Hi, I’m trying to activate the totalsegmentator on one of the examples of CT there’s in the slicer.
I get an error that the ml models are not connected and the result failes.
Thanks
Thanks for the reply, I’m pasting the error I got, hope you could help me solve it.
Processing started
Writing input file to C:/Users/assaf/slicer.org/__SlicerTemp__2025-04-30_09+51+06.674/total-segmentator-input.nii
Creating segmentations with TotalSegmentator AI…
Total Segmentator arguments: [‘-i’, ‘C:/Users/assaf/slicer.org/__SlicerTemp__2025-04-30_09+51+06.674/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/assaf/slicer.org/__SlicerTemp__2025-04-30_09+51+06.674/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–fast’]
Traceback (most recent call last):
File “C:\Users\assaf\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:\Users\assaf\slicer.org\Slicer 5.8.1\lib\Python\Lib\runpy.py”, line 87, in run_code
exec(code, run_globals)
File "C:\Users\assaf\slicer.org\Slicer 5.8.1\lib\Python\Scripts\TotalSegmentator.exe_main.py", line 7, in
File “C:\Users\assaf\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:\Users\assaf\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:\Users\assaf\slicer.org\Slicer 5.8.1\lib\Python\Lib\site-packages\totalsegmentator\nnunet.py”, line 29, in
from totalsegmentator.custom_trainers import nnUNetTrainer_MOSAIC_1k_QuarterLR_NoMirroring
File “C:\Users\assaf\slicer.org\Slicer 5.8.1\lib\Python\Lib\site-packages\totalsegmentator\custom_trainers.py”, line 2, in
from nnunetv2.training.nnUNetTrainer.variants.data_augmentation.nnUNetTrainerNoMirroring import nnUNetTrainerNoMirroring
File “C:\Users\assaf\slicer.org\Slicer 5.8.1\lib\Python\Lib\site-packages\nnunetv2\training\nnUNetTrainer\variants\data_augmentation\nnUNetTrainerNoMirroring.py”, line 5, in
from batchgeneratorsv2.helpers.scalar_type import RandomScalar
ModuleNotFoundError: No module named ‘batchgeneratorsv2’