.. index::
   single: matlab


.. _matlab:

MATLAB
======
to list Matlab versions, open a terminal window on the neuro cluster, and type 'matlab' followed by the tab key (twice), e.g.::

    matlab<tab><tab>


Graphics 
--------
If you experience poor graphics rendering, e.g. the screen doesn't refresh leaving a 'ghosting' appearance, then you may use a graphics processor to improve graphics performance. To use a graphics processor, preface the 'matlab' command with a 'g'. This may degrade overall performance and/or cause session errors, so use cautiously. An example is below::

    $ gmatlab-2010b

Compatibility with Mac
^^^^^^^^^^^^^^^^^^^^^^
There is a known problem displaying Java applications (including Matlab) remotely on Mac computers with the M1 chip. The screen will appear black while the mouse focus is on the Matlab window.

As a work-around, open a terminal window on the neuro cluster, and run the following commands::

    cd
    cat << END > java.opts
    -Dsun.java2d.xrender=false
    END

This will create a file called 'java.opts' in your home directory.

Now you may run Matlab from your home directory and the screen will appear normal. For example::

    cd
    matlab-2021a

If you prefer to run Matlab from a different directory, then copy the java.opts file to that directory.


SPM
---

The following MATLAB/SPM command shortcuts are available for your convenience:

    | matlab-spm2
    | matlab-spm5
    | matlab-spm8

To determine the specific MATLAB version used by a shortcut, run the 'ls' command followed by the path to the shortcut from a :ref:`terminal window <cli>`, e.g. ::

    ls -l `which matlab-spm2`


Toolboxes
---------

Toolboxes are located in /usr/local/matlab-tools. To request a toolbox, please email support-neuro@berkeley.edu.  Additional documentation is provided below:

    | `marsbar <http://marsbar.sourceforge.net/faq.html>`_
    | `snpm (versions 3 and 5b) <http://www.sph.umich.edu/ni-stat/SnPM/>`_
    | `wfu_toolboxes <http://fmri.wfubmc.edu/cms/software>`_
    | `mrDiffusion <http://white.stanford.edu/newlm/index.php/MrDiffusion>`_
    | `spm2DespoBasic <file:///usr/local/matlab-tools/spm/spm2DespoBasic/README.txt>`_


.. _matlab_install:

PC Installation
---------------
You may be authorized to run MATLAB on a personal computer for free. For more information, email me at support-neuro@berkeley.edu. Alternativey, use the `IST MATLAB FAQ <http://software.berkeley.edu/matlab>`_ to see if you qualify, and to request a license.