Methodological analysis related to physiological brain shift in the closed cranium is lacking. The spaceflight-associated neuro-ocular syndrome is attributed to the upward shift of the brain. We analyzed the relationship of brain shift and optic nerve shift by using MR volume data acquired in different body positions. The movement and rotation of each voxel, divided into 20 × 20 × 20 pixels3, were calculated using the block matching method. Experimental results show that the optic nerve transforms and deforms with the movement of the brain because of a change in body position.