We previously presented an image registration method, referred to hierarchical attribute matching mechanism for elastic registration (HAMMER), which demonstrated relatively high accuracy in inter-subject registration of MR brain images. However, the HAMMER algorithm requires the pre-segmentation of brain tissues, since the attribute vectors used to hierarchically match the corresponding pairs of points are defined from the segmented image. In many applications, the segmentation of tissues might be difficult, unreliable or even impossible to complete, which potentially limits the use of the HAMMER algorithm in more generalized applications. To overcome this limitation, we have used local spatial intensity histograms to design a new type of attribute vector for each point in an intensity image. The histogram-based attribute vector is rotationally invariant, and importantly it also captures spatial information by integrating a number of local intensity histograms from multi-resolution ...