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