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 $PATH, cat .bashrc, cat startup.m).
Really appreciate someone taking a look and walking me through a solution to my error?
Many Thanks!
Jenifer
- Running Freesurfer_v6 on RHEL Centos7.3
and matlab 2016b (with imaging processing toolbox)
- recon-all -s <FSID> -localGI
returns the following:
#@# Local Gyrification Index lh Thu Aug 10 15:39:03 CDT 2017
mris_compute_lgi --i lh.pial
ERROR: Matlab is required to run mris_compute_lgi! Linux localhost.localdomain 3.10.0-514.el7.x86_64 #1 SMP Wed Oct 19 11:24:13 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux
- matlab is in my path
[jjuranek@localhost subjects]$ 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
- 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.
- 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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