In order to allow accurate pre-operative localisation of functional targets in functional neurosurgery, we aim at constructing a three dimensional registrable cartography of the basal ganglia, based on histology. For doing this, a post mortem MR study was conducted on a cadaver’s head, and the brain was then extracted and processed for histology. The post mortem MR image will allow to report the cartography on the patient’s anatomy, by its registration with the patient’s MR image. In this paper, we focus on the problem of co-registering the histological and post mortem MR data of the same subject. First, realignment of the histological sections into a reliable three dimensional volume is performed. Then the reconstructed volume is registered with the post mortem MR image. To insure three dimensional integrity of the histological reconstructed volume, a reference volume is first constructed from photographs of the unstained surface of the frozen brain. This reference is then used as an intermediate volume for, on the one hand, independant alignment of each histological section with its corresponding optical section and on the other hand, three dimensional registration with the post mortem MR image.