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Hello FSL community, Does anyone have any advice on how to optimize registration when one is specifically interested in the brainstem? I have very little experience using FLIRT focused on this part of the brain -- is there any reason to expect it to fit brainstem worse than it fits cortex? I see that FIRST uses a two-stage process, first registering to the standard atlas, and then repeating this step using the brainstem mask as a -refweight. Is that the best way to do it? Considering the size and shape of this structure am I right to think that nonlinear registration (FNIRT) would be overkill? Thanks for any thoughts on this issue, Jonas ---- Jonas Kaplan, Ph.D. Research Assistant Professor Brain & Creativity Institute University of Southern California