See:
https://surfer.nmr.mgh.harvard.edu/fswiki
for information, including a tutorial.
In particular, the recon-all command will perform the subcortical segmentation. If you have freesurfer installed, then there is a sample subject, called bert, already processed. You can see its subcort results by typing:
tkmedit bert norm.mgz -segmentation mri/aseg.mgz \ $FREESURFER_HOME/tkmeditColorsCMA
and be sure to see:
https://surfer.nmr.mgh.harvard.edu/fswiki/SubcorticalSegmentation
On Sat, 2006-03-18 at 13:23 -0800, Shahabuddin Ansari wrote:
Hello,
I am new Freesurfer user. I need to segment subcortical regions of brain and wondering that if there is any doc or tutorial on the subject. I appreciate your comments.
Thanks Shahab
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