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
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’”.
I also cannot find the Liver Segments task, only Liver Vessels.
Thanks in advance