Hi Jennifer -
Ostensibly your pathways and environment variables look correct. I ran into
this problem once before, so I changed from BASH to the enhanced C shell
and it worked. You may want to try that. All you need to do is to exit out
of bash and set the environment in tcsh and it could work.
best,
Alan
On Thu, Aug 10, 2017 at 4:56 PM, Juranek, Jenifer <
jenifer.jura...@uth.tmc.edu> wrote:
> Hi,
>
> Hope someone can identify my user error...I've listed below key bits of
> info (system info, cmdline and error message, echo $PATH, cat .bashrc, cat
> startup.m).
>
> Really appreciate someone taking a look and walking me through a solution
> to my error?
>
> Many Thanks!
>
> Jenifer
>
>
> 1) Running Freesurfer_v6 on RHEL Centos7.3
>
> and matlab 2016b (with imaging processing toolbox)
>
> 2) recon-all -s <FSID> -localGI
>
> returns the following:
>
> #@# Local Gyrification Index lh Thu Aug 10 15:39:03 CDT 2017
>
> mris_compute_lgi --i lh.pial
>
> ERROR: Matlab is required to run mris_compute_lgi!
> Linux localhost.localdomain 3.10.0-514.el7.x86_64 #1 SMP Wed Oct 19
> 11:24:13 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux
>
>
> 3) matlab is in my path
>
> [jjuranek@localhost subjects]$ echo $PATH
> /home/jjuranek/freesurfer/bin:/home/jjuranek/freesurfer/
> fsfast/bin:/home/jjuranek/freesurfer/tktools:/home/jjuranek/fsl/bin:/home/
> jjuranek/freesurfer/mni/bin:/home/jjuranek/fsl/bin:/home/
> jjuranek/freesurfer/bin:/home/jjuranek/freesurfer/fsfast/
> bin:/home/jjuranek/freesurfer/tktools:/home/jjuranek/
> freesurfer/mni/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/
> usr/sbin:/bin:/sbin:/home/jjuranek/.local/bin:/home/
> jjuranek/bin:/home/jjuranek/matlab/R2016b/bin/matlab
>
>
> 4) my .bashrc file is as follows
>
> # .bashrc
>
> # Source global definitions
> if [ -f /etc/bashrc ]; then
> . /etc/bashrc
> fi
>
> # User specific aliases and functions
>
> export FREESURFER_HOME=/home/jjuranek/freesurfer
> source $FREESURFER_HOME/SetUpFreeSurfer.sh
>
> matlab=/home/jjuranek/matlab/R2016b/bin/matlab
> alias matlab=$matlab
>
> export PATH=$PATH:/home/jjuranek/matlab/R2016b/bin/matlab
>
> #/home/jjuranek/matlab/R2016b/bin/matlab
> #MATLAB is selecting SOFTWARE OPENGL rendering.
>
>
> 5) my startup.m file is as follows
>
> %------------ FreeSurfer -----------------------------%
> fshome = getenv('FREESURFER_HOME');
> fsmatlab = sprintf('%s/matlab',fshome);
> if (exist(fsmatlab) == 7)
> addpath(genpath(fsmatlab));
> end
> clear fshome fsmatlab;
> %-----------------------------------------------------%
>
> %------------ FreeSurfer FAST ------------------------%
> fsfasthome = getenv('FSFAST_HOME');
> fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
> if (exist(fsfasttoolbox) == 7)
> path(path,fsfasttoolbox);
> end
> clear fsfasthome fsfasttoolbox;
> %-----------------------------------------------------%
>
> %------------ FreeSurfer LGI ------------------------%
> FSH = getenv('FREESURFER_HOME');
>
> fshmatlab = sprintf('%s/matlab',FSH);
> path(path,fshmatlab);
> clear fshmatlab FSH;
>
>
>
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>
>
> 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
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> but does not contain patient information, please contact the sender and
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> dispose of the e-mail.
>
>
--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
*Alan N. Francis PhD*
Instructor - Imaging Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu <ezra_wegbr...@brown.edu>
afran...@mclean.harvard.edu
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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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
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