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 <alandarkene...@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.jura...@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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>>
>>
>> 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
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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
> al...@bwh.harvard.edu <ezra_wegbr...@brown.edu>
> afran...@mclean.harvard.edu
>
>
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>
>
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> 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
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> dispose of the e-mail.
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