A method for selecting vertices for performing deformable registration of imaged objects is provided. The selected vertices form corresponding pairs, each pair including a vertex from a first imaged object and a vertex from a second imaged object. The corresponding vertex pairs are sorted in order of distance between the vertices making up the corresponding vertex pair. The corresponding vertex pair with the greatest distance is given top priority. Corresponding vertex pairs that lie within a selected distance from the selected corresponding vertex pair are discarded. In this manner, the number of vertex pairs used for deformable registration of the imaged objects is reduced and therefore allows for processing times that are clinically acceptable.