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/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