Hello Huaiyu,

I would recommend installing a newer version of FreeSurfer.

Latest stable version is 8.2.0, and I believe that script should ship with versions of FreeSurfer >= 8.0.0.

Downloads for installers are available here: https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads

Best,

Jackson

From: Huaiyu Liu <huaiyu.liu@ucl.ac.uk>
Date: Wednesday, April 15, 2026 at 1:20 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] PAG and VTA delineation

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Dear Freesurfer developers,

I am using this tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/AANSegment) to segment my brainstem AAN nuclei. 

My freesurfer version is 7.3.2.

However, I couldn't find this segmentation shell script in my freesurfer.

SegmentAAN.sh

I wonder do I need to install it from somewhere else? Or do I need to install a recent freesurfer version?

Best,

Huaiyu

_________________________________________

Huaiyu Liu (Ted)
Postdoctoral Research Fellow
Department of Imaging Neuroscience, Functional Imaging Laboratory

University College London
12 Queen Square, London WC1N 3AR