A medical imaging system (200) includes a masking unit (234), an image registration unit (238), a motion estimator (240) and a motion compensating reconstructor (244). The masking unit constructs a mask for each reconstructed volumetric phase image of a plurality of reconstructed volumetric phase images that masks portions of a corresponding image external to an anatomical model fitted to a segmented at least one anatomical structure, 5 wherein the plurality of reconstructed volumetric phase images include a target phase and a plurality of temporal neighboring phases reconstructed from projection data. The image registration unit registers the masked reconstructed volumetric phase images. The motion estimator estimates motion between the target phase and the plurality of temporal neighboring phases according to the model based on the registered masked reconstructed 10 volumetric phase images. The motion compensating reconstructor reconstructs a motion compensated medical image from the projection data using the estimated motion of the registered masked reconstructed volumetric phase images.