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.Juranek@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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Alan N. Francis PhD
Instructor - Imaging Neuroscience
Brain Imaging Center

McLean Hospital

Harvard Medical School
115 Mill Street, Belmont, MA 02478
alanf@bwh.harvard.edu

afrancis@mclean.harvard.edu

                                                                                                          

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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 error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.