Abstract
Large-scale diffusion MRI tractography remains a significant challenge. Users must orchestrate a complex sequence of instructions that requires many software packages with complex dependencies and high computational cost. We developed MaPPeRTrac, a probabilistic tractography pipeline that simplifies and vastly accelerates this process on a wide range of high performance computing (HPC) environments. It fully automates the entire tractography pipeline, from management of raw MRI machine data to edge density imaging (EDI) of the structural connectome. Dependencies are containerized with Docker or Singularity and de-coupled from code to enable rapid proto-typing and modification. Data artifacts are strictly organized with the Brain Imaging Data Structure (BIDS) to ensure that they are findable, accessible, interoperable, and reusable following FAIR principles. The pipeline takes full advantage of HPC resources using the Parsl parallel programming frame-work, resulting in the creation of connectome datasets of unprecedented size. MaPPeRTrac is publicly available and tested on commercial and scientific hardware, so that it may accelerate brain connectome research for a broader user community.
Competing Interest Statement
The research is funded by the United States Department of Energy under the DOE Office of Science, Advanced Scientific Computing Research. Support is organized under The Co-Design for Artificial Intelligence and Computing at Scale for Extremely Large, Complex Datasets projects (Grant #KJ040301). Geoffrey Manley and Pratik Mukherjee disclose grants from the United States Department of Defense - TBI Endpoints Development Initiative (Grant #W81XWH-14-2-0176), TRACK-TBI Precision Medicine (Grant #W81XWH-18-2-0042), and TRACK-TBI NETWORK (Grant #W81XWH-15-9-0001); NIH-NINDS - TRACK-TBI (Grant #U01NS086090); and the National Football League (NFL) Scientific Advisory Board - TRACK-TBI LONGITUDINAL. The United States Department of Energy supports Dr. Manley for a precision medicine collaboration. One Mind has provided funding for TRACK-TBI patients stipends and support to clinical sites. He has received an unrestricted gift from the NFL to the UCSF Foundation to support research efforts of the TRACK-TBI NETWORK. Dr. Manley has also received funding from NeuroTruama Sciences LLC to support TRACK-TBI data curation efforts. Additionally, Abbott Laboratories has provided funding for add-in TRACK-TBI clinical studies. Amy Markowitz receives funding from the Department of Defense TBI Endpoints Development Initiative (Grant #W81XWH-14-2-0176) and TRACK-TBI NETWORK (Grant #W81XWH-15-9-0001). Ms. Markowitz also receives salary support from the United States Department of Energy precision medicine collaboration and the philanthropic organization, One Mind.
Footnotes
↵1 Transforming Research and Clinical Knowledge in Traumatic Brain Injury
Paper revised for clarity. Added Figures 1,3,5,6 and Tables 1,2,3,4 with data artifacts and detailed performance figures.
1 Transforming Research and Clinical Knowledge in Traumatic Brain Injury
7 https://alcf.anl.gov/support-center/cooley/cooley-system-overview