Dear Freesurfer experts,
Based on this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033337... , 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