This work describes a protocol for creating a population of pediatric, patient specific, computational dosimetry phantoms. Pediatric CT data are mapped to a detailed adult template using multi channel (MC) - large deformation diffeomorphic metric mapping (LDDMM) applied to whole body images. Challenges are studied and overcome using 2D LDDMM applied to simulated phantoms. The protocol involves automatic placement of landmarks, landmark based affine and LDDMM registration, followed by 4 applications of MC-LDDMM, with successively decreasing smoothness constraints. Deformed adult organ surfaces typically agree with pediatric organ surfaces within 1-2 voxels (∼2.3 mm).