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Hi - I'm not sure if you're saying that you'd like to improve the segmentation output by FAST or the effect of the cortical masking carried out by affine-transforming a simple cortical standard space mask onto the data - it sounds like it may be the latter, in which case you might want to use your own version of $FSLDIR/etc/standard/ avg152T1_strucseg_periph - or it may simply be that your subject is too different from the MNI152 for a purely affine transformation to give you a good match of the mask, in which case SIENAX can't help you there! Hope this helps - cheers, Steve. On 21 Oct 2006, at 17:57, Paul Geha wrote: > Hello, > > I am trying to do a cortical volume quantification using Sienax on > t1 images. When I run it I get > the output called t1_periph_render. This one shows that there are > some small areas in the > fusiform gyrus, and the orbito-frontal cortex. I tried to > increase the number of iteration with > the S option (to 15) in Sienax to improve this but this did not > work. However, if I run FAST on > the t1 image with the "use a priori probability maps for > initialising" I get a better peripheral > gray matter mask in t1_brain_seg1 image with no omissions, but > this one includes the sub-cortical > structures and the cerebellum, which I want to exclude. > > Can I improve Sienax segmentation in anyway? Please advise. > > thanks a lot, > > Paul > > Paul Geha M.D. > Northwestern University > The Feinberg School of Medicine > Department of Physiology M211 > 303 E. Chicago Ave. > Chicago, IL 60611 > Tel:312-503 2886 > Fax: 312-503-5101 ------------------------------------------------------------------------ --- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ------------------------------------------------------------------------ ---