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 require many software packages with complex dependencies and high computational cost. We developed MaPPeRTrac, a diffusion MRI tractography pipeline that si...
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| Veröffentlicht in: | bioRxiv |
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| Hauptverfasser: | , , , , , , , , |
| Format: | Paper |
| Sprache: | Englisch |
| Veröffentlicht: |
Cold Spring Harbor
Cold Spring Harbor Laboratory Press
24.12.2020
Cold Spring Harbor Laboratory |
| Ausgabe: | 1.3 |
| Schlagworte: | |
| ISSN: | 2692-8205, 2692-8205 |
| Online-Zugang: | Volltext |
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| Zusammenfassung: | Abstract Large scale diffusion MRI tractography remains a significant challenge. Users must orchestrate a complex sequence of instructions that require many software packages with complex dependencies and high computational cost. We developed MaPPeRTrac, a diffusion MRI tractography pipeline that simplifies and vastly accelerates this process on a wide range of high performance computing environments. It fully automates the entire tractography workflow, from management of raw MRI machine data to edge-density visualization of the connectome. Data and dependencies, handled by the Brain Imaging Data Structure (BIDS) and Containerization using Docker and Singularity, are de-coupled from code to enable rapid prototyping and modification. Data artifacts are designed to be findable, accessible, inter-operable, and reusable in accordance with FAIR principles. The pipeline takes full advantage of HPC resources using the Parsl parallel programming framework, resulting in 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 discloses 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 * A collaboration between the U.S. Department of Energy and TRACK-TBI1 * 1 Transforming Research and Clinical Knowledge in Traumatic Brain Injury |
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| Bibliographie: | SourceType-Working Papers-1 ObjectType-Working Paper/Pre-Print-1 content type line 50 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. |
| ISSN: | 2692-8205 2692-8205 |
| DOI: | 10.1101/2020.12.23.424191 |