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nimh-dsst / dsst-defacing-pipeline

Defacing algorithm to improve and evaluate accuracy for large datasets.
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Should not look under non-bids folders, or in particular under folder names with leading period #43

Open yarikoptic opened 5 months ago

yarikoptic commented 5 months ago

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 .