Hi Carlotta,
Either approach should work fine.
Cheers,
Paul
On 01/12/2018, Carlotta Fabris <[log in to unmask]> wrote:
> Thank you so much Paul!
>
> Once I have the atlas in the functional space, I can just use fslmeants with
> the --label option without having to use fslroi to extract all the rois from
> the atlas?
> What I was thinking was something like this:
> for roinum in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21; do
> fsl5.0-fslmaths <atlas> -thr $roinum -uthr $roinum -bin SubCort_ROIMask
> fsl5.0-fslmeants -i <fMRI data> -m SubCort_ROIMask -o
> SubCort_meants_roi${roinum}.txt
> done
>
> paste SubCort_meants_roi*.txt > SubCort_allmeants_roi.txt
>
> I hope my question is clear,
> Carlotta.
>
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