Dear Ted,
You can use this tool: https://surfer.nmr.mgh.harvard.edu/fswiki/AANSegment
Cheers,
/Eugenio

--

Juan Eugenio Iglesias

http://www.jeiglesias.com

From: Huaiyu Liu <huaiyu.liu@ucl.ac.uk>
Date: Monday, March 23, 2026 at 10:26 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Automatic delineation of PAG and VTA using FreeSurfer

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Dear FreeSurfer Team,

I hope you are well. My name is Ted and I am a postdoc working at the UCL, faculty of brain science

I am working with high-resolution T1-weighted MRI data and would like to identify an automated approach to delineate the periaqueductal gray (PAG) and ventral tegmental area (VTA) at the individual participant level.

I was wondering whether FreeSurfer provides:

1) Automated segmentation or masks for PAG and/or VTA
2) If so, how precise these segmentations are (e.g., spatial resolution, validation), and 
3) Whether these delineations are available at the single-subject level, rather than only in standard space

If FreeSurfer does not support this directly, I would also appreciate any recommendations for alternative tools or workflows.

Many thanks for your time and help in advance.

Best regards,
Huaiyu Liu (Ted)