External Email - Use Caution

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: 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

•    External Email - Use Caution        *
  
  

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 https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/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

Mail: aujoulat.lise@gmail.com / lise.aujoulat@etu.upmc.fr _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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 :

    External Email - Use Caution

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:

...

    External Email - Use Caution

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: 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

•    External Email - Use Caution        *
  
  

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 https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/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

Mail: aujoulat.lise@gmail.com / lise.aujoulat@etu.upmc.fr _______________________________________________ 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 Mail: aujoulat.lise@gmail.com / lise.aujoulat@etu.upmc.fr _______________________________________________ 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