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The invention relates to a deformable surface model-based magnetic-resonance (MR) image skull stripping method, which belongs to the image processing field, and is characterized in that: an initial surface model is built by utilizing a triangular mesh, and the initial surface model can approach a brain tissue surface through gradual deformation. The deformation process is required to satisfy two restriction conditions: firstly, the continuity and smoothness of the surface are guaranteed to avoid a broken layer and broken lines; and secondly, the model is promoted to move towards the surface of the image brain tissue. An ellipsoidal surface is innovatively adopted to initialize the surface model, firstly an initial skull margin is obtained through threshold segmentation, initial skull marginal points are used for fitting the ellipsoidal surface, then a spherical mesh model is obtained by segmenting a regular icosahedron, and finally mesh points of the spherical model are mapped to corresponding mesh points of the ellipsoidal surface through the affine transformation. Since a skull of the human being is approximately in an elliptical shape, by adopting the surface model, the convergence velocity of the algorithm can be facilitated to be rapider, the iterations is greatly reduced, and the operand is reduced.