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Hi, you probably want to use just SIENAX for all of this, which calls BET and FAST, and can give grey and white volumes, also optionally normalising for head size. You could easily add a couple of lines at the end bringing a standard-space mask for the auditory cortex into native space and applying to the FAST PVE outputs to get regional volumes. Cheers. On Tue, 29 Jun 2004, Anda Pacurar wrote: > Hello, > > I'm trying to perform for the first time volumetric measurements for > white/grey matter and CSF on a subject with Parkinson disease using fsl > and I would appreciate again your help. > > We have aquired T1 images (256X256X124) and I understand that I have to > > # run BET > > FAST Segmentation: > # remove the bias field > # set the number of input channels =1 > #set the number of classes= 3 (for white.gray matter and CSF) > # use a priory probability maps for initialization (Talairach template), > because at the end I would like to compare Parkinson group / Control Group > > My questions are: > 1. I would like to do segmentation only for primary auditory cortex so I > wonder is it a way to specify ROI mask? > 2. After the segmentation is done should I use SIENNA software to find > the volume for white/gray matter? > > Thank you. > Anda > 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