Probabilistic atlases for the human brain structure are more suitable than single brain atlases for representing population anatomy. In this study, we hypothesized the group-specific probabilistic atlas for accurate characteristic feature coding. Our proposed method for a new group comparison study, using a subpopulation specific probabilistic atlas, was based on this hypothesis. A knowledge-based automatic labeling technique using nonlinear registration was applied to encode group-specific regional probabilistic information. Direct atlas-based comparison using volume counting above the probability threshold, distance measurement and correlation analysis were performed based on the probabilistic atlas. Here, we applied this method for comparison between Korean and occidental groups. The results showed that this method could provide simple but intuitive regions of interest-based group analysis for the entire cortex area.