By default they are in talairach. But you can get mni305 by adding --nofixmni to the surfcluster command line

On 08/02/2016 03:36 PM, Sabin Khadka wrote:

Hi Doug, Thanks. Are these coordinates in talairach or MNI space? From previous post you mentioned these are in mni305 space but if I look at the log file it say TalX, TalY, TalZ. I am a little confused.

And how can I convert these coordinates to MNI152 space?

thanks for your help.

Cheers, Sabin Khadka

On Mon, Aug 1, 2016 at 9:24 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

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.

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