TotalSegmentator
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Error when running totalsegmentator `json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)`
Description
I'm trying to run total segmentator MRI but run into an error:
If you use this tool please cite: https://pubs.rsna.org/doi/10.1148/ryai.230024
Traceback (most recent call last):
File "/home/GRAMES.POLYMTL.CA/p118739/.conda/envs/total_env/bin/TotalSegmentator", line 8, in <module>
sys.exit(main())
File "/home/GRAMES.POLYMTL.CA/p118739/.conda/envs/total_env/lib/python3.9/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 "/home/GRAMES.POLYMTL.CA/p118739/.conda/envs/total_env/lib/python3.9/site-packages/totalsegmentator/python_api.py", line 129, in totalsegmentator
setup_totalseg()
File "/home/GRAMES.POLYMTL.CA/p118739/.conda/envs/total_env/lib/python3.9/site-packages/totalsegmentator/config.py", line 60, in setup_totalseg
config = json.load(f)
File "/home/GRAMES.POLYMTL.CA/p118739/.conda/envs/total_env/lib/python3.9/json/__init__.py", line 293, in load
return loads(fp.read(),
File "/home/GRAMES.POLYMTL.CA/p118739/.conda/envs/total_env/lib/python3.9/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
File "/home/GRAMES.POLYMTL.CA/p118739/.conda/envs/total_env/lib/python3.9/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/home/GRAMES.POLYMTL.CA/p118739/.conda/envs/total_env/lib/python3.9/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
Steps to reproduce
- Create an environment with python 3.9 or 3.11 (I used conda)
-
conda install pytorch==2.5.1 torchvision==0.20.1 torchaudio==2.5.1 pytorch-cuda=12.1 -c pytorch -c nvidia -
pip install TotalSegmentator -
TotalSegmentator -i $img -o segmentations --task total_mr