Tissues such as tendons, ligaments, articular cartilage, and menisci contain significant amounts of organised collagen which gives rise to the Magic Angle effect during magnetic resonance imaging (MRI). The MR intensity response of these tissues is dependent on the angle between the main field, B0, and the direction of the collagen fibres. Our previous work showed that by acquiring scans at as few as 7–9 different field orientations, depending on signal to noise ratio (SNR), the tissue microstructure can be deduced from the intensity variations across the set of scans. Previously our Magic Angle Directional Imaging (MADI) technique used rigid registration and manual final alignment, and did not assume any knowledge of the target anatomy being scanned. In the present work, fully automatic soft registration is incorporated into the MADI workflow and a priori knowledge of the target anatomy is used to reduce the required number of scans. Simulation studies were performed to assess how many scans are theoretically necessary. These findings were then applied to MRI data from a caprine knee specimen. Simulations suggested that using 3 scans might be sufficient, but in practice 4 scans were necessary to achieve high accuracy. 5 scans only offered marginal gains over 4 scans. A 15 scan dataset was used as a gold standard for quantitative voxel-to-voxel comparison of computed fibre directions, qualitative comparison of collagen tractography plots are also presented. The results are also encouraging at low SNR values, showing robustness of the method and applicability at low field.