Hi @themeo,
I had figured what was most likely causing this issue was a bad skull strip of the magnitude images. I remember reading some documentation by spm12 and FSL (both of which can handle phasediff images) about needing a very tight skull strip and to avoid any and all non-brain voxels as much as possible (FUGUE/Guide - FslWiki).
I used Freesurfer’s synthstrip (SynthStrip) to skull strip my magnitude images and ran the same processing again using fMRIPrep 22.1.1. I used Synthstrip since it seems to be able to handle any type of brain image very well.
Synthstrip’s skull stripping is already very robust and tight, and I think fMRIprep basically further skull stripped the already skull stripped magnitude image such that it made an extremely tight mask (i.e., too much brain voxel taken out). I think this is why now the “phasediff_fieldmap image” it generated came out very odd looking - it looks like a lot of voxels are just missing. However, the SDC correction applied to my functional images seemed to improve (almost even perfect).
So, I am not fully sure what to make of this. Maybe fMRIprep team should implement synthstrip under the hood to skull strip the magnitude image (of course erode it as well), and remove whatever current skull stripping utility they have and then it seem like this issue would be resolved.
I am including here screeshots of the images from the HTML report.
Distorted/Uncorrected functional:
SDC Corrected:
Best,
Jagan.