Dear Freesurfer experts,
Based on this
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033337.html
, I
wrote a short script to extract the centroids from Desikan-Killiany atlas.
######
for hemi in lh rh; do
mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels
for label in ${labels}; do
mri_surfcluster --in
/usr/local/freesurfer/subjects/fsaverage/surf/${hemi}.thickness --clabel
./labels/${label}.label --sum ./labels/sum.${label} --centroid --thmin 0
--hemi ${hemi} --subject fsaverage
tail -1 ./labels/sum.${label} | sed 's/ */ /g' | cut -d' ' -f6-8 >>
./labels/68parc.centroids.txt
done
done
#######
However, 1) the value is not precise enough, it is only one digit after
decimal point. And 2) I kept getting the same value for each hemisphere.
Eg,.
29.8 -20.7 18.0
29.8 -20.7 18.0
29.8 -20.7 18.0
29.8 -20.7 18.0
29.8 -20.7 18.0
29.8 -20.7 18.0
29.8 -20.7 18.0
I would appreciate if you have any suggestions regarding extracting
centroids and the aforementioned issues!
Thank you for your time!
Best,
Foucault
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