A system and method for co-registering image data includes generating a reference state model defined by deformable and non-deformable surfaces of a region of interest (ROI) of a patient. The reference state model is generated by identifying a deformable surface in a first image representing the ROI in a reference position, with the location of one or more anatomical reference points on the deformable surface tracked using at least one surface marker. Deformable and non-deformable surfaces of the ROI are identified within a medical image representing the ROI in a deformed position relative to the reference position. The non-deformable surface in the medical image is registered to positional coordinates of anatomical reference point(s) within the reference state model. The position of a target pixel in the medical image is projected to the reference state model based on a relative location of the target pixel between the deformable and non-deformable surfaces.
