A method and system for non-rigidly registering a fixed to a moving image utilizing a B-Spline based free form deformation (FFD) model is disclosed. The methodology utilizes sparse feature correspondences to estimate an elastic deformation field in a closed form. In a multi-resolution manner, the method is able to recover small to large non-rigid deformations. The resulting deformation field is globally smooth and guarantees one-to-one mapping between the images being registered. The method generally comprises the steps of: detecting feature points on the fixed image and feature points on the moving image; assigning a feature vector to each feature point; calculating the dissimilarity of each pair of feature vectors for feature pairs on the fixed image and the moving image; calculating the correspondence between feature pairs based on the dissimilarity measure; solving for a dense deformation field P using a closed form FFD model; and transforming the moving image and the feature points on the moving image using a current FFD deformation field estimate.