I am looking at bids_spec1.0.2.pdf (can’t find 1.0.3) and want to point out the ambiguity in the description regarding fieldmap
At BidsSpec 8.9 [Fieldmap data] it states the “The IntendedFor field may contain one or more filenames with paths relative to the subject subfolder…The IntendedFor field is optional and in case the fieldmaps do not correspond to any particular scans it does not have to be filled.”
The “optional” wording reads as if fmriprep would apply the fieldmap to all functional runs when the IntendedFor is not specified and would only apply to specific runs if files are specified in IntendedFor. This seems to be a common source of confusion as raised in Fmriprep: fieldmap present but ignored and that it causes situations where the IntendedFor field needs to be filled out manually after conversion Heudiconv heuristics for field maps
Could a possible solution be to modify default behavior of fmriprep to apply fieldmap to all func/ files if IntendedFor is not specified?