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MRtrix3 is a powerful diffusion MRI analysis toolbox. In our lab we use MRtrix3 to generate structural connectomes and perform higher-order/advanced diffusion tractography.

You can find MRtrix3 here. A good starting point with MRtrix3 is their beginner DWI tutorial.

For an example of how we leveraged MRtrix3 in the lab, please refer to Behan et al. 2017.