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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