An apparatus for mapping a structure in a body of a subject, said structure comprising a heart, the apparatus comprising: an imaging device for capturing a three-dimensional image of said structure, said structure having anatomical features that appear in said image; a probe linked to said processor and adapted for insertion into said structure, said probe having a position sensor for determining position and orientation information of said probe; a processor linked to said imaging device, said processor being operative for generating a functional model comprising a three-dimensional map of said structure comprising functional information relating to said structure measured at multiple points on said structure, said map exhibiting functional features of said structure, wherein said functional model comprises an electrical model when said probe is contacted with multiple contact points on said structure, and responsively to said position sensor of said probe said processor is operative to obtain position and orientation information associated with each of said contact points and wherein said structure comprises a heart, and wherein said functional information comprises a feature of a local electrocardiogram taken at each of said contact points; and a display device linked to said processor for displaying said functional information from said map in registration with said image characterised in that said processor is operative for registering said image with said map by automatically identifying at least one of said functional features with at least a corresponding one of said anatomical features in said image by using voltage values in said map to identify one of said functional features with a corresponding one of said anatomical features in the three-dimensional image that are known to generate such values. an imaging device for capturing a three-dimensional image of said structure, said structure having anatomical features that appear in said image; a probe linked to said processor and adapted for insertion into said structure, said probe having a position sensor for determining position and orientation information of said probe; a processor linked to said imaging device, said processor being operative for generating a functional model comprising a three-dimensional map of said structure comprising functional information relating to said structure measured at multiple points on said structure, said map exhibiting functional features of said structure, wherein said functional model comprises an electrical model when said probe is contacted with multiple contact points on said structure, and responsively to said position sensor of said probe said processor is operative to obtain position and orientation information associated with each of said contact points and wherein said structure comprises a heart, and wherein said functional information comprises a feature of a local electrocardiogram taken at each of said contact points; and a display device linked to said processor for displaying said functional information from said map in registration with said image characterised in that said processor is operative for registering said image with said map by automatically identifying at least one of said functional features with at least a corresponding one of said anatomical features in said image by using voltage values in said map to identify one of said functional features with a corresponding one of said anatomical features in the three-dimensional image that are known to generate such values.