On Wed, Feb 21, 2018 at 5:24 PM, zuxfoucault Wong <zuxfoucault@gmail.com> wrote:

Hi Kirstie,

Thank you very much for the suggestions!
I modified my snippet to prevent it from looping the same value and still got the same results?

######
input=($(cat ./names_68parc.txt))
labels=()
hemis=()
j=0
for i in "${input[@]}"; do
if [[ $i == lh_* ]]; then
hemis[j]="lh"
i=$(echo $i | sed 's/^lh_//g')
labels[j]="$i"
(( j++ ))
elif [[ $i == rh_* ]]; then
hemis[j]="rh"
i=$(echo $i | sed 's/^rh_//g')
labels[j]="$i"
(( j++ ))
fi
done

nlabel=68
if [[ ${#labels[@]} != $nlabel ]] && [[ ${#hemi[@]} != $nlabel ]]; then
echo " number of label not match "
fi

for hemi in lh rh; do
mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels
done

for ((i=0;i<${#labels[@]};i++)); do
mri_surfcluster --in /usr/local/freesurfer_orig/subjects/fsaverage/surf/${hemis[i]}.thickness --clabel ./labels/${hemis[i]}.${labels[i]}.label --sum ./labels/sum.${hemis[i]}.${labels[i]} --centroid --thmin 0 --hemi ${hemis[i]} --subject fsaverage
tail -1 ./labels/sum.${hemis[i]}.${labels[i]} | sed 's/ */ /g' | cut -d' ' -f6-8 >> ./labels/68parc.centroids.txt
done
######

The output message of mri_surfcluster:
######
thsign = abs, id = 0
version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman Exp $
hemi = rh
srcid = /usr/local/freesurfer_orig/subjects/fsaverage/surf/rh.thickness
srcsubjid = fsaverage
srcsurf = white
srcframe = 0
thsign = abs
thmin = 0
thmax = -1
fdr = -1
minarea = 0
xfmfile = talairach.xfm
clabelfile = ./labels/rh.lateraloccipital.label
clabelinv = 0
nth = -1
sumfile = ./labels/sum.rh.lateraloccipital
subjectsdir = /usr/local/freesurfer_orig/subjects
FixMNI = 1
Loading clabel ./labels/rh.lateraloccipital.label.
Found 5963 points in clabel.
------------- XFM matrix (RAS2RAS) ---------------
/usr/local/freesurfer_orig/subjects/fsaverage/mri/transforms/talairach.xfm
1.00000 0.00000 0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
----------------------------------------------------
Reading source surface /usr/local/freesurfer_orig/subjects/fsaverage/surf/rh.white
Done reading source surface
Computing metric properties
Loading source values
number of voxels in search space = 5963
Done loading source values (nvtxs = 163842)
overall max = 3.19752 at vertex 122846
overall min = 0 at vertex 0
surface nvertices 163842
metric props tot surface area 65020.839844
group_avg_vtxarea_loaded 1
masked surface area 4459.747559
NOT Adjusting threshold for 1-tailed test
thminadj = 0
Searching for Clusters ...
thmin=0.000000 (0.000000), thmax=-1.000000 (-1), thsignid=0, minarea=0.000000
Found 1 clusters
Max cluster size 82167.000000
INFO: fixing MNI talairach coordinates

On Wed, Feb 21, 2018 at 3:15 PM, Kirstie Whitaker <kw401@cam.ac.uk> wrote:
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 <zuxfoucault@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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