BrainForge: An online data analysis platform for integrative neuroimaging acquisition, analysis, and sharing

被引：2
作者：
Verner, Eric [1 ]
Petropoulos, Helen [1 ]
Baker, Bradley [1 ]
Bockholt, Henry Jeremy [1 ]
Fries, Jill [1 ]
Bohsali, Anastasia [1 ]
Raja, Rajikha [2 ]
Duc Hoai Trinh [1 ]
Calhoun, Vince [1 ]
机构：
[1] Triinst Ctr Translat Res Neuroimaging & Data Sci, Atlanta, GA 30322 USA
[2] Univ Arkansas Med Sci, Dept Radiol, Little Rock, AR 72205 USA
来源：
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE | 2023年 / 35卷 / 18期
基金：
美国国家科学基金会; 美国国家卫生研究院;
关键词：
cloud computing; containerization; high performance computing; neuroimaging; SOFTWARE; VISUALIZATION; MOVEMENT; IMAGES; TOOL;
D O I：
10.1002/cpe.6855
中图分类号：
TP31 [计算机软件];
学科分类号：
081202 ; 0835 ;
摘要：
BrainForge is a cloud-enabled, web-based analysis platform for neuroimaging research. This website allows users to archive data from a study and effortlessly process data on a high-performance computing cluster. After analyses are completed, results can be quickly shared with colleagues. BrainForge solves multiple problems for researchers who want to analyze neuroimaging data, including issues related to software, reproducibility, computational resources, and data sharing. BrainForge can currently process structural, functional, diffusion, and arterial spin labeling MRI modalities, including preprocessing and group level analyses. Additional pipelines are currently being added, and the pipelines can accept the BIDS format. Analyses are conducted completely inside of Singularity containers and utilize popular software packages including Nipype, Statistical Parametric Mapping, the Group ICA of fMRI Toolbox, and FreeSurfer. BrainForge also features several interfaces for group analysis, including a fully automated adaptive ICA approach.
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页数：11
相关论文
共 46 条
  • [1] Software as a Service for Data Scientists
    Allen, Bryce
    Bresnahan, John
    Childers, Lisa
    Foster, Ian
    Kandaswamy, Gopi
    Kettimuthu, Raj
    Kordas, Jack
    Link, Mike
    Martin, Stuart
    Pickett, Karl
    Tuecke, Steven
    [J]. COMMUNICATIONS OF THE ACM, 2012, 55 (02) : 81 - 88
  • [2] Tracking Whole-Brain Connectivity Dynamics in the Resting State
    Allen, Elena A.
    Damaraju, Eswar
    Plis, Sergey M.
    Erhardt, Erik B.
    Eichele, Tom
    Calhoun, Vince D.
    [J]. CEREBRAL CORTEX, 2014, 24 (03) : 663 - 676
  • [3] A baseline for the multivariate comparison of resting-state networks
    Allen, Elena A.
    Erhardt, Erik B.
    Damaraju, Eswar
    Gruner, William
    Segall, Judith M.
    Silva, Rogers F.
    Havlicek, Martin
    Rachakonda, Srinivas
    Fries, Jill
    Kalyanam, Ravi
    Michael, Andrew M.
    Caprihan, Arvind
    Turner, Jessica A.
    Eichele, Tom
    Adelsheim, Steven
    Bryan, Angela D.
    Bustillo, Juan
    Clark, Vincent P.
    Ewing, Sarah W. Feldstein
    Filbey, Francesca
    Ford, Corey C.
    Hutchison, Kent
    Jung, Rex E.
    Kiehl, Kent A.
    Kodituwakku, Piyadasa
    Komesu, Yuko M.
    Mayer, Andrew R.
    Pearlson, Godfrey D.
    Phillips, John P.
    Sadek, Joseph R.
    Stevens, Michael
    Teuscher, Ursina
    Thoma, Robert J.
    Calhoun, Vince D.
    [J]. FRONTIERS IN SYSTEMS NEUROSCIENCE, 2011, 5
  • [4] Towards a comprehensive framework for movement and distortion correction of diffusion MR images: Within volume movement
    Andersson, Jesper L. R.
    Graham, Mark S.
    Drobnjak, Ivana
    Zhang, Hui
    Filippini, Nicola
    Bastiani, Matteo
    [J]. NEUROIMAGE, 2017, 152 : 450 - 466
  • [5] An integrated approach to correction for off-resonance effects and subject movement in diffusion MR imaging
    Andersson, Jesper L. R.
    Sotiropoulos, Stamatios N.
    [J]. NEUROIMAGE, 2016, 125 : 1063 - 1078
  • [6] How to correct susceptibility distortions in spin-echo echo-planar images: application to diffusion tensor imaging
    Andersson, JLR
    Skare, S
    Ashburner, J
    [J]. NEUROIMAGE, 2003, 20 (02) : 870 - 888
  • [7] [Anonymous], 2010, REC PASSW BAS KEY 1
  • [8] Voxel-based morphometry - The methods
    Ashburner, J
    Friston, KJ
    [J]. NEUROIMAGE, 2000, 11 (06) : 805 - 821
  • [9] Ashburner J., 2014, SPM12 MANUAL, V2464
  • [10] The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services
    Avesani, Paolo
    McPherson, Brent
    Hayashi, Soichi
    Caiafa, Cesar F.
    Henschel, Robert
    Garyfallidis, Eleftherios
    Kitchell, Lindsey
    Bullock, Daniel
    Patterson, Andrew
    Olivetti, Emanuele
    Sporns, Olaf
    Saykin, Andrew J.
    Wang, Lei
    Dinov, Ivo
    Hancock, David
    Caron, Bradley
    Qian, Yiming
    Pestilli, Franco
    [J]. SCIENTIFIC DATA, 2019, 6 (1)
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