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The brain shape is deformed regionally by kinds of cerebral diseases and the degree of progress. Therefore quantitative evaluation of the deformation using MR images is effective for diagnosis of cerebral diseases. To evaluate the cerebral deformation, almost conventional methods are based on normalization of the brain shape which deforms the evaluating brain into the standardized brain. Because the normalization process does not take into account anatomical features such as the cerebral sulci and gyri, in some cases the normalization process produces that one sulcus of the evaluating brain miss-corresponds to the other sulcus of the standardized brain. This paper proposes a homologous brain shape modeling method for quantitative evaluation of the brain shape in MR images. We define a new image feature called sulcal-distribution index (SDI) to represent the 3-D distribution of sulci, and the proposed method deforms a template brain model so that SDI of the deformed brain model calculated from the evaluating brain MR images is similar to SDI of the template brain model. By using SDI, the proposed method can take into account anatomical features of the cerebral sulci. The experimental results showed that the proposed method homologically modeled the brain shape with a mean displacement of 1.3 mm.