A phantom and associated method for calibrating registration in a multi-modal medical diagnostic imaging system are presented. The phantom features a plurality of emission point sources arranged in multiple parallel planes along the length of the phantom, with enough planes to allow mode registration to be calibrated over the length of an entire full-body scan. According to the method, calibration scans are performed at each of several scan positions along the length of the phantom, with at least two planes of emission point sources covered by the scan at each position.