Hi Foucault,
In the snippet you added you don’t define the labels variable (which you
subsequently loop over in for label in ${labels}).
There are two possible mistakes that are easy to fix. One may be that you
forgot to read in the labels! And the other is that to get all the values in an
array you need ${labels[@]}.
I don’t think you need greater precision than you have. The regions are pretty
far apart in mm terms :)
Kirstie
Sent from my iPhone, please excuse any typos or excessive brevity
> On 21 Feb 2018, at 03:44, zuxfoucault Wong <zuxfouca...@gmail.com> wrote:
>
> 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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