A method and apparatus is provided to perform material decomposition based on spectral computed tomography (CT) projection data generated using registered reconstructed images. Registration is performed in the image domain, whereas material decomposition is performed in the sinogram domain. In the sinogram domain, material decomposition can include beam-hardening corrections. For at least two energy components, CT images are reconstructed, and registration is performed among the CT images. In certain implementations, the registered images are forward projected, and material decomposition is based on the resultant forward projections. In other implementations, motion images are generated from differences between the reconstructed CT images pre- and post-registration. The projection data is then corrected using forward projections of the motion images, and material decomposition is performed using the motion-corrected projection data.
