Systems and methods are provided for registering maps with images, involving segmentation of three-dimensional images and registration of images with an electro- anatomical map using physiological or functional information in the maps and the images, rather than using only location information. A typical application of the invention involves registration of an electro-anatomical map of the heart with a preacquired or real-time three-dimensional image. Features such as scar tissue in the heart, which typically exhibits lower voltage than healthy tissue in the electro-anatomical map, can be localized and accurately delineated on the three-dimensional image and map.
