Hi Doug, I tried to pick up from the thread below to get MNI coordinates of each destrieux parcellation region.
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html
I created label files from mri_annotation2label --subject fsaverage --hemi lh(/rh) --annotation aparc.a2009s --outdir label_destrieux # which works fine
And I tried to get the coordinates of each labels using
mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness --clabel <label file> --sum <output file> --centroid --thmin 0 --hemi lh --subject fsaverage
But, all left labels would produce the same coordinates and so does right labels. (I've attached few example files here with). Also, it says TalX, TalY, TalZ are these coordinates in MNI or Talairach?
Thanks for help.
Anyone?
Cheers, Sabin Khadka
On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka mr.sabinkhadka@gmail.com wrote:
Hi Doug, I tried to pick up from the thread below to get MNI coordinates of each destrieux parcellation region.
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html
I created label files from mri_annotation2label --subject fsaverage --hemi lh(/rh) --annotation aparc.a2009s --outdir label_destrieux # which works fine
And I tried to get the coordinates of each labels using
mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness --clabel <label file> --sum <output file> --centroid --thmin 0 --hemi lh --subject fsaverage
But, all left labels would produce the same coordinates and so does right labels. (I've attached few example files here with). Also, it says TalX, TalY, TalZ are these coordinates in MNI or Talairach?
Thanks for help.
Try setting thmin to something small but non-zero (eg, 10e-6)
On 8/1/16 10:23 AM, Sabin Khadka wrote:
Anyone?
Cheers, Sabin Khadka
On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka <mr.sabinkhadka@gmail.com mailto:mr.sabinkhadka@gmail.com> wrote:
Hi Doug, I tried to pick up from the thread below to get MNI coordinates of each destrieux parcellation region. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html I created label files from mri_annotation2label --subject fsaverage --hemi lh(/rh) --annotation aparc.a2009s --outdir label_destrieux # which works fine And I tried to get the coordinates of each labels using mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness --clabel <label file> --sum <output file> --centroid --thmin 0 --hemi lh --subject fsaverage But, all left labels would produce the same coordinates and so does right labels. (I've attached few example files here with). Also, it says TalX, TalY, TalZ are these coordinates in MNI or Talairach? Thanks for help.
ps. you can always just load the xyz in the label into matlab and compute the centroid
On 8/1/16 10:23 AM, Sabin Khadka wrote:
Anyone?
Cheers, Sabin Khadka
On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka <mr.sabinkhadka@gmail.com mailto:mr.sabinkhadka@gmail.com> wrote:
Hi Doug, I tried to pick up from the thread below to get MNI coordinates of each destrieux parcellation region. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html I created label files from mri_annotation2label --subject fsaverage --hemi lh(/rh) --annotation aparc.a2009s --outdir label_destrieux # which works fine And I tried to get the coordinates of each labels using mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness --clabel <label file> --sum <output file> --centroid --thmin 0 --hemi lh --subject fsaverage But, all left labels would produce the same coordinates and so does right labels. (I've attached few example files here with). Also, it says TalX, TalY, TalZ are these coordinates in MNI or Talairach? Thanks for help.
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Sabin Khadka