Operating system: Windows 10
Slicer version:5.6.2 + CPU
Dear support,
I tried to run totalsegmentator but it failed after a while with the “returned non-zero exit status 1”.
Could you help me to understand what is the probleme?
I copied below the message error of the pop-up window.
“Processing started
Writing input file to C:/Users/c.guillerminet/AppData/Local/Temp/Slicer/__SlicerTemp__2025-04-01_14+46+42.002/total-segmentator-input.nii
Creating segmentations with TotalSegmentator AI…
Total Segmentator arguments: [‘-i’, ‘C:/Users/c.guillerminet/AppData/Local/Temp/Slicer/__SlicerTemp__2025-04-01_14+46+42.002/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/c.guillerminet/AppData/Local/Temp/Slicer/__SlicerTemp__2025-04-01_14+46+42.002/segmentation’, ‘–task’, ‘body’, ‘–fast’]
Traceback (most recent call last):
File “C:\Users\c.guillerminet\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\runpy.py”, line 197, in _run_module_as_main
return run_code(code, main_globals, None,
File “C:\Users\c.guillerminet\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\runpy.py”, line 87, in run_code
exec(code, run_globals)
File "C:\Users\c.guillerminet\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Scripts\TotalSegmentator.exe_main.py", line 7, in
File “C:\Users\c.guillerminet\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\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 “C:\Users\c.guillerminet\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\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 “C:\Users\c.guillerminet\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\totalsegmentator\nnunet.py”, line 40, in
from totalsegmentator.dicom_io import dcm_to_nifti, save_mask_as_rtstruct
File “C:\Users\c.guillerminet\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\totalsegmentator\dicom_io.py”, line 13, in
import dicom2nifti
File "C:\Users\c.guillerminet\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\dicom2nifti_init.py”, line 19, in
from dicom2nifti.convert_dicom import dicom_series_to_nifti
File “C:\Users\c.guillerminet\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\dicom2nifti\convert_dicom.py”, line 17, in
import dicom2nifti.common as common
File “C:\Users\c.guillerminet\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\dicom2nifti\common.py”, line 16, in
from pydicom.pixels import apply_modality_lut
ModuleNotFoundError: No module named ‘pydicom.pixels’
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"
Sincerely yours,
Camille