GroupAFQ and BIDS error

yeatmanlab / pyAFQ

Automated Fiber Quantification ... in Python

http://yeatmanlab.github.io/pyAFQ/

BSD 2-Clause "Simplified" License

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GroupAFQ and BIDS error #1039

Closed radhi-bhalerao closed 8 months ago

radhi-bhalerao commented 1 year ago

I keep getting this error while initializing a GroupAFQ object “No dwi found for subject PDa### and session 1. Skipping.”

myafq = GroupAFQ( bids_path=('/data/morrison/data/parkinsons/retro_clin_dti_bids/Nifti'), viz_backend_spec='plotly_no_gif', bids_filters= {'suffix': 'dwi', 'session': '1', 'datatype': 'dwi'})

Any suggestions of maybe what I'm doing wrong in the bids organization?

arokem commented 1 year ago

Does this dataset validate as BIDS-compliant? You can easily check here: https://bids-standard.github.io/bids-validator/

I suspect that the file PDa001_dti.nii.gz might cause some issues unless it is recorded in the .bidsignore file of the dataset.

36000 commented 8 months ago

Another option here is to use ignore BIDS and use ParticipantAFQ:

myafq = ParticipantAFQ(
  '/data/morrison/data/parkinsons/retro_clin_dti_bids/Nifti/derivatives/sub-PDa001/ses-1/sub-PDa001_ses-1_dwi.nii',
  '/data/morrison/data/parkinsons/retro_clin_dti_bids/Nifti/derivatives/sub-PDa001/ses-1/sub-PDa001_ses-1_dwi.bval',
  '/data/morrison/data/parkinsons/retro_clin_dti_bids/Nifti/derivatives/sub-PDa001/ses-1/sub-PDa001_ses-1_dwi.bvec',
  some_path_to_output_folder)