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Hi !
This worked just fine! Thank you!

Le ven. 1 févr. 2019 à 12:11, Niels Bergsland <theniels@gmail.com> a écrit :

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Hi,
Not Andrew but you need to install tcsh:

I guess you're on a Debian-based Linux system (e.g. Ubuntu)? If so, the following will do it:

sudo apt-get install tcsh


On Fri, Feb 1, 2019 at 9:59 AM Lise_A <aujoulat.lise@gmail.com> wrote:

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Hi Andrew,

Thanks for your quick reply. I had already tried running the line without prepending "bash" to the front, but I would get another error message saying "there's no such file or directory":

lise.aujoulat@ICM-COHEN-LF001 ~ $ recon-all -i sample-001.nii.gz -s bert -all
bash: /usr/local/freesurfer/bin/recon-all : /bin/tcsh : mauvais interpréteur: Aucun fichier ou dossier de ce type

image.png

Where do you think the problem would come from?

Le jeu. 31 janv. 2019 à 18:02, Hoopes, Andrew <AHOOPES@mgh.harvard.edu> a écrit :

Hi Lise, recon-all is not a bash script, so prepending `bash` to the front of the command will break things. Just running `recon-all -i sample-001.nii.gz -s bert -all` should work fine.

 

best

Andrew

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Lise_A <aujoulat.lise@gmail.com>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, January 31, 2019 at 9:14 AM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Pb testing the FreeSurfer Installation

 

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Dear Sir or Madam,

 

I've just installed the last version of FreeSurfer for Linux (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz), but I got some troubles testing it:

 

When trying to follow Example 2 (https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Download), I get a "syntax error message":

 

lise.aujoulat@ICM-COHEN-LF001 ~ $ export SUBJECTS_DIR=/home/lise.aujoulat/Bureau/SUBJECTS_DATA
lise.aujoulat@ICM-COHEN-LF001 ~ $  bash recon-all -i sample-001.nii.gz -s bert -all
/usr/local/freesurfer/bin/recon-all: recon-all: ligne 31: erreur de syntaxe près du symbole inattendu « ( »
/usr/local/freesurfer/bin/recon-all: recon-all: ligne 31: `set inputargs = ($argv);'

 

You can find a screen shot attached to this email.

It seems that no one encountered this problem so far.

 

I had installed the macOS version some months ago on my personal computer and encountered no problem at that time.

 

How could I fix this?

 

Thanks for your help,

 

Lise

--

 

Lise AUJOULAT

MSc student in Integrative Biology and Physiology, Sorbonne University, Paris, France.

Phone number: + 33 6 87 97 30 32

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


--
Lise AUJOULAT
MSc student in Integrative Biology and Physiology, Sorbonne University, Paris, France.
Phone number: + 33 6 87 97 30 32
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


--
Lise AUJOULAT
MSc student in Integrative Biology and Physiology, Sorbonne University, Paris, France.
Phone number: + 33 6 87 97 30 32