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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