Hi,
You need to use a little shell scripting to do this.
Also, you don't need to use an upper threshold, as nothing in the cluster_index file will be above the largest value. So all you need to do is extract the third highest value, which is just the highest index minus 3. You can do this with:
maxval=`fslstats cluster_index -P 100`
maxval=`echo $maxval - 3 | bc`
And then do:
fslmaths -dt int cluster_index -thr $maxval -bin cluster_mask
You can find more information about scripting at:
http://fsl.fmrib.ox.ac.uk/fslcourse/lectures/scripting/index.html
All the best,
Mark
On 7 Jan 2014, at 11:04, [log in to unmask] wrote:
> Hi,
> i’m using function cluster and fslmaths for extracting first the 3 biggest first clusters.
> I’m looking for an automatic detection of the biggest cluster. Depending on the subject it takes different numbers. Does this function have something similar as has Matlab.
> I need something like this
>
> fslmaths -dt int cluster_index -thr cluster_index(end-3) -uthr cluster_index(end) -bin cluster_mask
>
> thanks and Happy New Year,
> Darya
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