Dear Alexandre,

It seems that problem is that you need the latest dev version to use this feature.

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: Alexandre Obert <obert.alexandre@gmail.com>
Date: Thursday, 26 October 2017 at 16:31
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>, "Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.uk>
Subject: Re: freesurfer errors-windows bash

Dear Eugenio, 

The freesurfer version commands tells me that I run the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c version. 

Before using segmentHA_T1.sh command, I run the recon-all -all -s bert one and it worked. 

Of course, recon-all also worked, telling be how to use it properly. 

Regards, 

Alexandre

2017-10-26 17:08 GMT+02:00 Alexandre Obert <obert.alexandre@gmail.com>:

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