This paper presents a method for estimating the internal structures of a patient brain by deforming a standard brain atlas. Conventional deformation methods need several landmarks from the brain surface contour to fit the atlas to the patient brain shape. However, since the number and shapes of small sulci on the brain surface are different from each other, the determination of the accurate correspondence between small sulcus is difficult for experienced neurosurgeons. Moreover, the relationship between the surface shape and internal structure of the brain is unclear. Therefore, even if the deformed atlas is fitted to the patient brain shape exactly, the use of the deformed atlas does not always guarantee the reliable estimation of the internal structure of the patient brain. To solve these problems, we propose a new method for estimate the internal structure of a patient brain by the finite element method (FEM). In the deformation, our method select the landmarks from the contours of both the brain surface and the detectable internal structures from MR images.