DTI, may be the only feasible technique to study micorstructural changes occurring during the brain development. The main aims of this study was to design a complete new pipeline to perform micro-structural diffusion analysis in neonatal brain and to compare DTI to CHARMED and NODDI, which provides new microstructural metrics such as the intra-cellular volume fraction (nic) and the orientation dispersion index (ODI). High quality subject template was generated using DTI-TK tensor registration tools, which allows the accurate definitions of 13 ROIs. FA, nic and ODI were able to depict fine microstructural differences in early maturation fiber tracts.