We have installed the Matlab toolboxes FSL-ROI and NIFTI on the cluster for general use. More information on the toolboxes can be found here: http://wiki.poldracklab.org/index.php/FSL-ROI and http://www.rotman-baycrest.on.ca/~jimmy/NIFTI/
In order to run them, you'll need to add the following two lines to your Matlab scripts, your cluster startup.m file (put in ~/matlab/startup.m), or the Matlab command window when using the Matlab GUI:
addpath('/usr/local/packages/MATLAB/fslroi');
addpath('/usr/local/packages/MATLAB/NIFTI');
-Josh