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), 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