This paper describes an automated procedure for creating detailed patient-specific pediatric dosimetry phantoms from a small set of segmented organs in a child's CT scan. The algorithm involves full body mappings from adult template to pediatric images using multichannel large deformation diffeomorphic metric mapping (MC-LDDMM). The parallel implementation and performance of MC-LDDMM for this application is studied here for a sample of 4 pediatric patients, and from 1 to 24 processors. 93.84% of computation time is parallelized, and the efficiency of parallelization remains high until more than 8 processors are used. The performance of the algorithm was validated on a set of 24 male and 18 female pediatric patients. It was found to be accurate typically to within 1-2 voxels (2-4 mm) and robust across this large and variable data set.