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Human brain atlases constructed from magnetic resonance images are extremely important for brain and cognition researches. With these atlases or brain maps, researchers can accurately analyze and compare different brain images. In this paper, the research progresses of brain atlas construction from magnetic resonance images are reviewed. Firstly, the development of human brain atlases from magnetic resonance images was introduced, including the technical skills required as well as the limitations. Then the basic technical methods for atlas construction are described. Finally, the statistical methods used for quantitative atlas-based analysis were reviewed, such as voxel-based morphometry and tract-based spatial statistical analysis. By analyzing the current research status, the limitations in the existing methodology and the trend of future development were put forward.