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
External Email - Use Caution 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)