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
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
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/HippocampalSubfieldsAndNucleiO fAmygdala). 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
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.commailto: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/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
freesurfer@nmr.mgh.harvard.edu
-
Alexandre Obert -
Iglesias Gonzalez, Eugenio