1. The process of registering an anatomical image of the thorax and abdomen of a patient with a functional image of the thorax and abdomen of the patient comprising the steps: a. obtaining an anatomical image of the thorax and abdomen of the patient, b. obtaining a functional image of the thorax and abdomen of the patient, the functional image containing functional and anatomical features, c. extracting the anatomical features of the anatomical and functional images, d. registering the anatomical and functional images by a process comprising the step: 1. transforming the scans using nonrigid B-Spline free form deformations using the anatomical features extracted from the anatomical and functional images.