mrTools provides a set of Matlab tools to analyze fMRI data. It can do basic analyses like correlation analyses used in retinotopy experiments, event-related, population RF and GLM analyses. It can display the results of analyses on inplane anatomies, flat maps and surfaces. It is designed to make it easy to write your own script and programs in Matlab to analyze your data. See here for published work showing what you can do with mrTools.
There are tutorials available for doing retinotopy, pRF, event-related analysis, classification and GLM.