A shape data generation method for transforming a reference shape of an organ to obtain a target shape of an organ of an individual patient, comprising: accepting a setting of source points on a reference shape identified from data of predefined vertices and a setting of target points on a target shape which is obtained from a plurality of segment images, wherein each of the target points corresponds to a different one of the source points; generating a first shape by transforming the reference shape so as to place each of the source points on a corresponding target point of the target points according to a Thin Plate Spline, TPS, Warp method; identifying (S27, S51), from among a plurality of vertices of the first shape, one or plural first vertices such that each vertex of the identified one or plural first vertices satisfies a condition that a normal line of the vertex crosses with the target shape, a condition that the vertex is not included in the source points, and a condition that a minimum of respective distances between the vertex and the source points and any other first vertices on the reference shape is longer than a predetermined first distance; transforming, according to the TPS Warp method, the first shape so as to move each identified first vertex, v, of the one or plural identified first vertices a second distance in a direction, n(v), of the normal line at the identified first vertex, wherein the second distance is determined by multiplying a distance (kn(v)) between the identified first vertex and a point at which the normal line at the identified first vertex crosses with the target shape by a ratio of a current number of repetition times, t, to a predetermined number of repetition times, T, and the source points are handled as fixed points and not moved in the transforming; repeating the identifying and the transforming T-1 times setting the transformed first shape of the previous repetition as the first shape of the current repetition; and displaying the transformed first shape after the identifying and the transforming are executed the predetermined number of repetition times, T. accepting a setting of source points on a reference shape identified from data of predefined vertices and a setting of target points on a target shape which is obtained from a plurality of segment images, wherein each of the target points corresponds to a different one of the source points; generating a first shape by transforming the reference shape so as to place each of the source points on a corresponding target point of the target points according to a Thin Plate Spline, TPS, Warp method; identifying (S27, S51), from among a plurality of vertices of the first shape, one or plural first vertices such that each vertex of the identified one or plural first vertices satisfies a condition that a normal line of the vertex crosses with the target shape, a condition that the vertex is not included in the source points, and a condition that a minimum of respective distances between the vertex and the source points and any other first vertices on the reference shape is longer than a predetermined first distance; transforming, according to the TPS Warp method, the first shape so as to move each identified first vertex, v, of the one or plural identified first vertices a second distance in a direction, n(v), of the normal line at the identified first vertex, wherein the second distance is determined by multiplying a distance (kn(v)) between the identified first vertex and a point at which the normal line at the identified first vertex crosses with the target shape by a ratio of a current number of repetition times, t, to a predetermined number of repetition times, T, and the source points are handled as fixed points and not moved in the transforming; repeating the identifying and the transforming T-1 times setting the transformed first shape of the previous repetition as the first shape of the current repetition; and displaying the transformed first shape after the identifying and the transforming are executed the predetermined number of repetition times, T.