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Thanks Varina My processing has to be cluster-compatible, and MATLAB is not admissible on our cluster, so SPM is not an option. Also, in this particular case, I'm trying to find out whether the FAST classification is better when CSF has already been masked out by another procedure. Best wishes Rolf On 2 October 2011 16:33, Wolf, Varina Louise <[log in to unmask]> wrote: > Rolf, > > I don't know if this will help you or not, but I get great tissue segmented masks for grey, white, csf using SPM-8, just using the Segment feature. This feature is easy to use: just feed your T1 image into the GUI and out comes the 3 segmented maps. I'm using the grey matter mask inside FAST and it seems to be working with my resting state data in that it cuts back on the noise sources found outside grey. > > Thanks for your help earlier, > Varina > > ________________________________________ > From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of Rolf A. Heckemann [[log in to unmask]] > Sent: Sunday, October 02, 2011 4:00 AM > To: [log in to unmask] > Subject: [FSL] FAST bug > > I still haven't found a solution for the issue of fast not working as > expected, so I'm reposting this: > > I am trying to obtain a two-class tissue segmentation of the brain > matter of an image. I have a bias-corrected full image (full.nii) and > a mask for the brain portion (excluding CSF, mask.nii). So I do > > fslmaths full -mas mask masked > fast -n 2 -g -N masked > > I get a grey matter probability map in masked_pve_0 as expected. But > the white matter portion, masked_pve_1, is a float-type image with > only two values, 0 and 1. I would have expected masked_pve_1 to > contain intermediate values, just as masked_pve_0 does. > > I would much appreciate your help. > > Regards > > Rolf > > > -- > Rolf A Heckemann, MD PhD > Médecin chercheur > Fondation Neurodis > CERMEP - Imagerie du Vivant > Hôpital Neurologique Pierre Wertheimer > 59 Boulevard Pinel > 69003 Lyon > France -- Rolf A Heckemann, MD PhD Médecin chercheur Fondation Neurodis CERMEP - Imagerie du Vivant Hôpital Neurologique Pierre Wertheimer 59 Boulevard Pinel 69003 Lyon France