Thanks for your helpful videos! If I am trying to do two step registration with the first step being linear registration of a T1 image to a T2 image, is it OK to use the FEAT tool and upload the T2 image where you have uploaded the functional data? Then subsequently use FNIRT to perform spatial normalization to MNI space?
I am trying to align rat brain fMRI to P56 Atlas template. And I'm not quite satisfied with the result. What are the tips for rat brains? And more importantly, how can I manually edit transformation matrices, delete skulls etc?