Histology-based validation of magnetic resonance imaging (MRI) is essential to confirm imaging technique specificity and accuracy. One-to-one correspondence is complicated by histological preparation and differences in MRI and histology contrast mechanisms. A new approach, based on local structure orientation (LSO) and using microstructural features, is proposed. LSO facilitates registration based on direct correspondence between tissue fibre structure to emulate a common contrast mechanism. Using a physical phantom derived from a chicken heart with embedded fibrous structures, residual displacement was 14.1 mm for advanced mean squares (AMS), 2.2 mm for modified AMS (AMSR), and 3.3 mm for mutual information (MI).