I have just added the latest version of Sue's functional connectivity toolbox to the NITRC site: http://www.nitrc.org/projects/conn . In addition to extracting the ROI timecourses and estimating ROI-to-ROI correlation measures, it performs seed-to-voxel analyses (maps of functional connectivity values between an ROI and every voxel), includes a pre-processing step that removes confounds (regressing-out motion parameters and noise signals obtained from white matter and CSF areas), and performs a number of second-level random effect analyses. Hope you find it useful