Each of my functional scans (acquired from a Simenese Prisma scanner) have an associated SBRef scan as well. Usually, before using BIDS, I used these as inplane images for registration and normalization.
I noted that in the BIDS format there is both an option to include SBRef images in the functional directory, as well as an inplane image in the anatomy directory.
I was wondering, in addition to including my SBRef in the functional directory, should I also use one of them as an inplane image in the anatomy directory?
Does fmriprep make use of the inplane and/or the SBRef image for its pre-processing?