It could be that the error is due to a matlab path issue according to some previous posts, and it is true I cannot find matlab with getmatlab command. I have trouble setting up MATLABPATH.

First, I can open matlab from terminal with commands matlab12 or matlab 13, I have 2 versions that I use for other applications, located at
/usr/local/MATLAB/R2012b and /usr/local/MATLAB/R2013a (the files matlab12 and matlab13 used to call matlab are in /usr/local/bin)

and I have a startup.m file in $HOME/matlab where the freesurfer matlab files are visible to matlab.

However, when I call env from terminal, matlabpath does not show up.

I must mention that the default shell was bash, and I changed it to .tcsh when installing FS, which works well, without issues

I guess I have to modify my /etc/csh.cshrc file to include matlab path, but several trials have failed, example

setenv MATLABPATH /usr/local/MATLAB/R2012b does not help when calling getmatlab

Please advise,

Thank you,

Octavian

---------- Forwarded message ----------
From: Octavian Lie <octavian.lie@gmail.com>
Date: Mon, Nov 17, 2014 at 8:11 AM
Subject: outer pial error
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>

Dear All,

I tried to get an outer pial surface on a previously processed pt subjid, and I got the following error.

(recon-all was running another subject in a separate window, for what's worth)

Please advise,

Octavian

recon-all -localGI -s subjid

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20131217
Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20131217
INFO: SUBJECTS_DIR is /usr/local/fs5.3/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/fs5.3/freesurfer
-rw-rw-r-- 1 ovl ovl 3224039 Nov 17 07:58 /usr/local/fs5.3/freesurfer/subjects/subjid/scripts/recon-all.log
Linux ovl-Wild-Dog-Performance 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
/usr/local/fs5.3/freesurfer/subjects/subjid/surf
#--------------------------------------------
#@# Local Gyrification Index lh Mon Nov 17 08:03:50 CST 2014

mris_compute_lgi --i lh.pial

=================
rm -Rf /usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial
=================
=================
mkdir -p /usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial
=================
=================
mris_fill -c -r 1 lh.pial /usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=================
reading surface from lh.pial...
writing filled volume to /usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
conforming output volume
setting resolution for intermediate calculations to 1.0000
=================
make_outer_surface('/usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit
=================
ERROR:: Too many arguments.
Linux ovl-Wild-Dog-Performance 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s subjid exited with ERRORS at Mon Nov 17 08:03:54 CST 2014