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Dear Ellen, If your images are not already in a similar orientation to the standard MNI images (as seen in FSLView) then I would recommend running fslreorient2std on your images as the first step, and then run the rest of the steps. This normally fixes this problem. All the best, Mark On 13 Dec 2011, at 17:04, Ellen Guller wrote: > sorry to jump in on this post- but I seem to be having the rare problem of registration failure. After running <fslvbm_2_template -a> my segmented\registered (GM_to_T.nii) images are flipped (not systematically, some are A-P flipped, some I/S)) and the labels in FSLview are not correct. However, the bet images (*brain.nii), and segmented (*struct_GM.nii) images are fine. Is there something I can do to fix the registration? > > Thanks, > > ~Ellen >