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Hi - it looks like this may possibly be a bug - if you could upload the input and output images Matthew could look into this. Please upload the files in a single compressed tarfile to http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi And then email me the upload ID. Cheers, Steve. On 12 Feb 2010, at 00:56, Torsten Rohlfing wrote: > Dear FSL team: > > I am having some trouble with FAST in FSL 4.1.5. The segmentation of a > fairly normal-looking 3T SPGR creates a "whole" of CSF inside the > frontal > WM. I am attaching some slice screenshots with the problem area > marked by a > read circle in the SPGR. > > I am running fast as > > fast -A prior0.nii prior1.nii prior2.nii -P -v --nopve -B -b -p -o > image > > I am also attaching the input WM prior and output WM probability image > slices: the prior is virtually 100% certain of WM in the problem > area, so > that does not seem to explain the problem. Also, if I run fast with no > priors, I get essentially the same result in that area. > > I'd appreciate any suggestions, if this seems to be a problem > related to the > way I am running fast. > > I would also be happy to upload the original SPGR image and prior > maps, if > anyone wants to try this hands-on. > > Thanks in advance! > Torsten > > < > fast4_spgr.jpeg><fast4_prior_wm.jpeg><fast4_seg.jpeg><fast4_p_wm.jpeg> --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------