Using a well-characterized multi-site diffusion MRI (dMRI) dataset of early Parkinson’s disease (PD), this study suggests that DTI-TK and TBSS perform at the same accuracy of detection if skeletonwise analysis are conducted. However, DTI-TK is more sensitive than TBSS. Further, results from voxelwise or ROI-based analysis should be reported with caution as this study found a significant smoothing effect to detect differences in scalar dMRI-derived measures. Overall, our findings suggest that the conclusions for the hypothesis being tested are strongly dependent upon the choice of analytic techniques as different analysis techniques can lead to different conclusions.