Techniques for registration of multiple measurement modes of a body include receiving first and second data from different modes. Each includes measured values with coordinate values. For two mechanically aligned modes, any non-rigid registration is performed. For some modes, the non-rigid registration includes a coarse transformation and multiple fine scale transformations. The coarse transformation maximizes a coarse similarity measure. The second data is sub-divided into contiguous sub-regions. Fine transformations are determined between the sub-regions and corresponding portions of the first data to maximize a fine similarity measure. Sub-dividing and determining fine transformations repeats until stop conditions are satisfied. Transformations between the last-divided sub-regions are interpolated. Any of the fine similarity measure, a search region, interpolation method, sub-division location, and the use of rigid or non-rigid fine transformations are adaptive to properties of the first or second data so that the registration is automatic without human intervention.