Hi Douglas,
Thank you, works perfectly.
But, I need to know first which structures id's are inside each file. I preferred to extract all the brain map with Matlab, as Bruce commented.

Now I try to match the coordinates, according to the linked you posted.
The brain space in results is of 256x256x256 voxels. What are the dimensions of each voxel here?
If I need to compare that results to another analysis that come from SPM, so case #2 is the way? And then, I'll need in fact the coordinates from mri_cor2label?

Thanks for the fast and useful replies.
Adiel

2017-07-24 22:11 GMT+03:00 Douglas Greve <greve@nmr.mgh.harvard.edu>:

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>:
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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