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 <kw...@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 <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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