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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