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
External Email - Use Caution Dear Freesurfer developers,
I am using this tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/AANSegmenthttps://secure-web.cisco.com/1XD9LLQnRJF77R_wsTSJMenKzi1tmGnEXcYl0tRY2Xeca6TPmHxwPjsFZueDPP4-jKdbUCT9ss1yDwJCMtBTu_T0FXh9xN8evhAH75xVPbr4uCodNrWjGfFVX-8VJQhrGnn0Ws6eAg5fuUI6qOG0CCxXH2xGBP0h8Bew_nu_DaAG8_XedxtwNNFkoj4Nc19RO1pt3Zz6qEOagxx-RWz26haJLm7xPEeXRncOuEr4UpQXUb9CG3dys-PiAOe-KaXlR_8lJytzUCcFaYFWisn6dFDJJ8U7skKka-GmoP3muL7iK8CPkDzBNk443Rz5yUIw_OjQODMHm5yEE4RLmNcecmQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FAANSegment) 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