[18F]-FP-DTBZ PET provides reliable information for the diagnosis of Parkinson’s disease. Quantitative analysis of PET images requires a precise segmentation of the region of interest. Two [18F]-FP-DTBZ PET image quantification methods, multi-atlas based and template based methods were compared in this study. A total of 68 subjects were included, each of them underwent 3D T1-weighted MR imaging and [18F]-FP-DTBZ PET imaging. Twenty subjects were used to build atlases and 48 were used for validation. Using dice coefficient and ICC coefficient for evaluation, we observed that the multi-atlas based method showed better performance than the template based method.