I’m dealing with small FOV “slab” data and the bbregister approach to the EPI-to-T1w registration does not perform well. I’ve previously used the ANTs SyN-based diffeomorphic registration for these types of tricky issues.
Is it possible to use the diffeomorphic registration with in the fmriprep pipeline? If not, how and where would you recommend running it?
The displacement I was referring to was temporal lobe and cerebellum which you can clearly move in the animated fixed/moving visualisation.
I haven’t tried the ANTs approach on this registration, but have in the past where it seemed to do better than bbregister. Do you reckon it would make sense to try a two-step registration with bbregister first and the the diffeomorphic approach?
It would be great if you could share an annotated screenshot so we would be certain we are on the same page.
The SyN based susceptibility correction used in this run of FMRIPREP does already the diffeomorphic realignment of the bold image to contrast matched t1w image. It’s constrained to the phase encoding direction and regions of the brain where such distortions usually happen. In essence we are already combining non linear coregistration with BBR.
Having said that I find this corregistration pretty good and don’t quite understand what do you mean by “the temporal lobe is moving in and out of alignment”…