The updated version of dcm2bids (version 3/1/0) is adding a “bids::” before the actual location of the functional MRI scan in the IntendedForField. When this is added, fMRIprep can’t find our distortion scan. Is there a simple solution for this that doesn’t involve our having to update the json file with a script?
dcm2bids 3.1.0 is outputting (here fMRIprep can’t find the distortion scan)
In short, no. But a python script with the json package should solve your issue easily. Also, fMRIPrep should eventually honor the BIDS URI, which would no longer produce the error. Additionally, we are thinking of having dcm2bids instead output B0FieldSource/Identifier pairs in a future release.
The correct version without the BIDS URI should not have sub-0001/ in front.