I have a MacBook Pro M4 and I have the same error… I tried force reinstalling the python packages and still get the same error… I am running 5.7.0
Processing started
Writing input file to /private/var/folders/72/n0v1btkn7q5gdq7rg3_s_1s00000gn/T/Slicer-carlosarrieta/__SlicerTemp__2024-11-09_11+14+38.364/total-segmentator-input.nii
Creating segmentations with TotalSegmentator AI…
Total Segmentator arguments: [‘-i’, ‘/private/var/folders/72/n0v1btkn7q5gdq7rg3_s_1s00000gn/T/Slicer-carlosarrieta/__SlicerTemp__2024-11-09_11+14+38.364/total-segmentator-input.nii’, ‘-o’, ‘/private/var/folders/72/n0v1btkn7q5gdq7rg3_s_1s00000gn/T/Slicer-carlosarrieta/__SlicerTemp__2024-11-09_11+14+38.364/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–device’, ‘cpu’]
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 30, in
from nnunetv2.inference.predict_from_raw_data import nnUNetPredictor
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/nnunetv2/inference/predict_from_raw_data.py”, line 22, in
from nnunetv2.inference.data_iterators import PreprocessAdapterFromNpy, preprocessing_iterator_fromfiles,
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/nnunetv2/inference/data_iterators.py”, line 12, in
from nnunetv2.preprocessing.preprocessors.default_preprocessor import DefaultPreprocessor
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/nnunetv2/preprocessing/preprocessors/default_preprocessor.py”, line 25, in
from nnunetv2.preprocessing.cropping.cropping import crop_to_nonzero
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/nnunetv2/preprocessing/cropping/cropping.py”, line 5, in
from acvl_utils.cropping_and_padding.bounding_boxes import get_bbox_from_mask, crop_to_bbox, bounding_box_to_slice
File “/Applications/Slicer.app/Contents/lib/Python/lib/python3.9/site-packages/acvl_utils/cropping_and_padding/bounding_boxes.py”, line 5, in
import blosc2
ModuleNotFoundError: No module named ‘blosc2’
Traceback (most recent call last):
File “/Applications/Slicer.app/Contents/bin/Python/slicer/util.py”, line 3295, in tryWithErrorDisplay
yield
File “/Applications/Slicer.app/Contents/Extensions-33089/TotalSegmentator/lib/Slicer-5.7/qt-scripted-modules/TotalSegmentator.py”, line 307, in onApplyButton
self.logic.process(self.ui.inputVolumeSelector.currentNode(), self.ui.outputSegmentationSelector.currentNode(),
File “/Applications/Slicer.app/Contents/Extensions-33089/TotalSegmentator/lib/Slicer-5.7/qt-scripted-modules/TotalSegmentator.py”, line 1002, in process
self.processVolume(inputFile, inputVolume,
File “/Applications/Slicer.app/Contents/Extensions-33089/TotalSegmentator/lib/Slicer-5.7/qt-scripted-modules/TotalSegmentator.py”, line 1076, in processVolume
self.logProcessOutput(proc)
File “/Applications/Slicer.app/Contents/Extensions-33089/TotalSegmentator/lib/Slicer-5.7/qt-scripted-modules/TotalSegmentator.py”, line 848, in logProcessOutput
raise CalledProcessError(retcode, proc.args, output=proc.stdout, stderr=proc.stderr)
subprocess.CalledProcessError: Command ‘[’/Applications/Slicer.app/Contents/bin/…/bin/PythonSlicer’, ‘/Applications/Slicer.app/Contents/lib/Python/bin/TotalSegmentator’, ‘-i’, ‘/private/var/folders/72/n0v1btkn7q5gdq7rg3_s_1s00000gn/T/Slicer-carlosarrieta/__SlicerTemp__2024-11-09_11+20+01.602/total-segmentator-input.nii’, ‘-o’, ‘/private/var/folders/72/n0v1btkn7q5gdq7rg3_s_1s00000gn/T/Slicer-carlosarrieta/__SlicerTemp__2024-11-09_11+20+01.602/segmentation’, ‘–ml’, ‘–task’, ‘total’, ‘–fast’]’ returned non-zero exit status 1.