PLSGUI has a nice built-in intensity extraction feature for voxels / regions and so does BrainVoyager, but I think SPM requires the MarsBar add-on and requires some fiddling. I'm not sure about AFNI. I think these tools would be about equally difficult to use as the bulk of the preparation time will be in programming your design matrix. That said, if you go with PLSGUI, you have the advantage of being able to set up exploratory connectivity analyses later without much extra effort (e.g., task analysis, seed analysis).