@article{ae82c8eb11d743d29ce6b93194e06e38,
title = "MaPPeRTrac: A Massively Parallel, Portable, and Reproducible Tractography Pipeline",
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 costs. We developed MaPPeRTrac, an edge-centric tractography pipeline that simplifies and accelerates this process in a wide range of high-performance computing (HPC) environments. It fully automates either probabilistic or deterministic tractography, starting from a subject{\textquoteright}s magnetic resonance imaging (MRI) data, including structural and diffusion MRI images, to the edge density image (EDI) of their structural connectomes. Dependencies are containerized with Singularity (now called Apptainer) and decoupled from code to enable rapid prototyping and modification. Data derivatives are 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 framework, resulting in the creation of connectome datasets of unprecedented size. MaPPeRTrac is publicly available and tested on commercial and scientific hardware, so it can accelerate brain connectome research for a broader user community. MaPPeRTrac is available at: https://github.com/LLNL/mappertrac.",
keywords = "Connectomes, Edge density imaging, FAIR, High performance computing, Tractography",
author = "Cai, {Lanya T.} and Joseph Moon and Camacho, {Paul B.} and Anderson, {Aaron T.} and Chwa, {Won Jong} and Brad Sutton and Markowitz, {Amy J.} and Palacios, {Eva M.} and Alexis Rodriguez and Manley, {Geoffrey T.} and Shivsundaram Shankar and Bremer, {Peer Timo} and Pratik Mukherjee and Madduri, {Ravi K.}",
note = "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).\u00A0Geoffrey Manley and Pratik Mukherjee disclose grants from the United States Department of Defense \u2013 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 \u2013 TRACK-TBI (Grant #U01NS086090); and the National Football League (NFL) Scientific Advisory Board \u2013 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 the research efforts of the TRACK-TBI NETWORK. Dr. Manley has also received funding from NeuroTrauma 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. In addition, we are grateful that Sam Payabvash and his group at Yale University School of Medicine have joined the efforts to test the latest release of MaPPeRTrac and pursue its application to a broad range of neuropathological research using EDI and connectomes. The TRACK-TBI Investigators: Shankar Gopinath, MD, Baylor College of Medicine; Ramesh Grandhi, MD MS, University of Utah; C. Dirk Keene, MD PhD, University of Washington; Michael McCrea, PhD, Medical College of Wisconsin; Randall Merchant, PhD, Virginia Commonwealth University; Laura B. Ngwenya, MD, PhD, University of Cincinnati; Ava Puccio, PhD, University of Pittsburgh; David Schnyer, PhD, UT Austin; Sabrina R. Taylor, PhD, University of California, San Francisco; John K. Yue, MD, University of California, San Francisco; Esther L. Yuh, MD, PhD, University of California, San Francisco; Ross Zafonte, DO, Harvard Medical School. 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 \u2013 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 \u2013 TRACK-TBI (Grant #U01NS086090); and the National Football League (NFL) Scientific Advisory Board \u2013 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 the research efforts of the TRACK-TBI NETWORK. Dr. Manley has also received funding from NeuroTrauma 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. In addition, we are grateful that Sam Payabvash and his group at Yale University School of Medicine have joined the efforts to test the latest release of MaPPeRTrac and pursue its application to a broad range of neuropathological research using EDI and connectomes. The TRACK-TBI Investigators: Shankar Gopinath, MD, Baylor College of Medicine; Ramesh Grandhi, MD MS, University of Utah; C. Dirk Keene, MD PhD, University of Washington; Michael McCrea, PhD, Medical College of Wisconsin; Randall Merchant, PhD, Virginia Commonwealth University; Laura B. Ngwenya, MD, PhD, University of Cincinnati; Ava Puccio, PhD, University of Pittsburgh; David Schnyer, PhD, UT Austin; Sabrina R. Taylor, PhD, University of California, San Francisco; John K. Yue, MD, University of California, San Francisco; Esther L. Yuh, MD, PhD, University of California, San Francisco; Ross Zafonte, DO, Harvard Medical School.",
year = "2024",
month = apr,
doi = "10.1007/s12021-024-09650-0",
language = "English (US)",
volume = "22",
pages = "177--191",
journal = "Neuroinformatics",
issn = "1539-2791",
publisher = "Humana Press",
number = "2",
}