Hi - use the -o output to cluster to get a cluster index image, then
you can threshold upper and lower in fslmaths to select one at a time.
Cheers.
On 23 Jan 2009, at 19:13, Cherif Sahyoun wrote:
> Hi,
>
> I'm trying to automate getting the mean FA from each subject for
> each output
> contrast of TBSS, within each cluster.
>
> If I binarise my contrast (at a certain threshold) and then apply it
> as a
> mask to all_FA_skeletonised with fslmeants, I get the mean FA for
> all sig.
> clusters together, but I'd like to break it down to a per-cluster
> output.
>
> Using the cluster command finds the clusters, but does not output
> individual
> images for each.
>
> Ideally I'd like a way to use the clusters from "cluster" as masks in
> fslmeants, so that I'd get one big table for each contrast... any
> thoughts?
> (or I should say any thoughts that would not involve drawing
> individual ROIs
> by hand :) )
>
> Thanks,
> Cherif
>
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Stephen M. Smith, Professor of Biomedical Engineering
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