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