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.gzhttps://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.commailto:aujoulat.lise@gmail.com / lise.aujoulat@etu.upmc.frmailto:lise.aujoulat@etu.upmc.fr