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I have a question relating to segmentation with FAST. I have been trying to use prior probabilities for initialization and for final segmentation in order to obtain more accurate segmentation of the basal ganglia, particularly the thalamus. I assume that in order to use prior probability masks the program tries to register the volume to be segmented to a template. Can the segmentation go very wrong if the volume to be segmented is tilted by a large angle in respect to standard space? I think FAST works better on deskulled volumes, but the skull can provide useful info for accurate registration to a template, so if I want to use priors, should I deskull the volume before or after segmentation? What happens if the brain I want to segment is much smaller or deformed in unusual ways as compared to the template? Can this result in inaccurate segmentation, due to poor registration with the template? Thanks for your help.... Stefano Marenco, MD Senior Staff Fellow Clinical Brain Disorders Branch NIMH 10 Center Drive, room 4S235 Bethesda, MD 20817 tel. (301) 435-8964 fax. (301) 480-7795 email: <mailto:[log in to unmask]> [log in to unmask]