Re: [Freesurfer] freesurfer errors-windows bash

2017-10-26 Thread Iglesias Gonzalez, Eugenio 
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 
Date: Thursday, 26 October 2017 at 16:31
To: "freesurfer@nmr.mgh.harvard.edu" , 
"Iglesias Gonzalez, Eugenio" 
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 
>:
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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Re: [Freesurfer] freesurfer errors-windows bash

2017-10-26 Thread Alexandre Obert 
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 :

> 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
>
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Re: [Freesurfer] freesurfer errors-windows bash

2017-10-26 Thread Iglesias Gonzalez, Eugenio 
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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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] freesurfer errors-windows bash

2017-10-26 Thread Alexandre Obert 
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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.