On 5/5/14 10:41 PM, Caka wrote:

Hi Douglas and all,

I have used the ‘recon-all’ command to segment the gray matter of 140 subjects. I have three questions:

(1) as the segmentation is done in the individual space, how can I register the results into the template brain? The results includes the surface and the vertex. Is it ‘mri_surf2surf’?

mri_surf2surf is used when mapping surface data to the surface of an average subject such as fsaverage. Is that what you want?

(2) If the gray matter is registered into the template brain, then same number of vertex in every region would be obtained. Then what information does the value of each vertex stands? Is it the cortical thickness changes?

I don't understand what you mean.

(3) We know that Freesurfer provides two kinds of brain region labeling, 68 regions and 77 regions in the cerebral cortex respectively. I am wondering whether I can use my own labeling, like 1000 regions? How can I do this?

Do you mean you've labeled 1000 regions on a brain? You would have to do that for a number of subjects (eg, 40), you can then build an atlas. The problem is that such small regions will not be very reliable doug

Thank you very much!

Qiongmin Ma _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer