Systems and computer-implemented methods of performing image registration. One method includes receiving a first image and a second image acquired from a patient at different times and, in each of the first image and the second image, detecting an upper boundary of an imaged object in an image coordinate system and detecting a lower boundary of the imaged object in the image coordinate system. The method further includes, based on the upper boundary and the lower boundary of each of the first image and the second image, cropping and padding at least one of the first image and the second image to create an aligned first image and an aligned second image and executing a registration model on the aligned first image and the aligned second image to compute a deformation field between the aligned first image and the aligned second image.