I am trying this pipeline on a dataset produced by heudiconv. There is .heudiconv/ folder which is not part of BIDS specification. Trying to run pipeline (see #42 for more on details) for a sample participant session
yoh@typhon:/mnt/DATA/data/yoh/1076_spacetop$ singularity run -B $PWD:$PWD:ro -B $PWD/derivatives:$PWD/derivatives:rw -B $PWD/scratch:$PWD/scratch:rw --scratch $PWD/scratch --pwd $PWD --net --network none ../dsst-defacing-pipeline/dsst-defacing-pipeline-test.sing -p 0001 -s 01 -- . derivatives/dss-defacing-1
results in
...
[]
Preparing for QC by visual inspection...
Traceback (most recent call last):
File "/opt/dsst-defacing-pipeline/run.py", line 192, in <module>
main()
File "/opt/dsst-defacing-pipeline/run.py", line 125, in main
raise ValueError(f'Could not find subject name in path: {defaceable}')
ValueError: Could not find subject name in path: .heudiconv/0001/ses-01
Ideally pipeline should not look under any .dotfolder .