MDT's object oriented modular design allows arbitrary user specification and combinations of dMRI compartment models, diffusion microstructure models, likelihood functions and optimization algorithms. Many diffusion microstructure models are included, and new models can be added simply by adding Python script files. GPU based computations allow for ~60x faster model fitting; e.g. the 81 volume example NODDI dataset can be fitted whole brain in about 40 seconds, which makes MDT ideal for population studies. MDT can be extended to other modalities and models such as quantitative MRI. The software is open source and freely available at https://github.com/cbclab.