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
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