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In the brain MR images, the boundary of each encephalic tissue is highly irregular. Traditional 3-D reconstruction algorithms are challenged. Owing to its powerful capacity in solving nonlinearity problems, the sphere-shaped support vector machines (SSSVMs) is applied in the 3-D reconstruction. Selecting parameters for SSSVM and the kernel function, however, is a complicated issue. Appropriate parameters can make the model more flexible and help to obtain more accurate data description. In this study, immune algorithm (IA) is used in searching for the optimal parameters. Immune SSSVM (ISSSVM) is proposed to reconstruct the 3-D encephalic tissues in MR images. As shown by the experiment of this study, each encephalic tissue can be reconstructed efficiently, and satisfied accuracy and visual effect can be obtained.