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Abstract
We created a set of resources to enable research based on openly-available diffusion MRI (dMRI) data from the Healthy Brain Network (HBN) study. First, we curated the HBN dMRI data (N = 2747) into the Brain Imaging Data Structure and preprocessed it according to best-practices, including denoising and correcting for motion effects, susceptibility-related distortions, and eddy currents. Preprocessed, analysis-ready data was made openly available. Data quality plays a key role in the analysis of dMRI. To optimize QC and scale it to this large dataset, we trained a neural network through the combination of a small data subset scored by experts and a larger set scored by community scientists. The network performs QC highly concordant with that of experts on a held out set (ROC-AUC = 0.947). A further analysis of the neural network demonstrates that it relies on image features with relevance to QC. Altogether, this work both delivers resources to advance transdiagnostic research in brain connectivity and pediatric mental health, and establishes a novel paradigm for automated QC of large datasets.
Measurement(s) | brain white matter |
Technology Type(s) | Diffusion Weighted Magnetic Resonance Imaging |
Sample Characteristic - Organism | Homo sapiens |
Sample Characteristic - Location | contiguous United States of America |
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1 Stanford University, Division of Developmental and Behavioral Pediatrics, Stanford, USA (GRID:grid.168010.e) (ISNI:0000000419368956); Stanford University, Graduate School of Education, Stanford, USA (GRID:grid.168010.e) (ISNI:0000000419368956)
2 Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Lifespan Informatics and Neuroimaging Center (PennLINC), Philadelphia, USA (GRID:grid.25879.31) (ISNI:0000 0004 1936 8972); Perelman School of Medicine, Children’s Hospital of Philadelphia Research Institute, Penn/CHOP Lifespan Brain Institute, Philadelphia, USA (GRID:grid.239552.a) (ISNI:0000 0001 0680 8770); Perelman School of Medicine, University of Pennsylvania, Department of Psychiatry, Philadelphia, USA (GRID:grid.25879.31) (ISNI:0000 0004 1936 8972)
3 Child Mind Institute, Center for the Developing Brain, New York City, USA (GRID:grid.428122.f) (ISNI:0000 0004 7592 9033)
4 Stanford University, Division of Developmental and Behavioral Pediatrics, Stanford, USA (GRID:grid.168010.e) (ISNI:0000000419368956); Stanford University, Graduate School of Education, Stanford, USA (GRID:grid.168010.e) (ISNI:0000000419368956); University of Modena and Reggio Emilia, Department of Biomedical, Metabolic and Neural Sciences, Modena, Italy (GRID:grid.7548.e) (ISNI:0000000121697570)
5 Child Mind Institute, Center for the Developing Brain, New York City, USA (GRID:grid.428122.f) (ISNI:0000 0004 7592 9033); Nathan Kline Institute for Psychiatric Research, Center for Biomedical Imaging and Neuromodulation, Orangeburg, USA (GRID:grid.250263.0) (ISNI:0000 0001 2189 4777)
6 Stanford University, Graduate School of Education, Stanford, USA (GRID:grid.168010.e) (ISNI:0000000419368956); Stanford University, Department of Psychiatry and Behavioral Sciences, School of Medicine, Stanford, USA (GRID:grid.168010.e) (ISNI:0000000419368956); University of Zurich, Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, Zurich, Switzerland (GRID:grid.7400.3) (ISNI:0000 0004 1937 0650); University of Zurich and ETH Zurich, Neuroscience Center Zurich, Zurich, Switzerland (GRID:grid.7400.3) (ISNI:0000 0004 1937 0650)
7 University of Washington, Department of Psychology, Seattle, USA (GRID:grid.34477.33) (ISNI:0000000122986657)
8 Stanford University, Department of Psychiatry and Behavioral Sciences, School of Medicine, Stanford, USA (GRID:grid.168010.e) (ISNI:0000000419368956)
9 Stanford University, Graduate School of Education, Stanford, USA (GRID:grid.168010.e) (ISNI:0000000419368956)
10 Old Dominion University, Norfolk, USA (GRID:grid.261368.8) (ISNI:0000 0001 2164 3177)
11 Carleton University, Northfield, USA (GRID:grid.261368.8)
12 Southern Methodist University, Dallas, USA (GRID:grid.263864.d) (ISNI:0000 0004 1936 7929)
13 University of California-Davis, Davis, USA (GRID:grid.27860.3b) (ISNI:0000 0004 1936 9684)
14 University of Pennsylvania, Philadelphia, USA (GRID:grid.25879.31) (ISNI:0000 0004 1936 8972)
15 Harvard University, Cambridge, USA (GRID:grid.38142.3c) (ISNI:000000041936754X)
16 University of Toronto, Toronto, Canada (GRID:grid.17063.33) (ISNI:0000 0001 2157 2938)
17 Duke University, Durham, USA (GRID:grid.26009.3d) (ISNI:0000 0004 1936 7961)
18 University of Michigan-Ann Arbor, Ann Arbor, USA (GRID:grid.214458.e) (ISNI:0000000086837370)
19 San Diego State University, San Diego, USA (GRID:grid.263081.e) (ISNI:0000 0001 0790 1491); University of California-San Diego, La Jolla, USA (GRID:grid.217200.6) (ISNI:0000 0004 0627 2787)
20 Concordia University, Montréal, Canada (GRID:grid.410319.e) (ISNI:0000 0004 1936 8630)
21 Katholieke Universiteit Leuven, Leuven, Belgium (GRID:grid.5596.f) (ISNI:0000 0001 0668 7884)
22 University of Manchester, Manchester, United Kingdom (GRID:grid.5379.8) (ISNI:0000000121662407)
23 University of Sydney, Camperdown, Australia (GRID:grid.1013.3) (ISNI:0000 0004 1936 834X)
24 University Medical Center Utrecht, Utrecht, Netherlands (GRID:grid.7692.a) (ISNI:0000000090126352)
25 Polytechnique Montreal, Montréal, Canada (GRID:grid.183158.6) (ISNI:0000 0004 0435 3292)
26 University of Rochester, Rochester, USA (GRID:grid.16416.34) (ISNI:0000 0004 1936 9174)
27 National Institute of Mental Health, Bethesda, USA (GRID:grid.416868.5) (ISNI:0000 0004 0464 0574)
28 Centre de Recherche de l’Institut Universitaire en Santé Mentale de Montréal, Montréal, Canada (GRID:grid.420732.0) (ISNI:0000 0001 0621 4067)
29 Linköping university, Linköping, Sweden (GRID:grid.5640.7) (ISNI:0000 0001 2162 9922)
30 Monash University, Clayton, Australia (GRID:grid.1002.3) (ISNI:0000 0004 1936 7857)
31 Temple University, Philadelphia, USA (GRID:grid.264727.2) (ISNI:0000 0001 2248 3398)
32 University of Greenwich, London, United Kingdom (GRID:grid.36316.31) (ISNI:0000 0001 0806 5472)
33 Indiana University-Bloomington, Bloomington, USA (GRID:grid.411377.7) (ISNI:0000 0001 0790 959X)
34 Georgia State University, Atlanta, USA (GRID:grid.256304.6) (ISNI:0000 0004 1936 7400)
35 University College London, London, United Kingdom (GRID:grid.83440.3b) (ISNI:0000000121901201)
36 Imperial College London, London, United Kingdom (GRID:grid.7445.2) (ISNI:0000 0001 2113 8111)
37 Brigham and Women’s Hospital, Boston, USA (GRID:grid.62560.37) (ISNI:0000 0004 0378 8294)
38 University of North Carolina at Chapel Hill, Chapel Hill, USA (GRID:grid.10698.36) (ISNI:0000000122483208)
39 University of Concepción, Concepción, Chile (GRID:grid.5380.e) (ISNI:0000 0001 2298 9663)
40 Universitätsmedizin der Johannes Gutenberg-Universität Mainz, Mainz, Germany (GRID:grid.410607.4)
41 University of Maryland-College Park, College Park, USA (GRID:grid.164295.d) (ISNI:0000 0001 0941 7177)
42 Philipps-Universität Marburg, Marburg, Germany (GRID:grid.10253.35) (ISNI:0000 0004 1936 9756)
43 Columbia University, New York, USA (GRID:grid.21729.3f) (ISNI:0000000419368729)
44 McGill University, Montreal, Canada (GRID:grid.14709.3b) (ISNI:0000 0004 1936 8649)
45 University of Pittsburgh, Pittsburgh, USA (GRID:grid.21925.3d) (ISNI:0000 0004 1936 9000)
46 University of Montréal, Montreal, Quebec, Canada (GRID:grid.14848.31) (ISNI:0000 0001 2292 3357)
47 Universidade de São Paulo, Ribeirão Preto, Brazil (GRID:grid.11899.38) (ISNI:0000 0004 1937 0722)
48 Heinrich-Heine University Dusseldorf, Düsseldorf, Germany (GRID:grid.411327.2) (ISNI:0000 0001 2176 9917)
49 Yale University, New Haven, USA (GRID:grid.47100.32) (ISNI:0000000419368710)
50 University of Chicago, Chicago, USA (GRID:grid.170205.1) (ISNI:0000 0004 1936 7822)
51 Brigham Young University, Provo, USA (GRID:grid.253294.b) (ISNI:0000 0004 1936 9115)
52 Child Mind Institute, New York, USA (GRID:grid.428122.f) (ISNI:0000 0004 7592 9033)
53 Institute of Neurosciences and Medicine, Forschungszentrum Jülich, Jülich, Germany (GRID:grid.8385.6) (ISNI:0000 0001 2297 375X)
54 McLean Hospital, Belmont, USA (GRID:grid.240206.2) (ISNI:0000 0000 8795 072X)
55 University of Oxford, Oxford, United Kingdom (GRID:grid.4991.5) (ISNI:0000 0004 1936 8948)
56 Auburn University, Auburn, USA (GRID:grid.252546.2) (ISNI:0000 0001 2297 8753)
57 Washington University in St Louis, Saint Louis, USA (GRID:grid.4367.6) (ISNI:0000 0001 2355 7002)
58 Université catholique de Louvain, Ottignies-Louvain-la-Neuve, Belgium (GRID:grid.7942.8) (ISNI:0000 0001 2294 713X)
59 University of Texas at Austin, Austin, USA (GRID:grid.89336.37) (ISNI:0000 0004 1936 9924)
60 University of Nottingham, Nottingham, United Kingdom (GRID:grid.4563.4) (ISNI:0000 0004 1936 8868)
61 Wayne State University, Detroit, USA (GRID:grid.254444.7) (ISNI:0000 0001 1456 7807)
62 University of Oslo, Oslo, Norway (GRID:grid.5510.1) (ISNI:0000 0004 1936 8921)
63 University of Michigan, Ann Arbor, USA (GRID:grid.214458.e) (ISNI:0000000086837370)
64 University of Virginia, Charlottesville, USA (GRID:grid.27755.32) (ISNI:0000 0000 9136 933X)
65 Trinity College Dublin, Dublin, Ireland (GRID:grid.8217.c) (ISNI:0000 0004 1936 9705)
66 Linköping University, Linköping, Sweden (GRID:grid.5640.7) (ISNI:0000 0001 2162 9922)
67 Stanford University, Stanford, USA (GRID:grid.168010.e) (ISNI:0000000419368956)
68 University of Cagliari, Cagliari, Italy (GRID:grid.7763.5) (ISNI:0000 0004 1755 3242)
69 Massachusetts General Hospital, Harvard Medical School, Boston, USA (GRID:grid.32224.35) (ISNI:0000 0004 0386 9924)
70 University of Florida, Gainesville, USA (GRID:grid.15276.37) (ISNI:0000 0004 1936 8091)
71 George Mason University, Fairfax, USA (GRID:grid.22448.38) (ISNI:0000 0004 1936 8032)
72 University of Alabama at Birmingham, Birmingham, USA (GRID:grid.265892.2) (ISNI:0000000106344187)
73 Boston University, Boston, USA (GRID:grid.189504.1) (ISNI:0000 0004 1936 7558)
74 Cornell University, Ithaca, USA (GRID:grid.5386.8) (ISNI:000000041936877X)
75 Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany (GRID:grid.419524.f) (ISNI:0000 0001 0041 5028)
76 National Neuroscience Institute, Singapore, Singapore (GRID:grid.276809.2) (ISNI:0000 0004 0636 696X)
77 University of Colorado School of Medicine, Aurora, USA (GRID:grid.430503.1) (ISNI:0000 0001 0703 675X)
78 Massachusetts Institute of Technology, Cambridge, USA (GRID:grid.116068.8) (ISNI:0000 0001 2341 2786)
79 Western Unviersity, London, Canada (GRID:grid.116068.8)
80 Psychological Institute of Russian Academy of Education, Moscow, Russia (GRID:grid.466465.3)
81 University of Illinois Urbana-Champaign, Champaign, USA (GRID:grid.35403.31) (ISNI:0000 0004 1936 9991)
82 University of Washington, Department of Psychology, Seattle, USA (GRID:grid.34477.33) (ISNI:0000000122986657); University of Washington, eScience Institute, Seattle, USA (GRID:grid.34477.33) (ISNI:0000000122986657)