The study on probabilistic connectivity of basal ganglia have not reported in mouse model. However, we have quantified fiber connectivity and visualized specific tractography pathway. The basal ganglia is a complex system of a subcortical nuclei network which plays a fundamental role in a wide range of processes related to motor and limbic functions. Altered neural connectivity of basal ganglia may contribute to a number of neurologic and psychiatric disease such as Parkinson’s disease. This study shows that probabilistic diffusion tractography allows for detailed 3D reconstruction of the projections of basal ganglia in ex vivo control and PD mouse brain.