It is now clear that the intention was to use each field map
acquisition just once. To make this more apparent in the BIDS layout,
and enable Heudiconv's "CustomAcquisitionLabel" strategy for matching
IntendedFor, we switch from using run- labels to acq- labels. The
label will be either the corresponding task label (if intended for
func) or the corresponding acquisition label (for dwi).
We still keep the ImagingVolume and Shims options: we'd rather not
assign IntendedFor than assign a mismatched one.
It seems that the conditional which handles protocol name with no
explicit field map numbering was left over from the initial draft (it
seems that protocols from Aachen, Frankfurt, and Mannheim always use
run-(1/2/3) while Mannheim has a naming strategy altogether
incompatible with this heuristic), but the conditional is kept (and
updated) just in case.
The heuristic did not handle DICOM series named "dwi_acq-(...)b0ref"
correctly - it placed them as "_sbref" into dwi/, while they should
have been "_epi" in func. These have an opposite phase encoding
direction to the main dwi acquisitions, and are intended for field map
correction.
This change assigns the correct folder and suffix to these files, and
adds dir-PA / dir-AP to the dwi and reference acquisitions. As a
result, QSIPrep should pick these up as field maps and apply
susceptibility distorsion correction.
