The Allen Brain Atlas provides most of their tracked brain data as 3d-files in the VTK-format. I found it difficult to find a converter for this format that would give me e.g. an obj-file. I came across the Graph Toolbox for Matlab which can read vtk-files and write obj-files. However, their importer did not work for that particular version of the vtk-format. Here is read_Allen_vtk.m, an m-file that I derived from read_vtk.m, which is able to extract all vertices and face-data from the vtk-files. You can then save them using write_obj() and open them in the 3d-tool of your choice. In the  upper image you see the hippocampus and entorhinal cortex of the mouse in Blender.