Yes! I got better results now! Thanks!!
On Thu, Feb 22, 2018 at 12:57 AM Kirstie Whitaker <kw...@cam.ac.uk> wrote:
> Hi Foucalt,
>
> I think you need to set the threshold to slightly larger than 0 otherwise
> you're taking the center of mass of the whole image (including the 0s) when
> really you want to exclude the 0s and only look at the individual regions.
>
> I changed --thmin 0 to --thmin 0.1 and the results looked good.
>
> Kx
>
> On 21 February 2018 at 09:28, zuxfoucault Wong <zuxfouca...@gmail.com>
> wrote:
>
>> Attach name file and result file.
>>
>> Thank you for your time!
>>
>> Best,
>> Foucault
>>
>> On Wed, Feb 21, 2018 at 5:24 PM, zuxfoucault Wong <zuxfouca...@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 <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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>>>
>>
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>
>
> --
> Kirstie Whitaker, PhD
>
> Research Fellow, Alan Turing Institute
> Research Associate, University of Cambridge
>
> *Mailing Address*
> Brain Mapping Unit
> Department of Psychiatry
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> Downing Street
> Cambridge CB2 3EB
>
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> *Website:* https://whitakerlab.github.io
> *Twitter:* @kirstie_j <https://twitter.com/kirstie_j>
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