Common Data Elements, Scalable Data Management Infrastructure, and Analytics Workflows for Large-Scale Neuroimaging Studies

被引:6
|
作者
Kuplicki, Rayus [1 ]
Touthang, James [1 ]
Al Zoubi, Obada [1 ]
Mayeli, Ahmad [1 ]
Misaki, Masaya [1 ]
Aupperle, Robin L. [1 ,2 ]
Teague, T. Kent [3 ,4 ,5 ]
McKinney, Brett A. [6 ,7 ]
Paulus, Martin P. [1 ]
Bodurka, Jerzy [1 ,8 ]
机构
[1] Laureate Inst Brain Res, Tulsa, OK 74136 USA
[2] Univ Tulsa, Dept Community Med, Oxley Coll Hlth Sci, Tulsa, OK 74104 USA
[3] Univ Oklahoma, Dept Surg, Sch Community Med, Tulsa, OK USA
[4] Univ Oklahoma, Dept Psychiat, Sch Community Med, Tulsa, OK USA
[5] Oklahoma State Univ, Dept Biochem & Microbiol, Ctr Hlth Sci, Tulsa, OK USA
[6] Univ Tulsa, Dept Math, Tulsa, OK 74104 USA
[7] Univ Tulsa, Tandy Sch Comp Sci, Tulsa, OK 74104 USA
[8] Univ Oklahoma, Stephenson Sch Biomed Engn, Norman, OK 73019 USA
来源
FRONTIERS IN PSYCHIATRY | 2021年 / 12卷
基金
美国国家卫生研究院;
关键词
human brain; neuroimaging; multi-level assessment; large-scale studies; common data element; data processing pipelines; scalable analytics; bids format; MOTION CORRECTION; FMRI; ACCURATE; ROBUST;
D O I
10.3389/fpsyt.2021.682495
中图分类号
R749 [精神病学];
学科分类号
100205 ;
摘要
Neuroscience studies require considerable bioinformatic support and expertise. Numerous high-dimensional and multimodal datasets must be preprocessed and integrated to create robust and reproducible analysis pipelines. We describe a common data elements and scalable data management infrastructure that allows multiple analytics workflows to facilitate preprocessing, analysis and sharing of large-scale multi-level data. The process uses the Brain Imaging Data Structure (BIDS) format and supports MRI, fMRI, EEG, clinical, and laboratory data. The infrastructure provides support for other datasets such as Fitbit and flexibility for developers to customize the integration of new types of data. Exemplar results from 200+ participants and 11 different pipelines demonstrate the utility of the infrastructure.
引用
收藏
页数:12
相关论文
共 47 条
  • [1] Large-scale automated synthesis of human functional neuroimaging data
    Yarkoni, Tal
    Poldrack, Russell A.
    Nichols, Thomas E.
    Van Essen, David C.
    Wager, Tor D.
    NATURE METHODS, 2011, 8 (08) : 665 - U95
  • [2] Reproducible Large-Scale Neuroimaging Studies with the OpenMOLE Workflow Management System
    Passerat-Palmbach, Jonathan
    Reuillon, Romain
    Leclaire, Mathieu
    Makropoulos, Antonios
    Robinson, Emma C.
    Parisot, Sarah
    Rueckert, Daniel
    FRONTIERS IN NEUROINFORMATICS, 2017, 11
  • [3] Robust regression for large-scale neuroimaging studies
    Fritsch, Virgile
    Da Mota, Benoit
    Loth, Eva
    Varoquauxa, Gael
    Banaschewski, Tobias
    Barker, Gareth J.
    Bokde, Arun L. W.
    Bruehl, Ruediger
    Butzek, Brigitte
    Conrod, Patricia
    Flor, Herta
    Garavan, Hugh
    Lemaitre, Herve
    Mann, Karl
    Nees, Frauke
    Paus, Tomas
    Schad, Daniel J.
    Schuemann, Gunter
    Frouin, Vincent
    Poline, Jean-Baptiste
    Thirion, Bertrand
    NEUROIMAGE, 2015, 111 : 431 - 441
  • [4] The benefits of prefetching for large-scale cloud-based neuroimaging analysis workflows
    Hayot-Sasson, Valerie
    Glatard, Tristan
    Rokem, Ariel
    PROCEEDINGS OF 16TH WORKSHOP ON WORKFLOWS IN SUPPORT OF LARGE-SCALE SCIENCE (WORKS21), 2021, : 42 - 49
  • [5] Common data elements and data management: Remedy to cure underpowered preclinical studies
    Lapinlampi, Niina
    Melin, Esbjorn
    Aronica, Eleonora
    Bankstahl, Jens P.
    Becker, Albert
    Bernard, Cristophe
    Gorter, Jan A.
    Grohn, Olli
    Lipsanen, Anu
    Lukasiuk, Katarzyna
    Loescher, Wolfgang
    Paananen, Jussi
    Ravizza, Teresa
    Roncon, Paolo
    Simonato, Michele
    Vezzani, Annamaria
    Kokaia, Merab
    Pitkanen, Asla
    EPILEPSY RESEARCH, 2017, 129 : 87 - 90
  • [6] The Functional Magnetic Resonance Imaging Data Center (fMRIDC): the challenges and rewards of large-scale databasing of neuroimaging studies
    Van Horn, JD
    Grethe, JS
    Kostelec, P
    Woodward, JB
    Aslam, JA
    Rus, D
    Rockmore, D
    Gazzaniga, MS
    PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 2001, 356 (1412) : 1323 - 1339
  • [7] Bridging Cognition and Genetics Using Large-scale Spatial Analysis of Neuroimaging and Neurogenetic Data
    Fox, Andrew S.
    Chang, Luke J.
    Gorgolewski, Krzysztof J.
    Yarkoni, Tal
    BIOLOGICAL PSYCHIATRY, 2015, 77 (09) : 377S - 377S
  • [8] Integrating the BIDS Neuroimaging Data Format and Workflow Optimization for Large-Scale Medical Image Analysis
    Shunxing Bao
    Brian D. Boyd
    Praitayini Kanakaraj
    Karthik Ramadass
    Francisco A. C. Meyer
    Yuqian Liu
    William E. Duett
    Yuankai Huo
    Ilwoo Lyu
    David H. Zald
    Seth A. Smith
    Baxter P. Rogers
    Bennett A. Landman
    Journal of Digital Imaging, 2022, 35 : 1576 - 1589
  • [9] Integrating the BIDS Neuroimaging Data Format and Workflow Optimization for Large-Scale Medical Image Analysis
    Bao, Shunxing
    Boyd, Brian D.
    Kanakaraj, Praitayini
    Ramadass, Karthik
    Meyer, Francisco A. C.
    Liu, Yuqian
    Duett, William E.
    Huo, Yuankai
    Lyu, Ilwoo
    Zald, David H.
    Smith, Seth A.
    Rogers, Baxter P.
    Landman, Bennett A.
    JOURNAL OF DIGITAL IMAGING, 2022, 35 (06) : 1576 - 1589
  • [10] Large-scale analysis of neuroimaging data on commercial clouds with content-aware resource allocation strategies
    Minervini, Massimo
    Rusu, Cristian
    Damiano, Mario
    Tucci, Valter
    Bifone, Angelo
    Gozzi, Alessandro
    Tsaftaris, Sotirios A.
    INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS, 2015, 29 (04): : 473 - 488