Copious documentation is available for froi. If you are only interested in how to use froi, the best documents to begin with are the html and/or pdf manual. It's recommended to download and print the pdf manual, as this version is guaranteed to be up-to-date; as well, it's easier to have something to look at when you're trying to learn the software.
You can also read an abridged version of the manual in html format, available in the list of links on the left. This version contains the first three chapters: introduction, roi basics, and further roi analyses.
As people use the software, there are bound to be frequently asked questions; those questions, along with answers, can be found in the faq.
Finally, those who want more in-depth information about froi can peruse the technical documentation section. Many people might find the manual pages for the command-line scripts useful; as well, you can find documentation for all of the matlab functions, perl modules, and data formats.