Dear Alexandre, You need to download the latest dev version to have access to the new hippocampus/amygdala segmentation. The other potential problem is that FreeSurfer is not sourced properly. Do other FreeSurfer commands work? E.g. do you get an output when you type: recon-all Cheers, /Eugenio
-- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alexandre Obert <obert.alexan...@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Thursday, 26 October 2017 at 16:10 To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] freesurfer errors-windows bash Dear all, I'm would like to run a hippocampal segmentation on my data. However, I'm a beginner with freesurfer thus, I juste try to run the commands with subject training data. I first try to run commands following the recent development (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala). However, terminal says that the command segmentHA.sh doesn't exist. I guess that it could be linked to the fact that I used bash in Windows but I can't find a way to check this..; Any idea ? Regards, Alexandre
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