I’m not sure it has been integrated into recon-all.  You can try mri_pglands_seg directly.

Yujing

From: Thakore, Radha <radhathakore@creighton.edu>
Sent: Monday, February 23, 2026 3:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Pineal Gland on v8

        External Email - Use Caution        

Hello,

I had a quick question about pineal gland segmentation. I heard that it would be possible to run pineal gland segmentation using FreeSurfer v.8. However, I am unsure about the Terminal input code with recon-all to specifically do that. 

Would you be able to help me with quantification of the pineal gland?

Thank you!

Sincerely,

Radha Thakore

M.D. Student | Class of 2028

Creighton University School of Medicine | Phoenix Campus