If you want all the coordinates for a given segment (eg, left hippo), then you can run mri_cor2label --i aparc+aseg.mgz --id 17 --l file.label
17 comes from $FREESURFER_HOME/FreeSurferColorLUT.txt
The coordinates will be in "tkregister space" which you can convert to MNI305 using the info from here:
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
using case #2
On 7/24/17 2:11 AM, 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 mailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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