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 <wie...@uwm.edu<mailto:wie...@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<http://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<http://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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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