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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 > 1213617743 > --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------