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Hi - yes, this is still related to the NEUROLOGICAL convention you are using in these Brainweb-derived files, which is a problem for FAST and many other NIFTI-reading programs at this point. If you run: fslswapdim t1_pn3_rf20_ns -x y z fixed fslorient -swaporient fixed fast -e -ov -os fixed You get a very nice segmentation. Otherwise the FAST output is L-R swapped relative to the input, which would explain your poor overlap measures. Cheers. On 6 Dec 2007, at 16:24, On Tsang wrote: > for archival purposes: > > Dear Steve, > > Thank you for your offer to help. The file I am attaching is the skull > stripped Brainweb T1-w phantom and I just used the default FAST > settings by > calling 'fast filename.nii'. From the output image, I extract the > different > tissue classes. Thank you again for your time. > > Best, > On Tsang --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------