  This manuscript presents a novel, tightly integrated pipeline for estimating
a connectome, which is a comprehensive description of the neural circuits in
the brain. The pipeline utilizes magnetic resonance imaging (MRI) data to
produce a high-level estimate of the structural connectivity in the human
brain. The Magnetic Resonance Connectome Automated Pipeline (MRCAP) is
efficient and its modular construction allows researchers to modify algorithms
to meet their specific requirements. The pipeline has been validated and over
200 connectomes have been processed and analyzed to date.
  This tool enables the prediction and assessment of various cognitive
covariates, and this research is applicable to a variety of domains and
applications. MRCAP will enable MR connectomes to be rapidly generated to
ultimately help spur discoveries about the structure and function of the human
brain.
