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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