Dear Sally,

You will need to download the development version to access this functionality.

However, if you have already run your subjects through recon-all with FS5.3, you can directly call segmentHA_T1.sh/ segmentHA_T2.sh/ segmentHA_T1_long.sh in the dev version (no need to run recon-all again with dev).

Cheers,

/Eugenio

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Sally Grace <sgrace@swin.edu.au>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, 6 June 2018 at 03:16
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Is amygdala nuclei segmentation possible in freesurfer version 5.3?

External Email - Use Caution

Hi there,

I wish to segment amygdala nuclei in Freesurfer Version 5.3, is it possible? I can find documentation only for Freesurfer version 6.0 here (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala). Can the scripts be adapted to Freesurfer v5.3?

Thanks in advance,

Sally.

HippocampalSubfieldsAndNucleiOfAmygdala - Free Surfer Wiki

surfer.nmr.mgh.harvard.edu

Segmentation of hippocampal subfields and nuclei of the amygdala (cross-sectional and longitudinal) This functionality has been available in the development version of FreeSurfer since August 31st 2017