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Clarmann von Clarenau V, Appelhoff S, Pachur T, Spitzer B. Over- and underweighting of extreme values in decisions from sequential samples. J Exp Psychol Gen 2024; 153:814-826. [PMID: 38271014 DOI: 10.1037/xge0001530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
People routinely make decisions based on samples of numerical values. A common conclusion from the literature in psychophysics and behavioral economics is that observers subjectively compress magnitudes, such that extreme values have less sway over people's decisions than prescribed by a normative model (underweighting). However, recent studies have reported evidence for anti-compression, that is, the relative overweighting of extreme values. Here, we investigate potential reasons for this discrepancy in findings and propose that it might reflect adaptive responses to different task requirements. We performed a large-scale study (n = 586) of sequential numerical integration, manipulating (a) the task requirement (averaging a single stream or comparing two interleaved streams of numbers), (b) the distribution of sample values (uniform or Gaussian), and (c) their range (1-9 or 100-900). The data showed compression of subjective values in the averaging task, but anticompression in the comparison task. This pattern held for both distribution types and for both ranges. In model simulations, we show that either compression or anticompression can be beneficial for noisy observers, depending on the sample-level processing demands imposed by the task. This suggests that the empirically observed patterns of over- and underweighting might reflect adaptive responses. (PsycInfo Database Record (c) 2024 APA, all rights reserved).
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Affiliation(s)
| | - Stefan Appelhoff
- Center for Adaptive Rationality, Max Planck Institute for Human Development
| | - Thorsten Pachur
- Center for Adaptive Rationality, Max Planck Institute for Human Development
| | - Bernhard Spitzer
- Center for Adaptive Rationality, Max Planck Institute for Human Development
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2
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Poldrack RA, Markiewicz CJ, Appelhoff S, Ashar YK, Auer T, Baillet S, Bansal S, Beltrachini L, Benar CG, Bertazzoli G, Bhogawar S, Blair RW, Bortoletto M, Boudreau M, Brooks TL, Calhoun VD, Castelli FM, Clement P, Cohen AL, Cohen-Adad J, D'Ambrosio S, de Hollander G, de la Iglesia-Vayá M, de la Vega A, Delorme A, Devinsky O, Draschkow D, Duff EP, DuPre E, Earl E, Esteban O, Feingold FW, Flandin G, Galassi A, Gallitto G, Ganz M, Gau R, Gholam J, Ghosh SS, Giacomel A, Gillman AG, Gleeson P, Gramfort A, Guay S, Guidali G, Halchenko YO, Handwerker DA, Hardcastle N, Herholz P, Hermes D, Honey CJ, Innis RB, Ioanas HI, Jahn A, Karakuzu A, Keator DB, Kiar G, Kincses B, Laird AR, Lau JC, Lazari A, Legarreta JH, Li A, Li X, Love BC, Lu H, Marcantoni E, Maumet C, Mazzamuto G, Meisler SL, Mikkelsen M, Mutsaerts H, Nichols TE, Nikolaidis A, Nilsonne G, Niso G, Norgaard M, Okell TW, Oostenveld R, Ort E, Park PJ, Pawlik M, Pernet CR, Pestilli F, Petr J, Phillips C, Poline JB, Pollonini L, Raamana PR, Ritter P, Rizzo G, Robbins KA, Rockhill AP, Rogers C, Rokem A, Rorden C, Routier A, Saborit-Torres JM, Salo T, Schirner M, Smith RE, Spisak T, Sprenger J, Swann NC, Szinte M, Takerkart S, Thirion B, Thomas AG, Torabian S, Varoquaux G, Voytek B, Welzel J, Wilson M, Yarkoni T, Gorgolewski KJ. The Past, Present, and Future of the Brain Imaging Data Structure (BIDS). ArXiv 2024:arXiv:2309.05768v2. [PMID: 37744469 PMCID: PMC10516110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown over time. We outline the principles behind the project, the mechanisms by which it has been extended, and some of the challenges being addressed as it evolves. We also discuss the lessons learned through the project, with the aim of enabling researchers in other domains to learn from the success of BIDS.
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Affiliation(s)
| | | | | | - Yoni K Ashar
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Tibor Auer
- School of Psychology, University of Surrey, Guildford, UK
- Artificial Intelligence and Informatics group, Rosalind Franklin Institute, Harwell Campus, Didcot, UK
| | - Sylvain Baillet
- McConnell Brain Imaging Centre, Montréal Neurological Institute, McGill University, Montréal, Canada
| | - Shashank Bansal
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Leandro Beltrachini
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Physics and Astronomy, Cardiff University, Wales, UK
| | - Christian G Benar
- Aix Marseille Université, INSERM, INS, Inst Neurosci Syst, Marseille, France
| | - Giacomo Bertazzoli
- Neurophysiology Lab, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
- Center for Mind/Brain Sciences - CIMeC, University of Trento, Rovereto, TN, Italy
- Brigham and Women's Hospital, Boston, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Ross W Blair
- Department of Psychology, Stanford University, Stanford, CA, USA
| | - Marta Bortoletto
- Neurophysiology Lab, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | | | - Teon L Brooks
- Department of Psychology, Stanford University, Stanford, CA, USA
| | - Vince D Calhoun
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State, Georgia Tech, Emory, Atlanta, GA, USA
| | - Filippo Maria Castelli
- European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy
- Bioretics srl, Cesena, Italy
| | - Patricia Clement
- Department of Medical Imaging, Ghent University Hospital, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Alexander L Cohen
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | | | - Sasha D'Ambrosio
- Dipartimento di Scienze della Salute dell'Università degli Studi di Milano, Milan, Italy
- Department of Clinical and Experimental Epilepsy, University College London, UK
| | - Gilles de Hollander
- Zurich Center for Neuroeconomics, Department of Economics, University of Zurich, Zurich, Switzerland
| | | | | | - Arnaud Delorme
- SCCN, University of California, San Diego, La Jolla CA USA
| | - Orrin Devinsky
- Department of Neurology, NYU Langone Medical Center, New York, NY, USA
| | - Dejan Draschkow
- Department of Experimental Psychology, University of Oxford, Oxford, UK
| | - Eugene Paul Duff
- UK Dementia Research Institute, Department of Brain Sciences, Imperial College London, London, UK
| | - Elizabeth DuPre
- Department of Psychology, Stanford University, Stanford, CA, USA
| | - Eric Earl
- Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
| | - Oscar Esteban
- Department of Radiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - Guillaume Flandin
- Wellcome Centre for Human Neuroimaging, University College London, London, England, UK
| | - Anthony Galassi
- Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
| | - Giuseppe Gallitto
- Center for Translational Neuro- and Behavioral Sciences, University Medicine Essen, Essen, Germany
- Department of Neurology, University Medicine Essen, Essen, Germany
| | - Melanie Ganz
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
- Neurobiology Research Unit, Copenhagen University Hospital, Copenhagen, Denmark
| | - Rémi Gau
- Origamin Lab, The Neuro, McGill University, Montreal, Quebec, Canada
| | - James Gholam
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Wales, UK
| | | | - Alessio Giacomel
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, England, UK
| | - Ashley G Gillman
- The Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, Townsville, Queensland, Australia
| | - Padraig Gleeson
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, England, UK
| | | | - Samuel Guay
- Université de Montréal, Montréal, QC, Canada
| | - Giacomo Guidali
- Department of Psychology & NeuroMI - Milan Centre for Neuroscience, University of Milano-Bicocca, Milan, Italy
| | - Yaroslav O Halchenko
- Center for Open Neuroscience, Department of Psychological and Brain Sciences, Dartmouth College, NH, USA
| | - Daniel A Handwerker
- Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
| | - Nell Hardcastle
- Department of Psychology, Stanford University, Stanford, CA, USA
| | - Peer Herholz
- McConnell Brain Imaging Centre, Montréal Neurological Institute, McGill University, Montréal, Quebec, Canada
| | - Dora Hermes
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Christopher J Honey
- Department of Psychological & Brain Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Robert B Innis
- Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
| | - Horea-Ioan Ioanas
- Center for Open Neuroscience, Department of Psychological and Brain Sciences, Dartmouth College, NH, USA
| | - Andrew Jahn
- Functional MRI Laboratory, University of Michigan, Ann Arbor, MI, USA
| | - Agah Karakuzu
- NeuroPoly Lab, Polytechnique Montréal, Montréal, Quebec, Canada
| | - David B Keator
- Change Your Brain Change Your Life Foundation, Costa Mesa, CA, USA
- Amen Clinics, Costa Mesa, CA, USA
- Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, CA, USA
| | - Gregory Kiar
- Center for Data Analytics, Innovation, and Rigor, Child Mind Institute, New York, NY USA
| | - Balint Kincses
- Center for Translational Neuro- and Behavioral Sciences, University Medicine Essen, Essen, Germany
- Department of Neurology, University Medicine Essen, Essen, Germany
| | - Angela R Laird
- Department of Physics, Florida International University, Miami, FL, USA
| | - Jonathan C Lau
- Department of Clinical Neurological Sciences, Western University, London, Ontario, Canada
| | - Alberto Lazari
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Jon Haitz Legarreta
- Department of Radiology, Brigham and Women's Hospital, Mass General Brigham/Harvard Medical School, Boston, MA, USA
| | - Adam Li
- Columbia University, New York, NY, USA
| | - Xiangrui Li
- Center for Cognitive and Behavioral Brain Imaging, The Ohio State University, Columbus, OH, USA
| | | | - Hanzhang Lu
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eleonora Marcantoni
- School for Psychology and Neuroscience and Centre for Cognitive Neuroimaging, University of Glasgow, Glasgow
| | - Camille Maumet
- Inria, Univ Rennes, CNRS, Inserm, IRISA UMR 6074, Empenn ERL U 1228, Rennes, France
| | - Giacomo Mazzamuto
- National Research Council - National Institute of Optics (CNR-INO), Florence, Italy
| | - Steven L Meisler
- Program in Speech and Hearing Bioscience and Technology, Harvard University, Cambridge, MA, USA
| | - Mark Mikkelsen
- Department of Radiology, Weill Cornell Medicine, New York, NY, USA
| | - Henk Mutsaerts
- Radiology and Nuclear Medicine, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Brain Imaging, Amsterdam, The Netherlands
| | - Thomas E Nichols
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Aki Nikolaidis
- Center for the Developing Brain, Child Mind Institute, New York, NY, USA
| | - Gustav Nilsonne
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Swedish National Data Service, Gothenburg University, Gothenburg, Sweden
| | | | - Martin Norgaard
- Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Thomas W Okell
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Robert Oostenveld
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands
- NatMEG, Karolinska Institutet, Stockholm, Sweden
| | - Eduard Ort
- Heinrich Heine University, Department of Biological Psychology of Decision Making, Düsseldorf, Germany
| | | | - Mateusz Pawlik
- Paris-Lodron-University of Salzburg, Department of Psychology, Centre for Cognitive Neuroscience, Salzburg, Austria
| | - Cyril R Pernet
- Neurobiology Research Unit, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Jan Petr
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
| | | | - Jean-Baptiste Poline
- Neuro Data Science ORIGAMI Laboratory, McConnell Brain Imaging Centre, Faculty of Medicine, McGill University, Montréal, Canada
| | - Luca Pollonini
- Department of Engineering Technology, University of Houston, Houston, TX
- Basque Center on Cognition, Brain and Language, Donostia-San Sebastián, Spain
| | | | - Petra Ritter
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Charitéplatz 1, Berlin 10117, Germany
- Department of Neurology with Experimental Neurology, Charité, Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charitéplatz 1, Berlin 10117, Germany
- Bernstein Focus State Dependencies of Learning and Bernstein Center for Computational Neuroscience, Berlin, Germany
- Einstein Center for Neuroscience Berlin, Charitéplatz 1, Berlin 10117, Germany
- Einstein Center Digital Future, Wilhelmstraße 67, Berlin 10117, Germany
| | - Gaia Rizzo
- Invicro, London, UK
- Division of Brain Sciences, Imperial College London, London, UK
| | - Kay A Robbins
- Department of Computer Science, University of Texas at San Antonio, San Antonio, TX, USA
| | - Alexander P Rockhill
- Department of Neurosurgery, Oregon Health & Science University, Portland, OR, USA
| | - Christine Rogers
- McGill Centre for Integrative Neuroscience (MCIN), Montréal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Ariel Rokem
- University of Washington, Department of Psychology and eScience Institute, Seattle, WA, USA
| | - Chris Rorden
- University of South Carolina, Department of Psychology, Columbia, SC, USA
| | | | | | - Taylor Salo
- Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael Schirner
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Charitéplatz 1, Berlin 10117, Germany
- Department of Neurology with Experimental Neurology, Charité, Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charitéplatz 1, Berlin 10117, Germany
- Bernstein Focus State Dependencies of Learning and Bernstein Center for Computational Neuroscience, Berlin, Germany
- Einstein Center for Neuroscience Berlin, Charitéplatz 1, Berlin 10117, Germany
- Einstein Center Digital Future, Wilhelmstraße 67, Berlin 10117, Germany
| | - Robert E Smith
- The Florey Institute of Neuroscience and Mental Health, Heidelberg, Victoria, Australia
- The Florey Department of Neuroscience and Mental Heath, The University of Melbourne, Parkville, Victoria, Australia
| | - Tamas Spisak
- Center for Translational Neuro- and Behavioral Sciences, University Medicine Essen, Essen, Germany
- Institute for Diagnostic and Interventional Radiology and Neuroradiology, University Medicine Essen, Essen, Germany
| | - Julia Sprenger
- Institut de Neurosciences de la Timone (INT), UMR7289, CNRS, Aix-Marseille Université, France
| | - Nicole C Swann
- University of Oregon, Department of Human Physiology, Eugene, OR, USA
| | - Martin Szinte
- Institut de Neurosciences de la Timone (INT), UMR7289, CNRS, Aix-Marseille Université, France
| | - Sylvain Takerkart
- Institut de Neurosciences de la Timone (INT), UMR7289, CNRS, Aix-Marseille Université, France
| | | | - Adam G Thomas
- Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
| | | | | | - Bradley Voytek
- Department of Cognitive Science, Halıcıoğlu Data Science Institute, and Neurosciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | | | - Martin Wilson
- University of Birmingham, Centre for Human Brain Health and School of Psychology, Birmingham, UK
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3
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Keller O, Appelhoff S, Paffhausen B, Wenzel T. Development and Sharing of Open Science Hardware: Lessons Learned from Wikimedia Fellowships. RIO 2023. [DOI: 10.3897/rio.9.e95174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The promise of open hardware as a branch of open science is a sustainable change of research instrumentation towards more openly documented and licensed designs. Methods, code, and data are already valued by journal editors and peer-reviews to judge if a study's result can be replicated with the information provided in a manuscript. The open hardware movement seeks to include laboratory tools and research instrumentation into the same category. Availability of and access to open hardware equipment are set to democratize professional lab work and field studies as well as enhance the transferability of methods to civic science settings. Here, we report four case studies from the first five years of the Wikimedia Program "Free Knowledge", an open science fellowship funded by Wikimedia Germany and partners. The project developers discuss and evaluate the impact related to key aspects typically attributed with open hardware: costs, availability, adaptability, community and educational value. The open hardware projects covered in this review span from natural sciences to life sciences to education.
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4
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Niso G, Botvinik-Nezer R, Appelhoff S, De La Vega A, Esteban O, Etzel JA, Finc K, Ganz M, Gau R, Halchenko YO, Herholz P, Karakuzu A, Keator DB, Markiewicz CJ, Maumet C, Pernet CR, Pestilli F, Queder N, Schmitt T, Sójka W, Wagner AS, Whitaker KJ, Rieger JW. Open and reproducible neuroimaging: From study inception to publication. Neuroimage 2022; 263:119623. [PMID: 36100172 PMCID: PMC10008521 DOI: 10.1016/j.neuroimage.2022.119623] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/17/2022] [Accepted: 09/09/2022] [Indexed: 10/31/2022] Open
Abstract
Empirical observations of how labs conduct research indicate that the adoption rate of open practices for transparent, reproducible, and collaborative science remains in its infancy. This is at odds with the overwhelming evidence for the necessity of these practices and their benefits for individual researchers, scientific progress, and society in general. To date, information required for implementing open science practices throughout the different steps of a research project is scattered among many different sources. Even experienced researchers in the topic find it hard to navigate the ecosystem of tools and to make sustainable choices. Here, we provide an integrated overview of community-developed resources that can support collaborative, open, reproducible, replicable, robust and generalizable neuroimaging throughout the entire research cycle from inception to publication and across different neuroimaging modalities. We review tools and practices supporting study inception and planning, data acquisition, research data management, data processing and analysis, and research dissemination. An online version of this resource can be found at https://oreoni.github.io. We believe it will prove helpful for researchers and institutions to make a successful and sustainable move towards open and reproducible science and to eventually take an active role in its future development.
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Affiliation(s)
- Guiomar Niso
- Psychological & Brain Sciences, Indiana University, Bloomington, IN, USA; Universidad Politecnica de Madrid, Madrid and CIBER-BBN, Spain; Instituto Cajal, CSIC, Madrid, Spain.
| | - Rotem Botvinik-Nezer
- Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USA.
| | - Stefan Appelhoff
- Center for Adaptive Rationality, Max Planck Institute for Human Development, Berlin, Germany
| | | | - Oscar Esteban
- Dept. of Radiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland; Department of Psychology, Stanford University, Stanford, CA, USA
| | - Joset A Etzel
- Department of Psychological and Brain Sciences, Washington University in St. Louis, St. Louis, MO, USA
| | - Karolina Finc
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
| | - Melanie Ganz
- Neurobiology Research Unit, Rigshospitalet, Copenhagen, Denmark; Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Rémi Gau
- Institute of Psychology, Université catholique de Louvain, Louvain la Neuve, Belgium
| | - Yaroslav O Halchenko
- Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USA
| | - Peer Herholz
- Montreal Neurological Institute-Hospital, McGill University, Montréal, Quebec, Canada
| | - Agah Karakuzu
- Biomedical Engineering Institute, Polytechnique Montréal, Montréal, Quebec, Canada; Montréal Heart Institute, Montréal, Quebec, Canada
| | - David B Keator
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA, USA
| | | | - Camille Maumet
- Inria, Univ Rennes, CNRS, Inserm - IRISA UMR 6074, Empenn ERL U 1228, Rennes, France
| | - Cyril R Pernet
- Neurobiology Research Unit, Rigshospitalet, Copenhagen, Denmark
| | - Franco Pestilli
- Psychological & Brain Sciences, Indiana University, Bloomington, IN, USA; Department of Psychology, The University of Texas at Austin, Austin, TX, USA
| | - Nazek Queder
- Montreal Neurological Institute-Hospital, McGill University, Montréal, Quebec, Canada; Department of Neurobiology and Behavior, University of California, Irvine, CA, USA
| | - Tina Schmitt
- Neuroimaging Unit, Carl-von-Ossietzky Universität, Oldenburg, Germany
| | - Weronika Sójka
- Faculty of Philosophy and Social Sciences, Nicolaus Copernicus University, Toruń, Poland
| | - Adina S Wagner
- Institute for Neuroscience and Medicine, Research Centre Juelich, Germany
| | | | - Jochem W Rieger
- Neuroimaging Unit, Carl-von-Ossietzky Universität, Oldenburg, Germany; Department of Psychology, Carl-von-Ossietzky Universität, Oldenburg, Germany.
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5
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Karakuzu A, Appelhoff S, Auer T, Boudreau M, Feingold F, Khan AR, Lazari A, Markiewicz C, Mulder M, Phillips C, Salo T, Stikov N, Whitaker K, de Hollander G. qMRI-BIDS: An extension to the brain imaging data structure for quantitative magnetic resonance imaging data. Sci Data 2022; 9:517. [PMID: 36002444 PMCID: PMC9402561 DOI: 10.1038/s41597-022-01571-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 07/19/2022] [Indexed: 11/16/2022] Open
Abstract
The Brain Imaging Data Structure (BIDS) established community consensus on the organization of data and metadata for several neuroimaging modalities. Traditionally, BIDS had a strong focus on functional magnetic resonance imaging (MRI) datasets and lacked guidance on how to store multimodal structural MRI datasets. Here, we present and describe the BIDS Extension Proposal 001 (BEP001), which adds a range of quantitative MRI (qMRI) applications to the BIDS. In general, the aim of qMRI is to characterize brain microstructure by quantifying the physical MR parameters of the tissue via computational, biophysical models. By proposing this new standard, we envision standardization of qMRI through multicenter dissemination of interoperable datasets. This way, BIDS can act as a catalyst of convergence between qMRI methods development and application-driven neuroimaging studies that can help develop quantitative biomarkers for neural tissue characterization. In conclusion, this BIDS extension offers a common ground for developers to exchange novel imaging data and tools, reducing the entrance barrier for qMRI in the field of neuroimaging.
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Affiliation(s)
- Agah Karakuzu
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montréal, QC, Canada. .,Montreal Heart Institute, Montreal, QC, Canada.
| | - Stefan Appelhoff
- Center for Adaptive Rationality, Max Planck Institute for Human Development, Berlin, Germany
| | - Tibor Auer
- NeuroModulation Lab, School of Psychology, University of Surrey, Guildford, UK
| | - Mathieu Boudreau
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montréal, QC, Canada.,Montreal Heart Institute, Montreal, QC, Canada
| | | | - Ali R Khan
- Department of Medical Biophysics, Robarts Research Institute, University of Western Ontario, London, Canada
| | - Alberto Lazari
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | | | - Martijn Mulder
- Department of Experimental Psychology, Utrecht University, Utrecht, the Netherlands
| | - Christophe Phillips
- GIGA Cyclotron Research Centre in vivo imaging, GIGA Institute, University of Liège, Liège, Belgium
| | - Taylor Salo
- Florida International University, Miami, FL, USA
| | - Nikola Stikov
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montréal, QC, Canada.,Montreal Heart Institute, Montreal, QC, Canada.,Center for Advanced Interdisciplinary Research, Ss. Cyril and Methodius University, Skopje, North Macedonia
| | | | - Gilles de Hollander
- Zurich Center for Neuroeconomics (ZNE), Department of Economics, University of Zurich, Zurich, Switzerland. .,Spinoza Centre for Neuroimaging, Amsterdam, The Netherlands.
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6
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Appelhoff S, Hertwig R, Spitzer B. Control over sampling boosts numerical evidence processing in human decisions from experience. Cereb Cortex 2022; 33:207-221. [PMID: 35266973 PMCID: PMC9758588 DOI: 10.1093/cercor/bhac062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/30/2022] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
When acquiring information about choice alternatives, decision makers may have varying levels of control over which and how much information they sample before making a choice. How does control over information acquisition affect the quality of sample-based decisions? Here, combining variants of a numerical sampling task with neural recordings, we show that control over when to stop sampling can enhance (i) behavioral choice accuracy, (ii) the build-up of parietal decision signals, and (iii) the encoding of numerical sample information in multivariate electroencephalogram patterns. None of these effects were observed when participants could only control which alternatives to sample, but not when to stop sampling. Furthermore, levels of control had no effect on early sensory signals or on the extent to which sample information leaked from memory. The results indicate that freedom to stop sampling can amplify decisional evidence processing from the outset of information acquisition and lead to more accurate choices.
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Affiliation(s)
- Stefan Appelhoff
- Corresponding author: Center for Adaptive Rationality, Max Planck Institute for Human Development, Lentzeallee 94, 14195 Berlin, Germany.
| | - Ralph Hertwig
- Center for Adaptive Rationality, Max Planck Institute for Human Development, Lentzeallee 94, 14195 Berlin, Germany
| | - Bernhard Spitzer
- Center for Adaptive Rationality, Max Planck Institute for Human Development, Lentzeallee 94, 14195 Berlin, Germany,Research Group Adaptive Memory and Decision Making, Max Planck Institute for Human Development, Lentzeallee 94, 14195 Berlin, Germany
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7
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Norgaard M, Matheson GJ, Hansen HD, Thomas A, Searle G, Rizzo G, Veronese M, Giacomel A, Yaqub M, Tonietto M, Funck T, Gillman A, Boniface H, Routier A, Dalenberg JR, Betthauser T, Feingold F, Markiewicz CJ, Gorgolewski KJ, Blair RW, Appelhoff S, Gau R, Salo T, Niso G, Pernet C, Phillips C, Oostenveld R, Gallezot JD, Carson RE, Knudsen GM, Innis RB, Ganz M. PET-BIDS, an extension to the brain imaging data structure for positron emission tomography. Sci Data 2022; 9:65. [PMID: 35236846 PMCID: PMC8891322 DOI: 10.1038/s41597-022-01164-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/11/2022] [Indexed: 11/15/2022] Open
Affiliation(s)
- Martin Norgaard
- Neurobiology Research Unit, Rigshospitalet, and Institute of Clinical Medicine, Univ. Copenhagen, København, Denmark.,Department of Psychology, Stanford University, California, USA
| | - Granville J Matheson
- Department of Psychiatry, Columbia University, New York, NY, 10032, USA.,Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet and Stockholm Health Care Services, Stockholm, Sweden
| | - Hanne D Hansen
- Neurobiology Research Unit, Rigshospitalet, and Institute of Clinical Medicine, Univ. Copenhagen, København, Denmark.,Athinoula A. Martinos Center for Biomedical Imaging, MGH/HST, Charlestown, MA, USA
| | - Adam Thomas
- Intramural Research Program, NIMH, Bethesda, USA
| | - Graham Searle
- Invicro and Division of Brain Sciences, Imperial College London, London, UK
| | - Gaia Rizzo
- Invicro and Division of Brain Sciences, Imperial College London, London, UK
| | - Mattia Veronese
- Centre for Neuroimaging Sciences, King's College London, London, UK.,Department of Information Engineering, University of Padua, Padua, Italy
| | - Alessio Giacomel
- Centre for Neuroimaging Sciences, King's College London, London, UK
| | - Maqsood Yaqub
- Amsterdam UMC, location VUmc, department of radiology and nuclear medicine, Amsterdam, Netherlands
| | - Matteo Tonietto
- Université Paris-Saclay, CEA, CNRS, Inserm, BioMaps, Service Hospitalier Frédéric Joliot, Orsay, France
| | - Thomas Funck
- INM-1, Jülich Forschungszentrum, Jülich, Germany
| | - Ashley Gillman
- Aust. e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, Townsville, Australia
| | - Hugo Boniface
- Centre d'Acquisition et de Traitement des Images, CEA, Paris, France
| | - Alexandre Routier
- Inria, Aramis project-team, Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtriére, Paris, France
| | - Jelle R Dalenberg
- Department of Neurology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Tobey Betthauser
- Wisconsin Alzheimer's Disease Research Center, Division of Geriatrics, Department of Medicine, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | | | | | | | - Ross W Blair
- Department of Psychology, Stanford University, California, USA
| | - Stefan Appelhoff
- Center for Adaptive Rationality, Max Planck Institute for Human Development, Berlin, Germany
| | - Remi Gau
- Institute of psychology, Université catholique de Louvain, Louvain la Neuve, Belgium
| | - Taylor Salo
- Department of Psychology, Florida International University, Miami, FL, USA
| | - Guiomar Niso
- Psychological Brain Sciences, Indiana University, Bloomington, IN, USA
| | - Cyril Pernet
- Neurobiology Research Unit, Rigshospitalet, and Institute of Clinical Medicine, Univ. Copenhagen, København, Denmark
| | - Christophe Phillips
- GIGA Cyclotron Research Centre in vivo imaging, University of Liege, Liege, Belgium
| | - Robert Oostenveld
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands.,NatMEG, Karolinska Institutet, Stockholm, Sweden
| | | | - Richard E Carson
- Department of Radiology and Biomedical Imaging, Yale University, New Haven, USA
| | - Gitte M Knudsen
- Neurobiology Research Unit, Rigshospitalet, and Institute of Clinical Medicine, Univ. Copenhagen, København, Denmark
| | - Robert B Innis
- Molecular Imaging Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, USA
| | - Melanie Ganz
- Neurobiology Research Unit, Rigshospitalet, and Institute of Clinical Medicine, Univ. Copenhagen, København, Denmark. .,Department of Computer Science, University of Copenhagen, Copenhagen, Denmark.
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8
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Robbins K, Truong D, Appelhoff S, Delorme A, Makeig S. Capturing the nature of events and event context using hierarchical event descriptors (HED). Neuroimage 2021; 245:118766. [PMID: 34848298 PMCID: PMC8925904 DOI: 10.1016/j.neuroimage.2021.118766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 10/27/2021] [Accepted: 11/26/2021] [Indexed: 10/25/2022] Open
Abstract
Event-related data analysis plays a central role in EEG and MEG (MEEG) and other neuroimaging modalities including fMRI. Choices about which events to report and how to annotate their full natures significantly influence the value, reliability, and reproducibility of neuroimaging datasets for further analysis and meta- or mega-analysis. A powerful annotation strategy using the new third-generation formulation of the Hierarchical Event Descriptors (HED) framework and tools (hedtags.org) combines robust event description with details of experiment design and metadata in a human-readable as well as machine-actionable form, making event annotation relevant to the full range of neuroimaging and other time series data. This paper considers the event design and annotation process using as a case study the well-known multi-subject, multimodal dataset of Wakeman and Henson made available by its authors as a Brain Imaging Data Structure (BIDS) dataset (bids.neuroimaging.io). We propose a set of best practices and guidelines for event annotation integrated in a natural way into the BIDS metadata file architecture, examine the impact of event design decisions, and provide a working example of organizing events in MEEG and other neuroimaging data. We demonstrate how annotations using HED can document events occurring during neuroimaging experiments as well as their interrelationships, providing machine-actionable annotation enabling automated within- and across-experiment analysis and comparisons. We discuss the evolution of HED software tools and have made available an accompanying HED-annotated BIDS-formated edition of the MEEG data of the Wakeman and Henson dataset (openneuro.org, ds003645).
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Affiliation(s)
- Kay Robbins
- Department of Computer Science, University of Texas San Antonio San Antonio, TX, United States.
| | - Dung Truong
- Swartz Center for Computational Neuroscience, Institute for Neural Computation, University of California San Diego, La Jolla, California, 92903-0559, United States
| | - Stefan Appelhoff
- Center for Adaptive Rationality, Max Planck Institute for Human Development, Berlin, Germany
| | - Arnaud Delorme
- Swartz Center for Computational Neuroscience, Institute for Neural Computation, University of California San Diego, La Jolla, California, 92903-0559, United States; Paul Sabatier University in Toulouse, Toulouse, France
| | - Scott Makeig
- Swartz Center for Computational Neuroscience, Institute for Neural Computation, University of California San Diego, La Jolla, California, 92903-0559, United States
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9
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Levitis E, van Praag CDG, Gau R, Heunis S, DuPre E, Kiar G, Bottenhorn KL, Glatard T, Nikolaidis A, Whitaker KJ, Mancini M, Niso G, Afyouni S, Alonso-Ortiz E, Appelhoff S, Arnatkeviciute A, Atay SM, Auer T, Baracchini G, Bayer JMM, Beauvais MJS, Bijsterbosch JD, Bilgin IP, Bollmann S, Bollmann S, Botvinik-Nezer R, Bright MG, Calhoun VD, Chen X, Chopra S, Chuan-Peng H, Close TG, Cookson SL, Craddock RC, De La Vega A, De Leener B, Demeter DV, Di Maio P, Dickie EW, Eickhoff SB, Esteban O, Finc K, Frigo M, Ganesan S, Ganz M, Garner KG, Garza-Villarreal EA, Gonzalez-Escamilla G, Goswami R, Griffiths JD, Grootswagers T, Guay S, Guest O, Handwerker DA, Herholz P, Heuer K, Huijser DC, Iacovella V, Joseph MJE, Karakuzu A, Keator DB, Kobeleva X, Kumar M, Laird AR, Larson-Prior LJ, Lautarescu A, Lazari A, Legarreta JH, Li XY, Lv J, Mansour L S, Meunier D, Moraczewski D, Nandi T, Nastase SA, Nau M, Noble S, Norgaard M, Obungoloch J, Oostenveld R, Orchard ER, Pinho AL, Poldrack RA, Qiu A, Raamana PR, Rokem A, Rutherford S, Sharan M, Shaw TB, Syeda WT, Testerman MM, Toro R, Valk SL, Van Den Bossche S, Varoquaux G, Váša F, Veldsman M, Vohryzek J, Wagner AS, Walsh RJ, White T, Wong FT, Xie X, Yan CG, Yang YF, Yee Y, Zanitti GE, Van Gulick AE, Duff E, Maumet C. Centering inclusivity in the design of online conferences-An OHBM-Open Science perspective. Gigascience 2021; 10:6355274. [PMID: 34414422 DOI: 10.1093/gigascience/giab051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
As the global health crisis unfolded, many academic conferences moved online in 2020. This move has been hailed as a positive step towards inclusivity in its attenuation of economic, physical, and legal barriers and effectively enabled many individuals from groups that have traditionally been underrepresented to join and participate. A number of studies have outlined how moving online made it possible to gather a more global community and has increased opportunities for individuals with various constraints, e.g., caregiving responsibilities. Yet, the mere existence of online conferences is no guarantee that everyone can attend and participate meaningfully. In fact, many elements of an online conference are still significant barriers to truly diverse participation: the tools used can be inaccessible for some individuals; the scheduling choices can favour some geographical locations; the set-up of the conference can provide more visibility to well-established researchers and reduce opportunities for early-career researchers. While acknowledging the benefits of an online setting, especially for individuals who have traditionally been underrepresented or excluded, we recognize that fostering social justice requires inclusivity to actively be centered in every aspect of online conference design. Here, we draw from the literature and from our own experiences to identify practices that purposefully encourage a diverse community to attend, participate in, and lead online conferences. Reflecting on how to design more inclusive online events is especially important as multiple scientific organizations have announced that they will continue offering an online version of their event when in-person conferences can resume.
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Affiliation(s)
- Elizabeth Levitis
- Section on Developmental Neurogenomics, National Institute of Mental Health, Bethesda, MD 20892, USA.,Centre for Medical Image Computing, Department of Computer Science, University College London, London, WC1E 6BT, UK
| | - Cassandra D Gould van Praag
- Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford, OX3 9DU, UK.,Department of Psychiatry, University of Oxford, Oxford, OX3 7JX, UK
| | - Rémi Gau
- Institute of Psychology, Université Catholique de Louvain, Louvain la Neuve 1348, Belgium
| | - Stephan Heunis
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, 5612 AP, The Netherlands
| | - Elizabeth DuPre
- NeuroDataScience - ORIGAMI laboratory, McGill University, Montreal, QC, H3A 2B4, Canada
| | - Gregory Kiar
- Department of Biomedical Engineering, McGill University, Montreal, QC, H3A 2B4, Canada.,Center for the Developing Brain, The Child Mind Institute, New York City, NY 10022, USA
| | | | - Tristan Glatard
- Department of Computer Science and Software Engineering, Concordia University, Montreal, QC, H3G 1M8, Canada
| | - Aki Nikolaidis
- Center for the Developing Brain, The Child Mind Institute, New York City, NY 10022, USA
| | | | - Matteo Mancini
- Department of Neuroscience, Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9RR, UK.,Cardiff University Brain Research Imaging Centre, Cardiff University, Cardiff, CF24 4HQ, UK.,NeuroPoly Lab, Polytechnique Montreal, Montreal, QC, H3T 1J4, Canada
| | - Guiomar Niso
- Departement of Psychological & Brain Sciences, Indiana University, Bloomington, IN 47405, USA.,ETSI Telecomunicación, Universidad Politécnica de Madrid and CIBER-BBN, 28040 Madrid, Spain
| | - Soroosh Afyouni
- Big Data Institute, University of Oxford, Oxford, OX3 7LF, UK.,Department of Psychology, University of Cambridge, CB2 3EB, Cambridge, UK
| | - Eva Alonso-Ortiz
- Department of Electrical Engineering, Polytechnique Montréal, Montréal, QC, H3T 1J4, Canada
| | - Stefan Appelhoff
- Center for Adaptive Rationality, Max Planck Institute for Human Development, Berlin 14195, Germany
| | - Aurina Arnatkeviciute
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, and Monash Biomedical Imaging, Monash University, Victoria, VIC, Clayton 3168, Australia
| | - Selim Melvin Atay
- Neuroscience and Neurotechnology, Middle East Technical University, Ankara 06800, Turkey
| | - Tibor Auer
- School of Psychology, University of Surrey, Guildford GU2 7XH, UK
| | - Giulia Baracchini
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, H3A 2B4, Canada.,Montréal Neurological Institute, Montréal, QC, H3A 2B4, Canada
| | - Johanna M M Bayer
- Centre for Youth Mental Health, University of Melbourne, Melbourne, VIC, 3010, Parkville, Melbourne, Australia.,Orygen Youth Health, Melbourne, VIC, 3052, Royal Park, Melbourne, Australia
| | | | - Janine D Bijsterbosch
- Department of Radiology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Isil P Bilgin
- Department of Biomedical Engineering, Cybernetics, The School of Biological Sciences, The University of Reading, Reading, RG6 6AH, UK
| | - Saskia Bollmann
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Steffen Bollmann
- School of Information Technology and Electrical Engineering, The University of Queensland, Brisbane, QLD 4072, Australia.,ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Rotem Botvinik-Nezer
- Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Molly G Bright
- Physical Therapy and Human Movement Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.,Biomedical Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL 60208, USA
| | - Vince D Calhoun
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State, Georgia Tech, Emory, Atlanta, GA 30303, USA
| | - Xiao Chen
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, 100101, Beijing, China.,Magnetic Resonance Imaging Research Center, Institute of Psychology, Chinese Academy of Sciences, 100101, Beijing, China.,International Big-Data Center for Depression Research, Chinese Academy of Sciences, Beijing 100101, Beijing, China
| | - Sidhant Chopra
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, and Monash Biomedical Imaging, Monash University, Victoria, VIC, Clayton 3168, Australia
| | - Hu Chuan-Peng
- School of Psychology, Nanjing Normal University, Nanjing 210024, China
| | - Thomas G Close
- Department of Biomedical Engineering, The University of Sydney, Sydney, NSW 2006, Australia.,National Imaging Facility, The University of Sydney, Sydney, NSW 2006, Australia
| | - Savannah L Cookson
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - R Cameron Craddock
- Department of Diagnostic Medicine, The University of Texas at Austin Dell Medical School, Austin, TX 78712, USA
| | - Alejandro De La Vega
- Department of Psychology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Benjamin De Leener
- Department of Computer and Software Engineering, Polytechnique Montreal, Montreal, QC H3T 1J4, Canada.,Research Centre, Sainte-Justine University Hospital Center, Montreal, QC, H3T 1C5, Canada
| | - Damion V Demeter
- Department of Psychology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Paola Di Maio
- Center for Systems, Knowledge Representation and Neuroscience, Edinburgh and Taipei, UK and Taiwan.,Institute for Globally Distributed Open Research and Education (IGDORE)
| | - Erin W Dickie
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1R8, Canada
| | - Simon B Eickhoff
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany.,Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich, Jülich 52425, Germany
| | - Oscar Esteban
- Department of Radiology, Lausanne University Hospital and University of Lausanne, Lausanne 1003, Switzerland
| | - Karolina Finc
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń 87-100, Poland
| | - Matteo Frigo
- Athena Project Team, Université Côte D'Azur, Inria, 06103 Nice, France
| | - Saampras Ganesan
- Melbourne Neuropsychiatry Centre, The University of Melbourne, Melbourne, VIC 3010, Australia.,Department of Biomedical Engineering, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Melanie Ganz
- Neurobiology Research Unit, Rigshospitalet, Copenhagen DK-2100, Denmark.,Department of Computer Science, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Kelly G Garner
- Queensland Brain Institute, University of Queensland, St. Lucia, QLD 4072, Australia.,School of Psychology, University of Birmingham, Birmingham, B15 2TT, UK.,School of Psychology, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Eduardo A Garza-Villarreal
- Laboratorio Nacional de Imagenología por Resonancia Magnética, Instituto de Neurobiología, Universidad Nacional Autónoma de México campus Juriquilla, Querétaro, Qro 76230, Mexico
| | - Gabriel Gonzalez-Escamilla
- Department of Neurology, Focus Program Translational Neuroscience (FTN), Rhine Main Neuroscience Network (rmn2), University Medical Center of the Johannes Gutenberg University Mainz, Mainz 55131, Germany
| | - Rohit Goswami
- Faculty of Physical Sciences, University of Iceland, 102 Reykjavík, Iceland.,Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - John D Griffiths
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada.,Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON M6J 1H4, Canada
| | - Tijl Grootswagers
- The MARCS Institute for Brain, Behaviour & Development, Western Sydney University, Sydney 2751, NSW, Australia
| | - Samuel Guay
- Department of Psychology, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Olivia Guest
- Donders Centre for Cognitive Neuroimaging, Radboud University, Nijmegen, 6525 EN, Netherlands
| | - Daniel A Handwerker
- Section on Functional Imaging Methods, Laboratory of Brain and Cognition, National Institute of Mental Health, Bethesda, MD 20892-9663, USA
| | - Peer Herholz
- NeuroDataScience - ORIGAMI laboratory, McGill University, Montreal, QC, H3A 2B4, Canada
| | - Katja Heuer
- Center for Research and Interdisciplinarity (CRI), INSERM U1284, Université de Paris, 75004 Paris, France.,Department of Neuropsychology, Max Planck Institute for Human Cognitive and Brain Sciences, 04103 Leipzig, Germany
| | - Dorien C Huijser
- Erasmus School of Social and Behavioral Sciences, Erasmus University Rotterdam, Rotterdam 3062, the Netherlands.,Developmental and Educational Psychology, Leiden University, Leiden 2333, the Netherlands
| | - Vittorio Iacovella
- Center for Mind/Brain Sciences - CIMeC, University of Trento, Rovereto 38068, Italy
| | - Michael J E Joseph
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada
| | - Agah Karakuzu
- NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montréal, Montréal, QC, H3T 1N8, Canada.,Montréal Heart Institute, University of Montréal, Montréal, QC, H1T 1C8, Canada
| | - David B Keator
- Psychiatry and Human Behavior, University of California Irvine, Irvine, CA 92697, USA
| | - Xenia Kobeleva
- Department of Neurology, University Hospital Bonn, 53127 Bonn, Germany.,Clinical Research, German Center for Neurodegenerative Diseases, 53127 Bonn, Germany
| | - Manoj Kumar
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA
| | - Angela R Laird
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Linda J Larson-Prior
- Psychiatric Research Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.,Arkansas Children's Nutrition Center, Little Rock, AR, USA.,Department of Neurology, Pediatrics, Neuroscience & Developmental Sciences, Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Alexandra Lautarescu
- Department of Perinatal Imaging and Health, Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King's College London, London SE5 8AF, UK.,Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 7EH, UK
| | - Alberto Lazari
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Jon Haitz Legarreta
- Department of Computer Science, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Xue-Ying Li
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing101408, China.,CAS Key Laboratory of Behavioral Science, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, China.,Sino-Danish Center for Education and Research, Graduate University of Chinese Academy of Sciences, Beijing 101408, China.,CFIN and PET Center, Aarhus University, 8000 Aarhus, Denmark
| | - Jinglei Lv
- School of Biomedical Engineering & Brain and Mind Center, University of Sydney, Sydney, NSW 2006, Australia
| | - Sina Mansour L
- Melbourne Neuropsychiatry Centre, The University of Melbourne, Melbourne, VIC 3010, Australia.,Department of Biomedical Engineering, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - David Meunier
- Aix Marseille Univ, CNRS, INT, Institut de Neurosciences de la Timone, 13005 Marseille, France
| | | | - Tulika Nandi
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 7LF, UK
| | - Samuel A Nastase
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA
| | - Matthias Nau
- Section on Learning and Plasticity, Laboratory of Brain and Cognition, National Institute of Mental Health, Bethesda, MD 20892-9663, USA.,Max-Planck-Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Stephanie Noble
- Radiology & Biomedical Imaging, Yale University, New Haven, CT 06519, USA
| | - Martin Norgaard
- Center for Reproducible Neuroscience, Department of Psychology, Stanford University, Stanford, CA 94305Ci, USA.,Neurobiology Research Unit, Department of Neurology, Rigshospitalet, Copenhagen University Hospital, Copenhagen 2100, Denmark
| | - Johnes Obungoloch
- Department of Biomedical Sciences and Engineering, Mbarara University of Science and Technology, Mbarara City, Uganda
| | - Robert Oostenveld
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, 6500 GL, The Netherlands.,NatMEG, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Edwina R Orchard
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, and Monash Biomedical Imaging, Monash University, Victoria, VIC, Clayton 3168, Australia
| | - Ana Luísa Pinho
- Université Paris-Saclay, Inria, CEA, 91120 Palaiseau, France
| | | | - Anqi Qiu
- Department of Biomedical Engineering, The N.1 Institute for Health, Smart Systems Institute, National University of Singapore, Singapore 117583, Singapore.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | | | - Ariel Rokem
- Department of Psychology & eScience Institute, University of Washington, Seattle, WA 98195, USA
| | - Saige Rutherford
- Department of Cognitive Neuroscience, Radboud University Medical Center, Nijmegen 6525 EN, The Netherlands.,Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Thomas B Shaw
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Warda T Syeda
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne, VIC 3053, Australia
| | | | - Roberto Toro
- Center for Research and Interdisciplinarity (CRI), INSERM U1284, Université de Paris, 75004 Paris, France.,Neuroscience Department, Institut Pasteur, 75015 Paris, France
| | - Sofie L Valk
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany.,Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich, Jülich 52425, Germany.,Otto Hahn Group Cognitive Neurogenetics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig 04303, Germany
| | - Sofie Van Den Bossche
- Department of Data Analysis, Faculty of Psychology and Educational Sciences, Ghent University, Ghent 9000, Belgium
| | - Gaël Varoquaux
- Université Paris-Saclay, Inria, CEA, 91120 Palaiseau, France.,Montreal Neurological Institute, McGill, Montreal, QC, H3A 2B4, Canada
| | - František Váša
- Department of Neuroimaging, Institute of Psychiatry Psychology & Neuroscience, King's College London SE5 8AF, London, UK
| | - Michele Veldsman
- Department of Experimental Psychology, University of Oxford, Oxfordshire, OX2 6GG, Oxford, UK
| | - Jakub Vohryzek
- Department of Psychiatry, University of Oxford, Oxford, OX3 7JX, UK.,Center for Music in the Brain, Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
| | - Adina S Wagner
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich, Jülich 52425, Germany
| | - Reubs J Walsh
- Department of Clinical, Neuro-, and Developmental Psychology, Vrije Universiteit Amsterdam, Amsterdam,1081BT, The Netherlands.,Center for Applied Transgender Studies , Chicago, USA
| | - Tonya White
- Department of Child and Adolescent Psychiatry, Erasmus University Medical Centre, Rotterdam, 3000CB, The Netherlands.,Department of Radiology and Nuclear Medicine, Erasmus University Medical Centre, Rotterdam 3000CB, The Netherlands
| | - Fu-Te Wong
- Institute of Linguistics, Academia Sinica, Taipei, Taiwan.,Institute of Medical Science, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Xihe Xie
- Department of Neuroscience, Weill Cornell Graduate School, New York City, NY 10065, USA
| | - Chao-Gan Yan
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, 100101, Beijing, China.,Department of Psychology, University of Chinese Academy of Sciences, 100101 Beijing, China.,International Big-Data Center for Depression Research, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yu-Fang Yang
- Department of Psychology, University of Würzburg, Würzburg 97074, Germany
| | - Yohan Yee
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
| | | | - Ana E Van Gulick
- Figshare, Cambridge, MA 02139, USA.,University Libraries, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Eugene Duff
- Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford, OX3 9DU, UK.,Department of Paediatrics, University of Oxford, Oxford, OX3 9DU, UK
| | - Camille Maumet
- Inria, Univ Rennes, CNRS, Inserm, IRISA UMR 6074, Empenn ERL U 1228, 35042 Rennes, France
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10
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Pavlov YG, Adamian N, Appelhoff S, Arvaneh M, Benwell CSY, Beste C, Bland AR, Bradford DE, Bublatzky F, Busch NA, Clayson PE, Cruse D, Czeszumski A, Dreber A, Dumas G, Ehinger B, Ganis G, He X, Hinojosa JA, Huber-Huber C, Inzlicht M, Jack BN, Johannesson M, Jones R, Kalenkovich E, Kaltwasser L, Karimi-Rouzbahani H, Keil A, König P, Kouara L, Kulke L, Ladouceur CD, Langer N, Liesefeld HR, Luque D, MacNamara A, Mudrik L, Muthuraman M, Neal LB, Nilsonne G, Niso G, Ocklenburg S, Oostenveld R, Pernet CR, Pourtois G, Ruzzoli M, Sass SM, Schaefer A, Senderecka M, Snyder JS, Tamnes CK, Tognoli E, van Vugt MK, Verona E, Vloeberghs R, Welke D, Wessel JR, Zakharov I, Mushtaq F. #EEGManyLabs: Investigating the replicability of influential EEG experiments. Cortex 2021; 144:213-229. [PMID: 33965167 DOI: 10.1016/j.cortex.2021.03.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/02/2021] [Accepted: 03/09/2021] [Indexed: 12/29/2022]
Abstract
There is growing awareness across the neuroscience community that the replicability of findings about the relationship between brain activity and cognitive phenomena can be improved by conducting studies with high statistical power that adhere to well-defined and standardised analysis pipelines. Inspired by recent efforts from the psychological sciences, and with the desire to examine some of the foundational findings using electroencephalography (EEG), we have launched #EEGManyLabs, a large-scale international collaborative replication effort. Since its discovery in the early 20th century, EEG has had a profound influence on our understanding of human cognition, but there is limited evidence on the replicability of some of the most highly cited discoveries. After a systematic search and selection process, we have identified 27 of the most influential and continually cited studies in the field. We plan to directly test the replicability of key findings from 20 of these studies in teams of at least three independent laboratories. The design and protocol of each replication effort will be submitted as a Registered Report and peer-reviewed prior to data collection. Prediction markets, open to all EEG researchers, will be used as a forecasting tool to examine which findings the community expects to replicate. This project will update our confidence in some of the most influential EEG findings and generate a large open access database that can be used to inform future research practices. Finally, through this international effort, we hope to create a cultural shift towards inclusive, high-powered multi-laboratory collaborations.
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Affiliation(s)
- Yuri G Pavlov
- University of Tuebingen, Germany; Ural Federal University, Russia.
| | | | | | | | | | | | | | | | | | | | | | | | | | - Anna Dreber
- Stockholm School of Economics, Sweden; University of Innsbruck, Austria
| | - Guillaume Dumas
- Université de Montréal, Montréal, Quebec, Canada; CHU Sainte-Justine Research Center, Montréal, Quebec, Canada
| | | | | | - Xun He
- Bournemouth University, UK
| | - José A Hinojosa
- Universidad Complutense de Madrid, Spain; Universidad Nebrija, Spain
| | | | | | | | | | | | | | - Laura Kaltwasser
- Berlin School of Mind and Brain, Humboldt-Universität zu Berlin, Germany
| | | | | | - Peter König
- University Osnabrück, Germany; University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Louisa Kulke
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | | | - Nicolas Langer
- University of Zurich, Switzerland; Neuroscience Center Zurich, Switzerland
| | | | - David Luque
- Universidad Autónoma de Madrid, Spain; Universidad de Málaga, Spain
| | | | - Liad Mudrik
- School of Psychological Sciences & Sagol School of Neuroscience, Tel Aviv University, Israel
| | | | | | | | - Guiomar Niso
- Indiana University, Bloomington, USA; Universidad Politecnica de Madrid and CIBER-BBN, Spain
| | | | | | | | | | | | | | | | | | - Joel S Snyder
- Department of Psychology, University of Nevada, Las Vegas, USA
| | | | | | | | | | | | - Dominik Welke
- Max-Planck-Institute for Empirical Aesthetics, Germany
| | - Jan R Wessel
- University of Iowa Hospitals and Clinics, Iowa City, USA; University of Iowa, Iowa City, USA
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11
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Knudsen GM, Ganz M, Appelhoff S, Boellaard R, Bormans G, Carson RE, Catana C, Doudet D, Gee AD, Greve DN, Gunn RN, Halldin C, Herscovitch P, Huang H, Keller SH, Lammertsma AA, Lanzenberger R, Liow JS, Lohith TG, Lubberink M, Lyoo CH, Mann JJ, Matheson GJ, Nichols TE, Nørgaard M, Ogden T, Parsey R, Pike VW, Price J, Rizzo G, Rosa-Neto P, Schain M, Scott PJ, Searle G, Slifstein M, Suhara T, Talbot PS, Thomas A, Veronese M, Wong DF, Yaqub M, Zanderigo F, Zoghbi S, Innis RB. Guidelines for the content and format of PET brain data in publications and archives: A consensus paper. J Cereb Blood Flow Metab 2020; 40:1576-1585. [PMID: 32065076 PMCID: PMC7370374 DOI: 10.1177/0271678x20905433] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
It is a growing concern that outcomes of neuroimaging studies often cannot be replicated. To counteract this, the magnetic resonance (MR) neuroimaging community has promoted acquisition standards and created data sharing platforms, based on a consensus on how to organize and share MR neuroimaging data. Here, we take a similar approach to positron emission tomography (PET) data. To facilitate comparison of findings across studies, we first recommend publication standards for tracer characteristics, image acquisition, image preprocessing, and outcome estimation for PET neuroimaging data. The co-authors of this paper, representing more than 25 PET centers worldwide, voted to classify information as mandatory, recommended, or optional. Second, we describe a framework to facilitate data archiving and data sharing within and across centers. Because of the high cost of PET neuroimaging studies, sample sizes tend to be small and relatively few sites worldwide have the required multidisciplinary expertise to properly conduct and analyze PET studies. Data sharing will make it easier to combine datasets from different centers to achieve larger sample sizes and stronger statistical power to test hypotheses. The combining of datasets from different centers may be enhanced by adoption of a common set of best practices in data acquisition and analysis.
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Affiliation(s)
- Gitte M Knudsen
- Neurobiology Research Unit, Rigshospital and University of Copenhagen, Copenhagen, Denmark
| | - Melanie Ganz
- Neurobiology Research Unit, Rigshospital and University of Copenhagen, Copenhagen, Denmark
| | - Stefan Appelhoff
- Center for Adaptive Rationality, Max Planck Institute for Human Development, Berlin, Germany
| | - Ronald Boellaard
- Department of Radiology and Nuclear Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Guy Bormans
- Laboratory for Radiopharmaceutical Research, KU, Leuven, Belgium
| | - Richard E Carson
- Department of Radiology and Biomedical Imaging, Yale University, New Haven, USA
| | - Ciprian Catana
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Department of Radiology, Boston, MA, USA
| | - Doris Doudet
- Department of Medicine/Neurology, Pacific Parkinson Research Center, Vancouver, Canada
| | - Antony D Gee
- Clinical PET Centre, King's College London, London, UK
| | - Douglas N Greve
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Department of Radiology, Boston, MA, USA
| | - Roger N Gunn
- Invicro and Division of Brain Sciences, Imperial College London, London, UK
| | - Christer Halldin
- Center for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet and Stockholm County Council, Stockholm, Sweden
| | - Peter Herscovitch
- Department of Positron Emission Tomography, National Institutes of Health, Bethesda, USA
| | - Henry Huang
- Department of Radiology and Biomedical Imaging, Yale University, New Haven, USA
| | - Sune H Keller
- Department of Clinical Physiology, Nuclear Medicine and PET, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Adriaan A Lammertsma
- Department of Radiology and Nuclear Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Rupert Lanzenberger
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Wien, Austria
| | - Jeih-San Liow
- Molecular Imaging Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, USA
| | | | - Mark Lubberink
- Uppsala University, Department of Surgical Sciences/Radiology and Nuclear Medicine, Uppsala University Hospital, Department of Medical Physics, Sweden
| | - Chul H Lyoo
- Department of Neurology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - J John Mann
- Department of Psychiatry, Molecular Imaging and Neuropathology Division, Columbia University, New York, USA
| | - Granville J Matheson
- Center for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet and Stockholm County Council, Stockholm, Sweden
| | - Thomas E Nichols
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Population Health, University of Oxford, UK
| | - Martin Nørgaard
- Neurobiology Research Unit, Rigshospital and University of Copenhagen, Copenhagen, Denmark
| | - Todd Ogden
- Columbia Mailman School of Public Health, Columbia University, New York, USA
| | - Ramin Parsey
- Department of Psychiatry, School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Victor W Pike
- Molecular Imaging Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, USA
| | - Julie Price
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Department of Radiology, Boston, MA, USA
| | - Gaia Rizzo
- Invicro and Division of Brain Sciences, Imperial College London, London, UK
| | - Pedro Rosa-Neto
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Canada.,Translational Neuroimaging Laboratory, McGill Centre for Studies in Aging, Douglas Mental Health University Institute, Montreal, Canada
| | - Martin Schain
- Columbia Mailman School of Public Health, Columbia University, New York, USA
| | - Peter Jh Scott
- Department of Radiology, University of Michigan, Ann Arbor, USA
| | - Graham Searle
- Invicro and Division of Brain Sciences, Imperial College London, London, UK
| | - Mark Slifstein
- Department of Psychiatry, School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Tetsuya Suhara
- Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology, Chiba, Japan
| | - Peter S Talbot
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Adam Thomas
- National Institute of Mental Health, Bethesda, USA
| | - Mattia Veronese
- Centre for Neuroimaging Sciences, King's College London, London, UK
| | - Dean F Wong
- Department of Radiology, Johns Hopkins Hospital, Baltimore, USA
| | - Maqsood Yaqub
- Department of Radiology and Nuclear Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | | | - Sami Zoghbi
- Molecular Imaging Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, USA
| | - Robert B Innis
- Molecular Imaging Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, USA
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12
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Appelhoff S, Sanderson M, Brooks TL, van Vliet M, Quentin R, Holdgraf C, Chaumon M, Mikulan E, Tavabi K, Höchenberger R, Welke D, Brunner C, Rockhill AP, Larson E, Gramfort A, Jas M. MNE-BIDS: Organizing electrophysiological data into the BIDS format and facilitating their analysis. J Open Source Softw 2019; 4:1896. [PMID: 35990374 PMCID: PMC9390980 DOI: 10.21105/joss.01896] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The development of the Brain Imaging Data Structure (BIDS; Gorgolewski et al., 2016) gave the neuroscientific community a standard to organize and share data. BIDS prescribes file naming conventions and a folder structure to store data in a set of already existing file formats. Next to rules about organization of the data itself, BIDS provides standardized templates to store associated metadata in the form of Javascript Object Notation (JSON) and tab separated value (TSV) files. It thus facilitates data sharing, eases metadata querying, and enables automatic data analysis pipelines. BIDS is a rich system to curate, aggregate, and annotate neuroimaging databases.
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Affiliation(s)
- Stefan Appelhoff
- Center for Adaptive Rationality, Max Planck Institute for Human Development, Berlin, Germany
| | - Matthew Sanderson
- Department of Cognitive Sciences, Macquarie University, Sydney, Australia
| | | | - Marijn van Vliet
- Department of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland
| | - Romain Quentin
- Human Cortical Physiology and Neurorehabilitation Section, NINDS, NIH, Bethesda, Maryland 20892
| | | | | | - Ezequiel Mikulan
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - Kambiz Tavabi
- Institute for Learning and Brain Sciences, University of Washington, Seattle, WA, USA
| | | | - Dominik Welke
- Max-Planck-Institute for Empirical Aesthetics, Frankfurt a.M., Germany
| | | | | | - Eric Larson
- Institute for Learning and Brain Sciences, University of Washington, Seattle, WA, USA
| | | | - Mainak Jas
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
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13
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Yarkoni T, Markiewicz CJ, de la Vega A, Gorgolewski KJ, Salo T, Halchenko YO, McNamara Q, DeStasio K, Poline JB, Petrov D, Hayot-Sasson V, Nielson DM, Carlin J, Kiar G, Whitaker K, DuPre E, Wagner A, Tirrell LS, Jas M, Hanke M, Poldrack RA, Esteban O, Appelhoff S, Holdgraf C, Staden I, Thirion B, Kleinschmidt DF, Lee JA, Visconti di Oleggio Castello M, Notter MP, Blair R. PyBIDS: Python tools for BIDS datasets. J Open Source Softw 2019; 4:1294. [PMID: 32775955 PMCID: PMC7409983 DOI: 10.21105/joss.01294] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
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14
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Holdgraf C, Appelhoff S, Bickel S, Bouchard K, D'Ambrosio S, David O, Devinsky O, Dichter B, Flinker A, Foster BL, Gorgolewski KJ, Groen I, Groppe D, Gunduz A, Hamilton L, Honey CJ, Jas M, Knight R, Lachaux JP, Lau JC, Lee-Messer C, Lundstrom BN, Miller KJ, Ojemann JG, Oostenveld R, Petridou N, Piantoni G, Pigorini A, Pouratian N, Ramsey NF, Stolk A, Swann NC, Tadel F, Voytek B, Wandell BA, Winawer J, Whitaker K, Zehl L, Hermes D. iEEG-BIDS, extending the Brain Imaging Data Structure specification to human intracranial electrophysiology. Sci Data 2019; 6:102. [PMID: 31239438 PMCID: PMC6592874 DOI: 10.1038/s41597-019-0105-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/24/2019] [Indexed: 11/09/2022] Open
Abstract
The Brain Imaging Data Structure (BIDS) is a community-driven specification for organizing neuroscience data and metadata with the aim to make datasets more transparent, reusable, and reproducible. Intracranial electroencephalography (iEEG) data offer a unique combination of high spatial and temporal resolution measurements of the living human brain. To improve internal (re)use and external sharing of these unique data, we present a specification for storing and sharing iEEG data: iEEG-BIDS.
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Affiliation(s)
- Christopher Holdgraf
- The Berkeley Institute for Data Science, Berkeley, USA.
- University of California at Berkeley, Berkeley, USA.
| | - Stefan Appelhoff
- Center for Adaptive Rationality, Max Planck Institute for Human Development, Berlin, Germany
| | - Stephan Bickel
- Feinstein Institute for Medical Research, Hofstra Northwell School of Medicine, New York, USA
| | - Kristofer Bouchard
- Biological Systems and Engineering Division, Lawrence Berkeley Lab, Berkeley, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Mainak Jas
- Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Med. School, Charlestown, USA
| | | | | | - Jonathan C Lau
- Department of Clinical Neurological Sciences, Division of Neurosurgery, Western University, London, Canada
| | | | | | - Kai J Miller
- Department of Neurosurgery, Mayo Clinic, Rochester, USA
| | | | - Robert Oostenveld
- Radboud University, Donders Institute for Brain, Cognition and Behaviour, Karolinska Institutet, Nijmegen, The Netherlands
| | - Natalia Petridou
- Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gio Piantoni
- UMC Utrecht Brain Center, Utrecht, The Netherlands
| | | | | | | | - Arjen Stolk
- University of California at Berkeley, Berkeley, USA
| | | | - François Tadel
- Universite Grenoble Alpes, Inserm, France
- CHU Grenoble Alpes, GIN, Grenoble, France
| | | | | | | | - Kirstie Whitaker
- Alan Turing Institute, London, UK
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Lyuba Zehl
- Institute for Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Dora Hermes
- Stanford University, Stanford, USA.
- UMC Utrecht Brain Center, Utrecht, The Netherlands.
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, USA.
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15
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Pernet CR, Appelhoff S, Gorgolewski KJ, Flandin G, Phillips C, Delorme A, Oostenveld R. EEG-BIDS, an extension to the brain imaging data structure for electroencephalography. Sci Data 2019; 6:103. [PMID: 31239435 PMCID: PMC6592877 DOI: 10.1038/s41597-019-0104-8] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/07/2019] [Indexed: 11/25/2022] Open
Abstract
The Brain Imaging Data Structure (BIDS) project is a rapidly evolving effort in the human brain imaging research community to create standards allowing researchers to readily organize and share study data within and between laboratories. Here we present an extension to BIDS for electroencephalography (EEG) data, EEG-BIDS, along with tools and references to a series of public EEG datasets organized using this new standard.
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Affiliation(s)
- Cyril R Pernet
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, Scotland.
| | - Stefan Appelhoff
- Center for Adaptive Rationality, Max Planck Institute for Human Development, Berlin, Germany.
| | | | | | | | - Arnaud Delorme
- Swart Center for Computational Neuroscience, University of California San Diego, San Diego, California, USA
- CerCo, CNRS/Université Paul Sabatier, Toulouse, France
| | - Robert Oostenveld
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands.
- NatMEG, Karolinska Institutet, Stockholm, Sweden.
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16
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Regente J, de Zeeuw J, Bes F, Nowozin C, Appelhoff S, Wahnschaffe A, Münch M, Kunz D. Can short-wavelength depleted bright light during single simulated night shifts prevent circadian phase shifts? Appl Ergon 2017; 61:22-30. [PMID: 28237017 DOI: 10.1016/j.apergo.2016.12.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 06/06/2023]
Abstract
In single night shifts, extending habitual wake episodes leads to sleep deprivation induced decrements of performance during the shift and re-adaptation effects the next day. We investigated whether short-wavelength depleted (=filtered) bright light (FBL) during a simulated night shift would counteract such effects. Twenty-four participants underwent a simulated night shift in dim light (DL) and in FBL. Reaction times, subjective sleepiness and salivary melatonin concentrations were assessed during both nights. Daytime sleep was recorded after both simulated night shifts. During FBL, we found no melatonin suppression compared to DL, but slightly faster reaction times in the second half of the night. Daytime sleep was not statistically different between both lighting conditions (n = 24) and there was no significant phase shift after FBL (n = 11). To conclude, our results showed positive effects from FBL during simulated single night shifts which need to be further tested with larger groups, in more applied studies and compared to standard lighting.
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Affiliation(s)
- J Regente
- Charité University Medicine, Institute of Physiology, Sleep Research & Clinical Chronobiology, Berlin, Germany; Department of Psychiatry, Psychotherapy and Psychosomatics, Immanuel Clinic Rüdersdorf, Medical School Brandenburg, Rüdersdorf near Berlin, Germany
| | - J de Zeeuw
- Charité University Medicine, Institute of Physiology, Sleep Research & Clinical Chronobiology, Berlin, Germany
| | - F Bes
- Charité University Medicine, Institute of Physiology, Sleep Research & Clinical Chronobiology, Berlin, Germany; Clinic for Sleep & Chronomedicine, St-Hedwig-Krankenhaus, D-10115 Berlin, Germany
| | - C Nowozin
- Charité University Medicine, Institute of Physiology, Sleep Research & Clinical Chronobiology, Berlin, Germany; Clinic for Sleep & Chronomedicine, St-Hedwig-Krankenhaus, D-10115 Berlin, Germany
| | - S Appelhoff
- Charité University Medicine, Institute of Physiology, Sleep Research & Clinical Chronobiology, Berlin, Germany
| | - A Wahnschaffe
- Charité University Medicine, Institute of Physiology, Sleep Research & Clinical Chronobiology, Berlin, Germany; Clinic for Sleep & Chronomedicine, St-Hedwig-Krankenhaus, D-10115 Berlin, Germany
| | - M Münch
- Charité University Medicine, Institute of Physiology, Sleep Research & Clinical Chronobiology, Berlin, Germany; Clinic for Sleep & Chronomedicine, St-Hedwig-Krankenhaus, D-10115 Berlin, Germany.
| | - D Kunz
- Charité University Medicine, Institute of Physiology, Sleep Research & Clinical Chronobiology, Berlin, Germany; Clinic for Sleep & Chronomedicine, St-Hedwig-Krankenhaus, D-10115 Berlin, Germany
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