This book constitutes the proceedings of the 16th International Workshop, CDMRI 2025, held in conjunction with MICCAI 2025, the 28th International Conference on Medical Image Computing and Computer-Assisted Intervention. The workshop took place in Daejeon, South Korea, on September 27, 2025. The 8 full papers presented in this book were carefully reviewed and selected from 10 submissions. They focus on all aspects of diffusion MRI acquisition, analysis, and application, bringing us closer to reliable clinical tools.