1. A method for correcting and reconstructing a plurality of projection images based on detected patient motion that occurs during an imaging procedure, the method executed by an imaging system including a computer with an electronic processing unit and a memory module storing a projection matrix calculation module and a reconstruction module, both executable by the electronic processing unit, the method comprising: obtaining, at the computer, a plurality of projection images generated by a scanner during the imaging procedure, each of the plurality of projection images including at least three markers, each of the at least three markers having a measured three-dimensional position and measured positions on a detector panel of the scanner in a first dimension and a second dimension; determining, with the electronic processing unit, a position error vector for each of the plurality of projection images based on the at least three markers in each of the plurality of projection images, the position error vector defining patient motion in the projection image; combining each position error vector for each of the plurality of projection images with geometric parameters associated with the scanner to derive a projection matrix for each of the plurality of projection images; and generating reconstructed images corrected for patient motion from the plurality of projection images and the projection matrix for each of the plurality of projection images.