You have to run recon-all on your T1-weighted image (see the tutorials on the wiki), then run the hippo/amyg segmentation as found here
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala


On 10/13/2020 12:32 PM, Elena Aggius-Vella wrote:

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Dear freesurfer,

This is Elena Aggius Vella.
I'm writing to ask for your help.
I need to do amygdala segmentation based on anatomy.... I see freesurfer has a nice tool to do it, but i'm new in freesurfer. Is it possible to have any help on this?

many many thanks
elena

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