Given a Deep-Brain-Stimulation patient’s scan session, I tried to do the following:
run dcm2bids (dicom to bids)
run qsiprep, which is a bids-app.
To convert dicom to bids using dcm2bids I have to create rules on how to name each type of scan. One of these scans is FGATIR, a sequence in which white matter is dark, widely used for getting good contrast in thalamic regions. A more generic name could be 'White Matter null" or Wmn.
Anyway, in BIDS I cannot find an appropriate suffix for this scan type, and ended up using a file "sub-x_ses-y_acq-FGATIR_t1w.nii.gz.
But then qsiprep interpreted this as being just another t1w scan, and averaged it with the regular t1w scan, which gives a very bad result. So using the suffix t1w is obviously not the way to go. But it seems BIDS will not allow custom suffixes like _FGATIR.nii.gz. How to deal with this? Can a file be non-BIDS-ifyable?
You can open issues on the BIDS standard GitHub repo to suggest inclusion of additional file types. In the meantime, if it is not a T1w variant, you can give it a custom suffix and then include those files in your .bidsignore. If it is a T1w variance, then the acq-<> label is fine and you can filter it out from qsiprep with a bids filter file.