We are developing an imaging system that enables the brain of a freely moving animal to be imaged with microPET while simultaneously observing its behaviour. Towards this end, we investigated the feasibility of reconstructing a motion-tracked volume of interest (VOI) in the presence of an extraneous activity compartment with unknown motion. A dual phantom study was performed to simulate movements of a freely moving animal. Both phantoms were moved through discrete positions but only one phantom (representing the head) was tracked. The multiple acquisition frames (MAF) and LOR rebinning methods were applied based on the measured motion of the tracked phantom. We also investigated alternative approaches that are hybrids of these two methods. We found that LOR rebinning causes up to 90% ‘lost events’ (events that would have been measured had motion not occurred) when applied to a freely moving target and this fraction can be significantly reduced using the hybrid approaches, resulting in improved image quality. The MAF-based motion correction yields good results but is not practical for unconstrained motion due to the assumption of no motion within each time segment. We conclude that it is feasible to reconstruct a target VOI in the presence of extraneous activity whose motion is unknown, provided the target motion is accurately tracked.