Brain Connectomics: Opportunities for High-Performance Computing

Alan Kaplan | 18-FS-009


The human brain is estimated to contain approximately 100 trillion neural connections. This complex map of connectivity, the human connectome, underlies cognitive processes and informs disease states. Studying the human connectome has been hampered by the difficulty of collecting and processing suitable data for analysis. The Human Connectome Project (HCP) was created to acquire and collect the largest, most cohesive set of brain data to accelerate neuroscience research. Recently, the HCP released a magnetic resonance dataset of brain imagery with unprecedented scale and organization as well as high-quality spatial and temporal resolution. However, using this high-resolution brain imagery to estimate neurological connectivity networks requires high-performance computing (HPC) capabilities.

In this project, we explored the feasibility of using Lawrence Livermore National Laboratory's computing resources to effectively estimate brain connectivity networks from the HCP's large imagery set. Specifically, we addressed the challenge of advancing computation of individual structural and functional connectomes. We hosted the latest version of the HCP dataset and developed software to handle the computationally-intensive tasks required to generate connectomes on the entire HCP cohort (~1200 subjects). As a result, the opportunity to quantify the structural connections inside the brain at a high level of detail are now available. Instead of working with pairwise measures that describe the connectivity between a few hundred anatomical regions, we now have the capability to express complex geometric networks in the brain.

Impact on Mission

Our research leveraged Livermore's core competencies in high-performance computing, simulation, and data science and enhanced HPC capabilities by addressing computing network topology at scale from large amounts of data. In addition, this project paved the way for new scientific and neural engineering advances that strengthen the Laboratory's bioscience and bioengineering core competencies and support the chemical and biological countermeasures R&D challenge. This project also supports NNSA's goal of advancing the scientific, technical, and engineering competencies that are the foundation of the NNSA mission.

Publications, Presentations, Etc.

Kaplan, A. 2019. "Large Scale Connectome Generation." Presentation at Society for Brain Mapping & Therapeutics. LLNL-PRES-769612.