Hi, I took a look at this and saw that the error comes from the "getmatlab" script ($FREESURFER_HOME/fsfast/bin/getmatlab). It is a CSH script, which I thought might be the issue.

Specifically, the script checks for the existence of matlab by (unsurprisingly)

set MATLAB = `which matlab`;

On Dr. J's system, this was problematic due to "matlab" being aliased, so calling "getmatlab" directly exited with the error. Hard-coding the path for matlab in the "getmatlab" script is a (non-portable) solution.

However, I am not sure why it would throw an error, in any case. I tried it on my system and it returned the correct location of matlab. I am running CentOS 7.3 and using Freesurfer v5.3 (x86_64-unknown-linux-gnu-stable5-20130513). The version of "getmatlab" is Revision 1.2

Chris

On Fri, Aug 11, 2017 at 12:27 PM, Alan Francis alandarkenergy@gmail.com wrote:

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/fsfa st/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 ezra_wegbreit@brown.edu afrancis@mclean.harvard.edu

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