I’ve got a study where the protocol collects two separate T1w images in a session, one of which is non-normalized. The non-normalized image contains much poorer contrast, and while fmriprep will merge multiple T1w anatomicals using Freesufer’s
mri_robust_template, my worry is that this merging will aversely affect the quality of the new image. To prevent this, I have not converted the non-normalized image to BIDS, so only the better contrast T1w image is used in fmriprep. Is this an appropriate approach, or should I be converting both to BIDS and having them merge?
For reference, here are snapshots of the images: