motr comes in two flavors, a Windows version and a Linux version; both need MATLAB (version 2009b or later and the Image processing, Signal processing and Statistics toolboxes; the Linux version also needs the MATLAB compiler).
Both versions can be run on your local computer; the Linux version can also run on a cluster (this splits tracking up into multiple separate jobs and makes it faster).
Simple install (zipped files):
a) Go to https://github.com/motr/motr and click on the button that says Download ZIP (on the righthand side of the page).
b) Extract the zipped files to a directory.
c) Start MATLAB
d) Add the directory with the motr files to your MATLAB path
Slightly more complicated install (clone the git repository):
a) If you don't already have a copy, download and install a copy of git (I like tortoisegit: http://code.google.com/p/tortoisegit/).
b) Make a directory for the motr files, right click and select "Git clone". Enter the URL of the motr repository: https://github.com/motr/motr and make sure the Directory name is where you want the motr files to go. Click "OK".
c) Add the motr directory to your MATLAB path
note: Running motr on a cluster
The details of this are going to vary depending on where you are. You'll need to find someone computer savvy (if you aren't yourself) at your local institution to help with the details. However, if you are running Windows, a good place to start would be to download an NX client for Windows (see Appendices