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Hi, I have an experiment with several functional scans that I would like to align to each other, and then align them to the structural scan (stay in native space though). Preferably, I would align run 2-n to run 1, and then have the same transformation to coregister to the structural scan. I know that in SPM and Brainvoyager, it is possible to do motion correction on run 2-n aligned to the first volume of run 1, but I was wondering how to do that in FSL. Also, should I first use a betted functional to coregister to my structural, and then use this matrix to coregister the unbetted functional? Or does EPI-align work well with the functional scans that are not betted? I can then mask the functional scan after coregistration Thanks!