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Hi - yes, FAST calls FLIRT internally if you turn on either of the "priors" options. Because FAST always needs BET (deskulling) to have been run before calling FAST, it registers to an already-stripped template image (MNI152). In fact, in general, registration is slightly more robust on skull-stripped images. Yes, it is possible for inaccurate registrations (or if the subject looks nothing like the standard image) to decrease the FAST output quality when using priors - that is one reason why we do not use priors by default. To get deep grey, which is known to be hard from T1-only, you are better off combining with a second image and using MFAST - for example a PD image. Cheers, Steve. On Thu, 4 Mar 2004, Marenco, Stefano (NIH/NIMH) wrote: > 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] > > > > Stephen M. Smith DPhil Associate Director, FMRIB and Analysis Research Coordinator Oxford University Centre for Functional MRI of the Brain John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve