Precise brain phantoms are important for evaluating the quality of segmentation tools for brain MRI. Here we suggested the construction of a 3D physical brain phantom as gold standard to validate the performance of those tools. Folding patterns of grey and white matter compartments were replicated using 3D-printed models from a real structural brain scan. T1 and T2 intensities of these brain regions in a 3 Tesla MRI were mimicked by a 0.6% agar mixture containing the appropriate concentrations of the paramagnetic compounds Ferumoxide and Manganese chloride. With its 3D-printed brain-like design, the phantom showed to be a promising alternative to existing methods for MRI segmentation validation.