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Hi, I think it's just that after the PVE estimation (including the MRF on the mixeltype classification) the hard segmentation is re-evaluated using the PVE outputs. Cheers. On 18 Jun 2008, at 20:30, Rolf Heckemann wrote: > Thanks, my procedure does indeed yield files identical to the _pveseg > output, solving my immediate problem. > > I would still like to understand the difference between _seg and > _pveseg output. > > Regards > > Rolf > > > On Tue, Jun 17, 2008 at 11:29:08AM +1000, Steve Smith wrote: >> Hi, you could use the *_pveseg output file for this? >> Cheers. >> >> >> >> On 16 Jun 2008, at 22:36, Rolf Heckemann wrote: >> >>> Is there a straightforward way to create hard segmentations like >>> those >>> in fast4's _seg file output from the _pve files? I tried to >>> generate >>> one using a max value approach (see below), but it looks slightly >>> different from the original _seg. Do I need to apply some kind of >>> smoothing to get exactly the same result? Thanks. >>> >>> # T1 weighted image named a01 >>> # a01_seg and a01_pve_? generated with fast4 >>> >>> # Generate a file containing the maximum of three pve values per >>> voxel >>> fslmaths a01_pve_1 -max a01_pve_2 -max a01_pve_3 max >>> >>> # Extract from each individual pve those voxels that match the >>> maximum >>> # and set them to a value reflecting the tissue class >>> fslmaths max -sub a01_pve_1 -abs -bin -sub 1 -abs t1 >>> fslmaths max -sub a01_pve_2 -abs -bin -sub 1 -abs -mul 2 t2 >>> fslmaths max -sub a01_pve_3 -abs -bin -sub 1 -abs -mul 3 t3 >>> >>> # Combine the classes for comparison with a01_seg >>> fslmaths t1 -add t2 -add t3 -uthr 3 tseg >>> >>> # Histogram comparison >>> fslstats tseg -h 4 >>> 4088262.000000 >>> 249205.000000 >>> 721571.000000 >>> 516642.000000 >>> >>> fslstats a01_seg -h 4 >>> 4088262.000000 >>> 282874.000000 >>> 707927.000000 >>> 496617.000000 >>> >>> # Difference image -- screenshot uploaded to >>> # http://www.soundray.org/pve-seg-screenshot.png >>> fslmaths a01_seg -sub tseg diff >>> >>> >>> -- > > > -- > Rolf A Heckemann, PhD > Research Associate > Division of Neuroscience and Mental Health > MRC Clinical Sciences Centre > Imperial College London > Hammersmith Hospital Campus > Du Cane Road > London W12 0HS > United Kingdom > 1213784793 > --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------