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;