Hi Adiel

in matlab you could do something like:

cd $SUBJECTS_DIR/<subject id>/mri
matlab

[v,M,mr] = load_mgh('aseg.mgz');
left_hippo_indices = find(v == 17);

where the '17' comes from $FREESURFER_HOME/FreeSurferColorLUT.txt and is the index for left hippocampus.

Is that would you mean? Or you could use mri_extract_labels to build volumes that have only the labels you want in them.

cheers
Bruce

On Mon, 24 Jul 2017, עדיאל חרבש wrote:

Hi Bruce,
Thanks for the reply.
By "coordinates" I mean all the voxels that belong to a certain structure. I
think it's called "labels"? I interest in the main structures like
Hippocampus, Thalamus, Cerebellum, Amygdala, corpus callosum, etc. If the
standard segmentation segments in that specificity only the lobes, it can be
good enough...
I see the .mgz files, but can not extract them... How should I do that?

Thank for the patience..
Adiel


2017-07-23 18:09 GMT+03:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
      Hi Adiel

      what kind of coordinates do you mean, and which brain structures
      are you interested in? Our standard segmentation is sampled into
      the volume in files named aparc*+aseg.mgz, but the Brodmann area
      estimates are on the surface.

      cheers
      Bruce


      On Sun, 23 Jul 2017, עדיאל חרבש wrote:

            Hi,
            I'm very new to Freesurfer, and actually work with
            some exist results of
            other people. The results are from the call of
            "-recon all -autorun".
            I try to get all the coordinates of each of the
            structures of the brain,
            that segmented. I can find on files only the volumes
            of some structures and
            something that look like detailed coordinates of
            Brodman Areas only. But I
            can't find the detailed coordinates of all
            structures in brain.

            I'll be grateful if someone can guide me where can I
            find it, or what should
            I do to get these results.

            Thanks,
            Adiel



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