Although the transformation of brain tissue during craniotomy is a well-known phenomenon, there has been a lack of methodological analysis related to physiological brain shift in the closed cranium. In this study, we analyzed brain shift and transformation using MRI volume data acquired in different body positions. The volume data were divided into voxels. Each voxel of the prone or the right volume was registered using voxels of the supine or the left volume as templates, and movement and rotation of each voxel were recorded. Experimental result shows that the displacement in the depth of the brain tended to be conspicuous and rigid compared to the displacement of the brain surface.