The quantification of neonatal brain development has a significant role in understanding, prevention, diagnosis and treatment of nervous system diseases in infancy time. On the other hand, brain development and its morphological changes are very fast during the first weeks after birth. So, age-related brain atlases representing sharp anatomical features of a neonatal population are indispensable. In this paper, we constructed two neonatal brain atlases for the age ranges of 39-40 and 41-42 weeks' gestational age with 16 T1-weighted magnetic resonance images using an improved groupwise registration. Neonatal images were normalized to the newly created and previously available neonatal atlases. The similarity between these atlases and normalized images was calculated via mutual information. The mean of mutual information between normalized images and the new atlases using the proposed algorithm is larger. This result confirms the greater similarity between normalized images and the atlases created in this paper. Besides, neonatal brain development was analyzed using deformation based morphometry and brain anatomical changes could be seen in local regions.