1. A method for generating a diagnostic three dimensional image of a patient comprising: obtaining a plurality of images of the patient using an imaging modality device, wherein each of the plurality of images is obtained at a given time in sequence; estimating a registration vector for each of the plurality of images at the given time based on a motion function and an image transformation function, wherein each of the plurality of images is defined by a measurement noise occurring at the given time added to the image transformation function operating on the registration vector with respect to a reference image, and wherein the registration vector is a function of a breathing motion of a prior registration vector added to a transition noise value at the given time; estimating motion parameters based on a sequence of estimated registration vector; iteratively refining the estimated registration vector and the estimated motion parameters; and upon iteratively refining the estimated registration vector and the estimated motion parameters, generating the diagnostic three dimensional image of the patient using the estimated registration vector for each of the plurality of images at the given time and the estimated motion parameters.