Hi again,
I figured it out- converted .mgz to nii.gz with "mri_convert", then gunzip the nii.gz files, and get the file with the labels as a brain map.
Thanks for the direction!

Adiel


---------- Forwarded message ----------
From: עדיאל חרבש <adiel204@gmail.com>
Date: 2017-07-24 9:11 GMT+03:00
Subject: Re: [Freesurfer] help with finding exact and detailed coordinates of brain areas
To: Freesurfer support list ‫‎<freesurfer@nmr.mgh.harvard.edu>‎‬


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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