Volumetric registration of brain MR images presents a challenging problem due to the wide variety of sulcal folding patterns. We present a novel volumetric registration method based on an intermediate parameter space in which the shape differences are normalized. First, we generate a 3D harmonic map of each brain volume to unit ball which is used as an intermediate space. Cortical surface features and volumetric intensity are then used to find a simultaneous surface and volume registration. We present a finite element method for the registration by using a tetrahedral volumetric mesh for registering the interior volumetric information and the corresponding triangulated mesh at the surface points. This framework aligns the convoluted sulcal folding patterns as well as the subcortical structures by allowing simultaneous flow of surface and volumes for registration. We describe the methodology and FEM implementation and then evaluate the method in terms of the overlap between segmented structures in coregistered brains.