Marie, Thanks so much for your suggestion. You see it perfectly. I did not realize that matlab functionality was required to run lgi. Which essential components of matlab are suggested so that I may purchase the proper license(s)? Jenifer ________________________________
From: Marie Schaer [mailto:[EMAIL PROTECTED] Sent: Sat 4/19/2008 7:44 AM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] LGI: EXITS with ERRORS Jenifer, Have you installed Matlab on your computer? As far as I see it, either you don't have matlab, or the path to matlab is not set properly. You can cd into the surf directory (cd SB_09_H20089/surf) and try directly: mris_compute_lgi --debug --i lh.pial If it finishes in a few seconds with "getmatlab", then you have to add the matlab directory to you $PATH environment variable. Marie Quoting "Juranek, Jenifer " <[EMAIL PROTECTED]>: > I recently downloaded and installed fs4v03 (CentOS 4x86_64) on my > new 64bit linux box running RHEL 5 (Tikanga). I didn't see any > special notes on the download page for RHEL 5 (only RHEL 4 is noted). > > While test-driving my first dataset through the fsv403 pipeline, I > encountered some difficulties with my explorations of the new > feature of calculated local gyrification index. > I tried the following cmd lines...each yielded the same standard out > message pasted below > > Any ideas? > Jenifer > > [EMAIL PROTECTED] subjects]$ recon-all -subjid SB_09_H20089 -localGI > [EMAIL PROTECTED] subjects]$ recon-all -lgi -s SB_09_H20089 > [EMAIL PROTECTED] subjects]$ recon-all -lgi -sid SB_09_H20089 > > > [EMAIL PROTECTED] subjects]$ recon-all -lgi -s SB_09_H20089 > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects > Actual FREESURFER_HOME /usr/local/freesurfer > -rw-rw-r-- 1 jjuranek jjuranek 768975 Apr 18 17:30 > /usr/local/freesurfer/subjects/SB_09_H20089/scripts/recon-all.log > Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 > EST 2007 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/SB_09_H20089/surf > #-------------------------------------------- > [EMAIL PROTECTED] Local Gyrification Index lh Fri Apr 18 17:45:32 CDT 2008 > > mris_compute_lgi --i lh.pial > > Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 > EST 2007 x86_64 x86_64 x86_64 GNU/Linux > > recon-all exited with ERRORS at Fri Apr 18 17:45:32 CDT 2008 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
