Just use either "system" or the exclamation mark and type the FSL commands
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Albrecht, Daniel S.
[dsalbre...@mgh.harvard.edu]
Sent: Tuesday, August 04, 2015 4:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Using FSL commands through Matlab (Linux)
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
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