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-bounces@nmr.mgh.harvard.edu on behalf of Alexandre Obert obert.alexandre@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/HippocampalSubfieldsAndNucleiOfAmy...). 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