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/dicom2nifti/ **init**.py”, line 19, in   
from dicom2nifti.convert\_dicom import dicom\_series\_to\_nifti  
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/dicom2nifti/convert\_dicom.py”, line 17, in   
import dicom2nifti.common as common  
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/dicom2nifti/common.py”, line 16, in   
from pydicom.pixels import apply\_modality\_lut  
ModuleNotFoundError: No module named ‘pydicom.pixels’

I have already reinstalled PyTorch (but not manually) and TotalSegmentator. I’ve also already read [TotalSegmentator + Slicer 5.8.1 - “ModuleNotFoundError: No module named ‘pydicom.pixels’”](https://discourse.slicer.org/t/totalsegmentator-slicer-5-8-1-modulenotfounderror-no-module-named-pydicom-pixels/42386).

I also cannot find the Liver Segments task, only Liver Vessels.

Thanks in advance

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<div class="post-metadata">

**Author:** ![Celina\_Hallal](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/celina_hallal/32/12339_2.png) [@Celina\_Hallal](https://discourse.slicer.org/u/Celina_Hallal)\
**Post date:** [July 14, 2025, 2:32pm UTC](https://discourse.slicer.org/t/having-trouble-with-totalsegmentator/43710/2 "2025-07-14T14:32:46Z")

</div>

Ok, so I installed dicom2nifti v 2.5.1 using the Python console and the segmentation works! But I still can’t find some of the tasks like liver\_segments and abdominal\_muscles…