Hi Jon,

It looks like the matlab path is not set on your machine. Can you set the $PATH environment variable to include the path to the matlab functions as well? You can try to launch the command "getmatlab", if you get the answer that matlab is not installed, it means that the $PATH environment variable is not properly set. You can also look on the mailing list, there are a few explanations about this path issue, among which the following one: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25017.html

Let me know if you don't find how to make it work.

Best,

Marie


On Mar 18, 2013, at 10:44 AM, Jon Wieser <wieser@uwm.edu>
 wrote:

i am trying to computer the LGI local gyrification index with freesurfer. I have Matlab on my machine.
I got the following error:


recon-all -s freesurfer -localGI
Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012
Actual FREESURFER_HOME /Applications/freesurfer
-rw-rw-r--  1 wieser  admin  506264 Mar 18 12:37 /Studies/MJMRI/MJ0012/freesurfer/scripts/recon-all.log
Darwin psy-cerebellum.wifi.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun  7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
/Studies/MJMRI/MJ0012/freesurfer/surf
#--------------------------------------------
#@# Local Gyrification Index lh Mon Mar 18 12:43:04 CDT 2013
\n mris_compute_lgi --i lh.pial \n
ERROR: Matlab is required to run mris_compute_lgi!
Darwin psy-cerebellum.wifi.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun  7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64

recon-all -s freesurfer exited with ERRORS at Mon Mar 18 12:43:04 CDT 2013

For more details, see the log file /Studies/MJMRI/MJ0012/freesurfer/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



JOn

--
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
Milwaukee, WI 53211
Phone: 414-229-7145
Fax: 414-229-5219
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