In neurosurgery, localisation of deep brain structures is a crucial issue, which can be assisted by a 3-dimensional brain atlases. Our goal is to build such an atlas by fusing histological data with a 3D MR image of the same subject. This requires two steps: first a 2D realignment of the histological sections in order to obtain a three-dimensional block, then a 3D registration between this reconstructed block and the MR image. Both steps are based on the same robust registration algorithm.