Thanks, Mark, it works!
Quoting Mark Jenkinson <[log in to unmask]>:
> 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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