A shape data generation method relating to this invention includes: first generating first three-dimensional voxel data that represents a target object by using first tomographic images, in which a first region occupied by the target object is designated, among plural tomographic images； extracting, from the first tomographic images, brightness values of voxels included in the first region； second generating a function for calculating a probability that a voxel is included in the first region by using the extracted brightness values； calculating, for each voxel among voxels in a voxel space that includes the plural tomographic images, a probability by using a brightness value of the voxel and the function； and third generating second three-dimensional voxel data that represents the target object by using the first three-dimensional voxel data and probabilities calculated for the voxels in the voxel space.
