In the cancer treatment by the hadron-therapy, beams of Carbon nuclei present therapeutic advantages over proton beams. The knowledge of the fragmentation of Carbon nuclei when they interact with human tissues is important to evaluate the spatial profile of the energy deposition in the human body, hence maximizing the effectiveness in hitting the cancer with minimal damage to the neighbouring tissues. The measurement is also of interest for the evaluation of the biological damage by cosmic rays to astronauts in space missions. Nuclear emulsions allow to measure particle trajectories with space resolution at the micrometric level. In the Emulsion Cloud Chamber (ECC) technique, nuclear emulsion films are interleaved with plates of passive material in a multiple sandwich structure. This allows to integrate the target and the fragment detector in a very compact structure. The development of techniques of controlled fading of particle tracks in nuclear emulsions has opened the way to measurements of the specific ionisation over a very broad dynamic range. The data presented in this paper have been obtained by exposing an ECC to a beam of Carbon nuclei with 400 MeV/nucleon at the Heavy Ion Medical Accelerator in Chiba, Japan. The ECC consisted of emulsion films and, as passive material, of polycarbonate with a density similar to that of the human body. We report on the identification of nuclear fragments through the measurement of their specific ionisation, linked to the electrical charge. The results provide also features of the interactions such as the scattering angles for the different ions. We finally report the measurement of the partial charge-changing cross-sections, and in particular the production cross-section of low charge fragments, which is poorly known. The cross-sections obtained in this work are compared to those available from other experiments.