A method for motion estimation in CT systems is provided. The method includes dividing projection data, obtained by scanning a heart using the CT system, into a plurality of partial-angle-reconstruction (PAR) bins, reconstructing a plurality of PAR volumes from the PAR-binned projection data, obtaining, based on the plurality of reconstructed PAR volumes, a number of short-scan volumes, determining, based on the obtained number of short-scan volumes, a plurality of nodes throughout the heart, estimating, for each of the determined plurality of nodes, a plurality of model parameters of a motion model, and generating, based on the plurality of model parameters estimated for each of the plurality of nodes, parameters of a global motion model at each voxel of a volume of the heart. The method also includes reconstructing, based on the generated motion parameters of the global motion model at each voxel of the volume of the heart, a motion-compensated short-scan volume.