Overlap produces two tables describing ROI overlaps between two ROI images: one shows the number of pixels overlapping between a given pair of ROIs, and the second one translates this information into percent overlap between the ROIs (relative to the number of pixels in the first ROI).
java OverlapThis starts up the java interpreter and runs the Overlap application. You need to have set up your environment for java in order for this to work.
Note that although only the ROI images must be specified in the fields, the corresponding .plist files must exist and reside in the same location as the images they correspond to.