We suggest a method to reconstruct intermediate slices of 3D subcortical structures given by slices (2D cross-sections) using shape-based interpolation for sparse slices. This algorithm overcomes some limitations of previous interpolation methods of reconstruction. The method can find the intermediate slice cross-section of 3D structure with discontinuities and can work for non-overlapping contours on different cross-sections. The method used can be considered as "indirect interpolation", because the auxiliary information about structure shape, based on minimum distance to the contour from each point of the image, has been used. Variations of the parameters (bias, connectivity, tension) can help adjust the contour produced to the expected shape. We apply this approach to interpolate subcortical structures in the Talairach-Tournoux brain atlas.