Ah, that's probably correct. I think it worked on my system because I source
the FSL conf file in my .bashrc
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, August 04, 2015 4:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Using FSL commands through Matlab (Linux)
I don't think that will work because the shell where FSLDIR gets set is
not the same shell as that of the system command. Try putting those two
in the same string and then running system on that
On 08/04/2015 04:36 PM, Albrecht, Daniel S. wrote:
> Hello,
>
> Sorry if this isn’t the right forum for the question, but not sure
> where to direct it.
>
> I’m trying to incorporate some FSL commands into a Matlab script. I’m
> using a Linux machine and running Matlab 7.11.0 (2010b). I tried to
> access the FSL toolbox through Matlab using:
>
> setenv(‘FSLDIR’,’/autofs/cluster/pubsw/2/pubsw/Linux-2-2.3-x86_64/packages/fsl.64bit/5.0.7’)
> system(‘${FSLDIR}/etc/fslconf/fsl.sh’)
>
> But received a “permissions denied” error. Is there an easier way to
> access FSL through Matlab?
>
> Thanks,
>
> Daniel S. Albrecht, PhD
> Research Fellow in Radiology
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
> 149 Thirteenth Street, Room 2301
> Charlestown, MA 02129
> Phone: (617) 643-6748
> Fax: (617) 726-7422
> dsalbre...@mgh.harvard.edu
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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