We propose a new method for mapping onto a brain volume model including inner organs with complicated shapes such as lateral ventricles. The proposed method is based on a volumetric Self-organizing Deformable Model (vSDM) which allows to control the mapping positions of inner organs while preserving geometrical features before and after the mapping. The control sometimes causes the self-intersection of the volume model. The solution for the self-intersection in vSDM is to move vertices of the volume model. However, when the inner organ has complicated shape, the vertex movement cannot always correct the self-intersection. To solve this problem, we extend vSDM by introducing a new process of editing the mesh structure of the volume model. Moreover, by applying the proposed method to six brain volume models, a volumetric Statistical Shape Model (SSM) is constructed which represents the shape variations of not only brain surface but also brain inner organs. From experimental results, we confirmed the volumetric SSM has an acceptable performance compared with general surface SSMs generated by organ surface models.