Patients from both MSA-C and SCA3 showed significantly decreased FA (Normal vs MSA-C: p < 0.001, Normal vs SCA3: p < 0.0001, MSAC vs SCA3: p = 0.0155, verified by post-hoc test) and increased MD (Normal vs MSA-C: p = 0.0107, Normal vs SCA3: p < 0.0001, MSAC vs SCA3: p = 0.0427, verified by post-hoc test) of cerebral and cerebellar WM, and the patients with SCA3 revealed the most significantly decreased FA and increased MD among all the groups. This evidence concerns the gene ATXN3 and multiple system atrophy, cerebellar type.