MaPPeRTrac (Massively Parallel, Portable, and Reproducible Tractography) is a brain tractography workflow for high performance computing. It incorporates novel technologies to simplify and accelerate neuroimaging research. MaPPeRTrac’s data and dependencies are de-coupled from code to enable rapid prototyping and modification. The container enables high-performance, parallel, parametrized, and portable generation of the brain’s neural connectomes that is fast, efficient, well-tested, robust, and easy-to-use.