System and method for processing magnetic resonance imaging (MRI) data of an object to perform motion correction. The method comprises estimating, for each slice of the MRI data, parameters for a state space model using a filter that predicts the location of the object for temporally adjacent slices, wherein the state space model represents motion dynamics of the object throughout acquisition of a three-dimensional volume, registering the slices to a reference image based, at least in part, on the estimated parameters, reconstructing an image based, at least in part, on the registered two-dimensional slices, and outputting the reconstructed image.