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However, it turned out that the manual_correction.py script does not support wildcards for multiple contrasts:
$ python manual_correction.py -path-img /Users/user/data/dcm-xxxx/ -config /Users/user/data/dcm-xxxx/label_discs.yml----------------------------------------------------------------------------------------------------Parsing of arguments: Input folder .............. /Users/user/data/dcm-xxxx Label folder .............. /Users/user/data/dcm-xxxx/derivatives/labels Output folder ............. /Users/user/data/dcm-xxxx/derivatives/labels----------------------------------------------------------------------------------------------------Enter your name (Firstname Lastname). It will be used to generate a json sidecar with each corrected file: Jan userFILES_LABEL: 0%| | 0/2 [00:00<?, ?file/s]FILES_LABEL: 0%| | 0/2 [00:00<?, ?file/s]Traceback (most recent call last): File "/Users/user/code/manual-correction/venv/lib/python3.9/site-packages/nibabel/loadsave.py", line 87, in load stat_result = os.stat(filename)FileNotFoundError: [Errno 2] No such file or directory: '/Users/user/data/dcm-xxxx/sub-*/anat/sub-*_T1w.nii.gz'During handling of the above exception, another exception occurred:Traceback (most recent call last): File "/Users/user/code/manual-correction/manual_correction.py", line 904, in <module> main() File "/Users/user/code/manual-correction/manual_correction.py", line 843, in main utils.create_empty_mask(fname, fname_out) File "/Users/user/code/manual-correction/utils.py", line 298, in create_empty_mask img = nib.load(fname) File "/Users/user/code/manual-correction/venv/lib/python3.9/site-packages/nibabel/loadsave.py", line 89, in load raise FileNotFoundError(f"No such file or no access: '{filename}'")FileNotFoundError: No such file or no access: '/Users/user/data/dcm-xxxx/sub-*/anat/sub-*_T1w.nii.gz'
I wanted to label discs for all T1w and T2w images, so I used the following YML config file with wildcards (
*
) for several contrasts:However, it turned out that the
manual_correction.py
script does not support wildcards for multiple contrasts:The reason is this condition.
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