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;