fMRIprep (23.1.4) does not take the magnitude1 and phase files for correction, as it reports “Susceptibility distortion correction: None”. The fmap files are not mentioned anywhere, and they should be both named correctly according to BIDS (generated by nii2bids) under the fmap folder and contain the intendedFor sidecar (everything passes bids validation).
I have triple echo acquisition, I tried to point to the first echo, and to all 3 in the intendedFor, nothing changed.
magnitude1 is for the shortest echo, and phasediff.json contains info on both echos. I also added magnitude2 but did not help. They are generated by a gre_field_mapping_AP scanner sequence.
Running fMRIprep in singularity, reports that it finished successfully with no errrors.