Hi Lin,

You can try mri_binarize to obtain the mask - https://surfer.nmr.mgh.harvard.edu/fswiki/mri_binarize

FreeSurferColorLUT.txt in your Freesurfer install directory will give you a complete list of aparc/aseg labels.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Lin Cai
Sent: Tuesday, February 21, 2023 9:15 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] How to calculate the mean FA value in the hippocampus

        External Email - Use Caution        

Dear Freesurfer experts,

I want to calculate the mean FA value in the hippocampus.

Now I have already obtained the FA map for the whole brain in the native space.

And I have the aparc+aseg.mgz file after running the recon -all analysis.

Does someone know how to use freesurfer functions to obtain the hippocampus mask according to the DK atlas? I want to use this mask to calculate the mean FA value in the hippocampus.

Best regards,

Lin