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Alsaigh R, Mehmood R, Katib I, Liang X, Alshanqiti A, Corchado JM, See S. Harmonizing AI governance regulations and neuroinformatics: perspectives on privacy and data sharing. Front Neuroinform 2024; 18:1472653. [PMID: 39741922 PMCID: PMC11685213 DOI: 10.3389/fninf.2024.1472653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Accepted: 12/04/2024] [Indexed: 01/03/2025] Open
Affiliation(s)
- Roba Alsaigh
- Department of Computer Science, Faculty of Computing and Information Technology (FCIT), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rashid Mehmood
- Faculty of Computer and Information Systems, Islamic University of Madinah, Madinah, Saudi Arabia
| | - Iyad Katib
- Department of Computer Science, Faculty of Computing and Information Technology (FCIT), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Xiaohui Liang
- Department of Computer Science, University of Massachusetts, Boston, MA, United States
| | - Abdullah Alshanqiti
- Faculty of Computer and Information Systems, Islamic University of Madinah, Madinah, Saudi Arabia
| | - Juan M. Corchado
- BISITE Research Group, University of Salamanca, Salamanca, Spain
- Air Institute, IoT Digital Innovation Hub, Salamanca, Spain
- Department of Electronics, Information and Communication, Faculty of Engineering, Osaka Institute of Technology, Osaka, Japan
| | - Simon See
- NVIDIA AI Technology Center, NVIDIA Corporation, Santa Clara, CA, United States
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2
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Iyer S, Maxson Jones K, Robinson JO, Provenza NR, Duncan D, Lázaro-Muñoz G, McGuire AL, Sheth SA, Majumder MA. The BRAIN Initiative data-sharing ecosystem: Characteristics, challenges, benefits, and opportunities. eLife 2024; 13:e94000. [PMID: 39602224 PMCID: PMC11602185 DOI: 10.7554/elife.94000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/10/2024] [Indexed: 11/29/2024] Open
Abstract
In this paper, we provide an overview and analysis of the BRAIN Initiative data-sharing ecosystem. First, we compare and contrast the characteristics of the seven BRAIN Initiative data archives germane to data sharing and reuse, namely data submission and access procedures and aspects of interoperability. Second, we discuss challenges, benefits, and future opportunities, focusing on issues largely specific to sharing human data and drawing on N = 34 interviews with diverse stakeholders. The BRAIN Initiative-funded archive ecosystem faces interoperability and data stewardship challenges, such as achieving and maintaining interoperability of data and archives and harmonizing research participants' informed consents for tiers of access for human data across multiple archives. Yet, a benefit of this distributed archive ecosystem is the ability of more specialized archives to adapt to the needs of particular research communities. Finally, the multiple archives offer ample raw material for network evolution in response to the needs of neuroscientists over time. Our first objective in this paper is to provide a guide to the BRAIN Initiative data-sharing ecosystem for readers interested in sharing and reusing neuroscience data. Second, our analysis supports the development of empirically informed policy and practice aimed at making neuroscience data more findable, accessible, interoperable, and reusable.
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Affiliation(s)
- Sudhanvan Iyer
- Center for Medical Ethics and Health Policy, Baylor College of MedicineHoustonUnited States
| | - Kathryn Maxson Jones
- Center for Medical Ethics and Health Policy, Baylor College of MedicineHoustonUnited States
- Department of History, Purdue UniversityWest LafayetteUnited States
| | - Jill O Robinson
- Center for Medical Ethics and Health Policy, Baylor College of MedicineHoustonUnited States
| | - Nicole R Provenza
- Department of Neurosurgery, Baylor College of MedicineHoustonUnited States
| | - Dominique Duncan
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern CaliforniaLos AngelesUnited States
| | - Gabriel Lázaro-Muñoz
- Center for Bioethics, Harvard Medical SchoolBostonUnited States
- Department of Psychiatry, Massachusetts General HospitalBostonUnited States
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of MedicineHoustonUnited States
| | - Sameer A Sheth
- Department of Neurosurgery, Baylor College of MedicineHoustonUnited States
| | - Mary A Majumder
- Center for Medical Ethics and Health Policy, Baylor College of MedicineHoustonUnited States
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Meliss S, Pascua-Martin C, Skipper JI, Murayama K. The magic, memory, and curiosity fMRI dataset of people viewing magic tricks. Sci Data 2024; 11:1063. [PMID: 39353978 PMCID: PMC11445505 DOI: 10.1038/s41597-024-03675-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 07/23/2024] [Indexed: 10/03/2024] Open
Abstract
Videos of magic tricks offer lots of opportunities to study the human mind. They violate the expectations of the viewer, causing prediction errors, misdirect attention, and elicit epistemic emotions. Herein we describe and share the Magic, Memory, and Curiosity (MMC) Dataset where 50 participants watched 36 magic tricks filmed and edited specifically for functional magnetic imaging (fMRI) experiments. The MMC Dataset includes a contextual incentive manipulation, curiosity ratings for the magic tricks, and incidental memory performance tested a week later. We additionally measured individual differences in working memory and constructs relevant to motivated learning. fMRI data were acquired before, during, and after learning. We show that both behavioural and fMRI data are of high quality, as indicated by basic validation analysis, i.e., variance decomposition as well as intersubject correlation and seed-based functional connectivity, respectively. The richness and complexity of the MMC Dataset will allow researchers to explore dynamic cognitive and motivational processes from various angles during task and rest.
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Affiliation(s)
- Stefanie Meliss
- School of Psychology and Clinical Language Sciences, University of Reading, Reading, UK
- Experimental Psychology, University College London, London, UK
| | | | | | - Kou Murayama
- School of Psychology and Clinical Language Sciences, University of Reading, Reading, UK.
- Hector Research Institute of Education Sciences and Psychology, University of Tübingen, Tübingen, Germany.
- Research Institute, Kochi University of Technology, Kochi, Japan.
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4
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Giehl K, Mutsaerts HJ, Aarts K, Barkhof F, Caspers S, Chetelat G, Colin ME, Düzel E, Frisoni GB, Ikram MA, Jovicich J, Morbelli S, Oertel W, Paret C, Perani D, Ritter P, Segura B, Wisse LEM, De Witte E, Cappa SF, van Eimeren T. Sharing brain imaging data in the Open Science era: how and why? Lancet Digit Health 2024; 6:e526-e535. [PMID: 38906618 DOI: 10.1016/s2589-7500(24)00069-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/18/2024] [Accepted: 04/02/2024] [Indexed: 06/23/2024]
Abstract
The sharing of human neuroimaging data has great potential to accelerate the development of imaging biomarkers in neurological and psychiatric disorders; however, major obstacles remain in terms of how and why to share data in the Open Science context. In this Health Policy by the European Cluster for Imaging Biomarkers, we outline the current main opportunities and challenges based on the results of an online survey disseminated among senior scientists in the field. Although the scientific community fully recognises the importance of data sharing, technical, legal, and motivational aspects often prevent active adoption. Therefore, we provide practical advice on how to overcome the technical barriers. We also call for a harmonised application of the General Data Protection Regulation across EU countries. Finally, we suggest the development of a system that makes data count by recognising the generation and sharing of data as a highly valuable contribution to the community.
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Affiliation(s)
- Kathrin Giehl
- Department of Nuclear Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Institute of Neurosciences and Medicine (INM-2), Research Center Jülich, Jülich, Germany
| | - Henk-Jan Mutsaerts
- Radiology and Nuclear Medicine, Vrije Universiteit Medical Center, Amsterdam University Medical Center, Amsterdam, Netherlands; Amsterdam Neuroscience, Brain Imaging, Amsterdam, Netherlands
| | | | - Frederik Barkhof
- Radiology and Nuclear Medicine, Vrije Universiteit Medical Center, Amsterdam University Medical Center, Amsterdam, Netherlands; Amsterdam Neuroscience, Brain Imaging, Amsterdam, Netherlands; Queen Square Institute of Neurology and Centre for Medical Image Computing, University College London, London, UK
| | - Svenja Caspers
- Institute of Neuroscience and Medicine (INM-1), Research Center Jülich, Jülich, Germany; Institute for Anatomy I, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Gaël Chetelat
- Normandie université, UNICAEN, INSERM, U1237, NeuroPresage Team, Cyceron, Caen, France
| | | | - Emrah Düzel
- Faculty of Medicine, Institute for Cognitive Neurology and Dementia Research, University of Magdeburg, Magdeburg, Germany; Center for Neurodegenerative Diseases, Magdeburg, Germany
| | - Giovanni B Frisoni
- Department of Rehabilitation and Geriatrics, Memory Center, Geneva University and University Hospitals, Geneva, Switzerland
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Jorge Jovicich
- Center for Mind/Brain Sciences, University of Trento, Rovereto, Italy
| | - Silvia Morbelli
- Nuclear Medicine Unit, AOU Città Della Salute e Della Scienza di Torino, Turin, Italy; Department of Medical Sciences, University of Turin, Turin, Italy
| | - Wolfgang Oertel
- European Brain Council, Brussels, Belgium; Department of Neurology, University of Marburg, Marburg, Germany
| | - Christian Paret
- Department of Psychosomatic Medicine and Psychotherapy, Central Institute of Mental Health Mannheim, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Daniela Perani
- San Raffaele University and San Raffaele Scientific Institute, Milan, Italy
| | - Petra Ritter
- Berlin Institute of Health, Charité, Universitätsmedizin Berlin, Berlin, Germany; Department of Neurology with Experimental Neurology, Charité, Universitätsmedizin Berlin, Berlin, Germany; Bernstein Focus State Dependencies of Learning and Bernstein Center for Computational Neuroscience, Berlin, Germany; Einstein Center for Neuroscience Berlin, Berlin, Germany; Einstein Center Digital Future, Berlin, Germany
| | - Bàrbara Segura
- Medical Psychology Unit, Department of Medicine, Institute of Neurosciences, University of Barcelona, Barcelona, Spain; Hospital Clinic Foundation for Biomedical Research-August Pi i Sunyer Biomedical Research Institute, Barcelona, Spain; Biomedical Research Networking Center on Neurodegenerative Diseases Barcelona, Spain
| | - Laura E M Wisse
- Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Elke De Witte
- Neurosurgical Department, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Stefano F Cappa
- University Institute of Advanced Studies, Pavia, Italy; IRCCS Mondino Foundation, Pavia, Italy
| | - Thilo van Eimeren
- Department of Nuclear Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Department of Neurology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
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5
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Bradshaw A, Hughes N, Vallez-Garcia D, Chokoshvili D, Owens A, Hansen C, Emmert K, Maetzler W, Killin L, Barnes R, Brookes AJ, Visser PJ, Hofmann-Apitius M, Diaz C, Steukers L. Data sharing in neurodegenerative disease research: challenges and learnings from the innovative medicines initiative public-private partnership model. Front Neurol 2023; 14:1187095. [PMID: 37545729 PMCID: PMC10397390 DOI: 10.3389/fneur.2023.1187095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/02/2023] [Indexed: 08/08/2023] Open
Abstract
Efficient data sharing is hampered by an array of organizational, ethical, behavioral, and technical challenges, slowing research progress and reducing the utility of data generated by clinical research studies on neurodegenerative diseases. There is a particular need to address differences between public and private sector environments for research and data sharing, which have varying standards, expectations, motivations, and interests. The Neuronet data sharing Working Group was set up to understand the existing barriers to data sharing in public-private partnership projects, and to provide guidance to overcome these barriers, by convening data sharing experts from diverse projects in the IMI neurodegeneration portfolio. In this policy and practice review, we outline the challenges and learnings of the WG, providing the neurodegeneration community with examples of good practices and recommendations on how to overcome obstacles to data sharing. These obstacles span organizational issues linked to the unique structure of cross-sectoral, collaborative research initiatives, to technical issues that affect the storage, structure and annotations of individual datasets. We also identify sociotechnical hurdles, such as academic recognition and reward systems that disincentivise data sharing, and legal challenges linked to heightened perceptions of data privacy risk, compounded by a lack of clear guidance on GDPR compliance mechanisms for public-private research. Focusing on real-world, neuroimaging and digital biomarker data, we highlight particular challenges and learnings for data sharing, such as data management planning, development of ethical codes of conduct, and harmonization of protocols and curation processes. Cross-cutting solutions and enablers include the principles of transparency, standardization and co-design - from open, accessible metadata catalogs that enhance findability of data, to measures that increase visibility and trust in data reuse.
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Affiliation(s)
| | | | - David Vallez-Garcia
- Department of Radiology and Nuclear Medicine, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | | | - Andrew Owens
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Clint Hansen
- Department of Neurology, University Hospital Schleswig-Holstein, Campus Kiel and Kiel University, Kiel, Germany
| | - Kirsten Emmert
- Department of Neurology, University Hospital Schleswig-Holstein, Campus Kiel and Kiel University, Kiel, Germany
| | - Walter Maetzler
- Department of Neurology, University Hospital Schleswig-Holstein, Campus Kiel and Kiel University, Kiel, Germany
| | - Lewis Killin
- Synapse Research Management Partners, Barcelona, Spain
| | | | - Anthony J. Brookes
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Pieter Jelle Visser
- Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, University of Maastricht, Maastricht, Netherlands
| | | | - Carlos Diaz
- Synapse Research Management Partners, Barcelona, Spain
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Schroeder PA, Artemenko C, Kosie JE, Cockx H, Stute K, Pereira J, Klein F, Mehler DMA. Using preregistration as a tool for transparent fNIRS study design. NEUROPHOTONICS 2023; 10:023515. [PMID: 36908680 PMCID: PMC9993433 DOI: 10.1117/1.nph.10.2.023515] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 01/11/2023] [Indexed: 05/04/2023]
Abstract
Significance The expansion of functional near-infrared spectroscopy (fNIRS) methodology and analysis tools gives rise to various design and analytical decisions that researchers have to make. Several recent efforts have developed guidelines for preprocessing, analyzing, and reporting practices. For the planning stage of fNIRS studies, similar guidance is desirable. Study preregistration helps researchers to transparently document study protocols before conducting the study, including materials, methods, and analyses, and thus, others to verify, understand, and reproduce a study. Preregistration can thus serve as a useful tool for transparent, careful, and comprehensive fNIRS study design. Aim We aim to create a guide on the design and analysis steps involved in fNIRS studies and to provide a preregistration template specified for fNIRS studies. Approach The presented preregistration guide has a strong focus on fNIRS specific requirements, and the associated template provides examples based on continuous-wave (CW) fNIRS studies conducted in humans. These can, however, be extended to other types of fNIRS studies. Results On a step-by-step basis, we walk the fNIRS user through key methodological and analysis-related aspects central to a comprehensive fNIRS study design. These include items specific to the design of CW, task-based fNIRS studies, but also sections that are of general importance, including an in-depth elaboration on sample size planning. Conclusions Our guide introduces these open science tools to the fNIRS community, providing researchers with an overview of key design aspects and specification recommendations for comprehensive study planning. As such it can be used as a template to preregister fNIRS studies or merely as a tool for transparent fNIRS study design.
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Affiliation(s)
- Philipp A. Schroeder
- University of Tuebingen, Department of Psychology, Faculty of Science, Tuebingen, Germany
| | - Christina Artemenko
- University of Tuebingen, Department of Psychology, Faculty of Science, Tuebingen, Germany
| | - Jessica E. Kosie
- Princeton University, Social and Natural Sciences, Department of Psychology, Princeton, New Jersey, United States
| | - Helena Cockx
- Radboud University, Donders Institute for Brain, Cognition and Behaviour, Biophysics Department, Faculty of Science, Nijmegen, The Netherlands
| | - Katharina Stute
- Chemnitz University of Technology, Institute of Human Movement Science and Health, Faculty of Behavioural and Social Sciences, Chemnitz, Germany
| | - João Pereira
- University of Coimbra, Coimbra Institute for Biomedical Imaging and Translational Research, Coimbra, Portugal
| | - Franziska Klein
- University of Oldenburg, Department of Psychology, Neurocognition and functional Neurorehabilitation Group, Oldenburg (Oldb), Germany
- RWTH Aachen University, Medical School, Department of Psychiatry, Psychotherapy and Psychosomatics, Aachen, Germany
| | - David M. A. Mehler
- RWTH Aachen University, Medical School, Department of Psychiatry, Psychotherapy and Psychosomatics, Aachen, Germany
- University of Münster, Institute for Translational Psychiatry, Medical School, Münster, Germany
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7
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Reer A, Wiebe A, Wang X, Rieger JW. FAIR human neuroscientific data sharing to advance AI driven research and applications: Legal frameworks and missing metadata standards. Front Genet 2023; 14:1086802. [PMID: 37007976 PMCID: PMC10065194 DOI: 10.3389/fgene.2023.1086802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/21/2023] [Indexed: 03/16/2023] Open
Abstract
Modern AI supported research holds many promises for basic and applied science. However, the application of AI methods is often limited because most labs cannot, on their own, acquire large and diverse datasets, which are best for training these methods. Data sharing and open science initiatives promise some relief to the problem, but only if the data are provided in a usable way. The FAIR principles state very general requirements for useful data sharing: they should be findable, accessible, interoperable, and reusable. This article will focus on two challenges to implement the FAIR framework for human neuroscience data. On the one hand, human data can fall under special legal protection. The legal frameworks regulating how and what data can be openly shared differ greatly across countries which can complicate data sharing or even discourage researchers from doing so. Moreover, openly accessible data require standardization of data and metadata organization and annotation in order to become interpretable and useful. This article briefly introduces open neuroscience initiatives that support the implementation of the FAIR principles. It then reviews legal frameworks, their consequences for accessibility of human neuroscientific data and some ethical implications. We hope this comparison of legal jurisdictions helps to elucidate that some alleged obstacles for data sharing only require an adaptation of procedures but help to protect the privacy of our most generous donors to research … our study participants. Finally, it elaborates on the problem of missing standards for metadata annotation and introduces initiatives that aim at developing tools to make neuroscientific data acquisition and analysis pipelines FAIR by design. While the paper focuses on making human neuroscience data useful for data-intensive AI the general considerations hold for other fields where large amounts of openly available human data would be helpful.
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Affiliation(s)
- Aaron Reer
- Applied Neurocognitive Psychology Lab, Institute for Medicine and Healthcare, Department of Psychology, Oldenburg University, Oldenburg, Germany
- *Correspondence: Aaron Reer,
| | - Andreas Wiebe
- Chair for Intellectual Property and Information Law, Göttingen University, Göttingen, Germany
| | - Xu Wang
- Chair for Intellectual Property and Information Law, Göttingen University, Göttingen, Germany
| | - Jochem W. Rieger
- Applied Neurocognitive Psychology Lab, Institute for Medicine and Healthcare, Department of Psychology, Oldenburg University, Oldenburg, Germany
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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: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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Ehlers MR, Lonsdorf TB. Data sharing in experimental fear and anxiety research: From challenges to a dynamically growing database in 10 simple steps. Neurosci Biobehav Rev 2022; 143:104958. [DOI: 10.1016/j.neubiorev.2022.104958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
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10
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Bruña R, Vaghari D, Greve A, Cooper E, Mada MO, Henson RN. Modified MRI Anonymization (De-Facing) for Improved MEG Coregistration. BIOENGINEERING (BASEL, SWITZERLAND) 2022; 9:bioengineering9100591. [PMID: 36290559 PMCID: PMC9598466 DOI: 10.3390/bioengineering9100591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/02/2022] [Accepted: 10/17/2022] [Indexed: 01/28/2023]
Abstract
Localising the sources of MEG/EEG signals often requires a structural MRI to create a head model, while ensuring reproducible scientific results requires sharing data and code. However, sharing structural MRI data often requires the face go be hidden to help protect the identity of the individuals concerned. While automated de-facing methods exist, they tend to remove the whole face, which can impair methods for coregistering the MRI data with the EEG/MEG data. We show that a new, automated de-facing method that retains the nose maintains good MRI-MEG/EEG coregistration. Importantly, behavioural data show that this "face-trimming" method does not increase levels of identification relative to a standard de-facing approach and has less effect on the automated segmentation and surface extraction sometimes used to create head models for MEG/EEG localisation. We suggest that this trimming approach could be employed for future sharing of structural MRI data, at least for those to be used in forward modelling (source reconstruction) of EEG/MEG data.
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Affiliation(s)
- Ricardo Bruña
- Center for Cognitive and Computational Neuroscience, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Department of Radiology, Rehabilitation and Physical Therapy, Universidad Complutense de Madrid, IdISSC, 28040 Madrid, Spain
- Correspondence:
| | - Delshad Vaghari
- Department of Electrical & Computer Engineering, Tarbiat Modares University, Tehran P.O. Box 14115-111, Iran
| | - Andrea Greve
- Medical Research Council Cognition and Brain Sciences Unit, University of Cambridge, Cambridge CB2 7EF, UK
| | - Elisa Cooper
- Medical Research Council Cognition and Brain Sciences Unit, University of Cambridge, Cambridge CB2 7EF, UK
| | - Marius O. Mada
- Medical Research Council Cognition and Brain Sciences Unit, University of Cambridge, Cambridge CB2 7EF, UK
| | - Richard N. Henson
- Medical Research Council Cognition and Brain Sciences Unit, University of Cambridge, Cambridge CB2 7EF, UK
- Department of Psychiatry, University of Cambridge, Cambridge CB2 OSZ, UK
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Mercier MR, Dubarry AS, Tadel F, Avanzini P, Axmacher N, Cellier D, Vecchio MD, Hamilton LS, Hermes D, Kahana MJ, Knight RT, Llorens A, Megevand P, Melloni L, Miller KJ, Piai V, Puce A, Ramsey NF, Schwiedrzik CM, Smith SE, Stolk A, Swann NC, Vansteensel MJ, Voytek B, Wang L, Lachaux JP, Oostenveld R. Advances in human intracranial electroencephalography research, guidelines and good practices. Neuroimage 2022; 260:119438. [PMID: 35792291 PMCID: PMC10190110 DOI: 10.1016/j.neuroimage.2022.119438] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/23/2022] [Accepted: 06/30/2022] [Indexed: 12/11/2022] Open
Abstract
Since the second-half of the twentieth century, intracranial electroencephalography (iEEG), including both electrocorticography (ECoG) and stereo-electroencephalography (sEEG), has provided an intimate view into the human brain. At the interface between fundamental research and the clinic, iEEG provides both high temporal resolution and high spatial specificity but comes with constraints, such as the individual's tailored sparsity of electrode sampling. Over the years, researchers in neuroscience developed their practices to make the most of the iEEG approach. Here we offer a critical review of iEEG research practices in a didactic framework for newcomers, as well addressing issues encountered by proficient researchers. The scope is threefold: (i) review common practices in iEEG research, (ii) suggest potential guidelines for working with iEEG data and answer frequently asked questions based on the most widespread practices, and (iii) based on current neurophysiological knowledge and methodologies, pave the way to good practice standards in iEEG research. The organization of this paper follows the steps of iEEG data processing. The first section contextualizes iEEG data collection. The second section focuses on localization of intracranial electrodes. The third section highlights the main pre-processing steps. The fourth section presents iEEG signal analysis methods. The fifth section discusses statistical approaches. The sixth section draws some unique perspectives on iEEG research. Finally, to ensure a consistent nomenclature throughout the manuscript and to align with other guidelines, e.g., Brain Imaging Data Structure (BIDS) and the OHBM Committee on Best Practices in Data Analysis and Sharing (COBIDAS), we provide a glossary to disambiguate terms related to iEEG research.
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Affiliation(s)
- Manuel R Mercier
- INSERM, INS, Institut de Neurosciences des Systèmes, Aix-Marseille University, Marseille, France.
| | | | - François Tadel
- Signal & Image Processing Institute, University of Southern California, Los Angeles, CA United States of America
| | - Pietro Avanzini
- Institute of Neuroscience, National Research Council of Italy, Parma, Italy
| | - Nikolai Axmacher
- Department of Neuropsychology, Faculty of Psychology, Institute of Cognitive Neuroscience, Ruhr University Bochum, Universitätsstraße 150, Bochum 44801, Germany; State Key Laboratory of Cognitive Neuroscience and Learning and IDG/McGovern Institute for Brain Research, Beijing Normal University, 19 Xinjiekou Outer St, Beijing 100875, China
| | - Dillan Cellier
- Department of Cognitive Science, University of California, La Jolla, San Diego, United States of America
| | - Maria Del Vecchio
- Institute of Neuroscience, National Research Council of Italy, Parma, Italy
| | - Liberty S Hamilton
- Department of Neurology, Dell Medical School, The University of Texas at Austin, Austin, TX, United States of America; Institute for Neuroscience, The University of Texas at Austin, Austin, TX, United States of America; Department of Speech, Language, and Hearing Sciences, Moody College of Communication, The University of Texas at Austin, Austin, TX, United States of America
| | - Dora Hermes
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, United States of America
| | - Michael J Kahana
- Department of Psychology, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Robert T Knight
- Department of Psychology and the Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720, United States of America
| | - Anais Llorens
- Helen Wills Neuroscience Institute, University of California, Berkeley, United States of America
| | - Pierre Megevand
- Department of Clinical neurosciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Lucia Melloni
- Department of Neuroscience, Max Planck Institute for Empirical Aesthetics, Grüneburgweg 14, Frankfurt am Main 60322, Germany; Department of Neurology, NYU Grossman School of Medicine, 145 East 32nd Street, Room 828, New York, NY 10016, United States of America
| | - Kai J Miller
- Department of Neurosurgery, Mayo Clinic, Rochester, MN 55905, USA
| | - Vitória Piai
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Nijmegen, the Netherlands; Department of Medical Psychology, Radboudumc, Donders Centre for Medical Neuroscience, Nijmegen, the Netherlands
| | - Aina Puce
- Department of Psychological & Brain Sciences, Programs in Neuroscience, Cognitive Science, Indiana University, Bloomington, IN, United States of America
| | - Nick F Ramsey
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, UMC Utrecht, the Netherlands
| | - Caspar M Schwiedrzik
- Neural Circuits and Cognition Lab, European Neuroscience Institute Göttingen - A Joint Initiative of the University Medical Center Göttingen and the Max Planck Society, Göttingen, Germany; Perception and Plasticity Group, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Sydney E Smith
- Neurosciences Graduate Program, University of California, La Jolla, San Diego, United States of America
| | - Arjen Stolk
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Nijmegen, the Netherlands; Psychological and Brain Sciences, Dartmouth College, Hanover, NH, United States of America
| | - Nicole C Swann
- University of Oregon in the Department of Human Physiology, United States of America
| | - Mariska J Vansteensel
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, UMC Utrecht, the Netherlands
| | - Bradley Voytek
- Department of Cognitive Science, University of California, La Jolla, San Diego, United States of America; Neurosciences Graduate Program, University of California, La Jolla, San Diego, United States of America; Halıcıoğlu Data Science Institute, University of California, La Jolla, San Diego, United States of America; Kavli Institute for Brain and Mind, University of California, La Jolla, San Diego, United States of America
| | - Liang Wang
- CAS Key Laboratory of Mental Health, Institute of Psychology, Beijing, China; Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Jean-Philippe Lachaux
- Lyon Neuroscience Research Center, EDUWELL Team, INSERM UMRS 1028, CNRS UMR 5292, Université Claude Bernard Lyon 1, Université de Lyon, Lyon F-69000, France
| | - Robert Oostenveld
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Nijmegen, the Netherlands; NatMEG, Karolinska Institutet, Stockholm, Sweden
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12
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Jwa AS, Poldrack RA. The spectrum of data sharing policies in neuroimaging data repositories. Hum Brain Mapp 2022; 43:2707-2721. [PMID: 35142409 PMCID: PMC9057092 DOI: 10.1002/hbm.25803] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 01/19/2022] [Accepted: 01/28/2022] [Indexed: 02/05/2023] Open
Abstract
Sharing data is a scientific imperative that accelerates scientific discoveries, reinforces open science inquiry, and allows for efficient use of public investment and research resources. Considering these benefits, data sharing has been widely promoted in diverse fields and neuroscience has been no exception to this movement. For all its promise, however, the sharing of human neuroimaging data raises critical ethical and legal issues, such as data privacy. Recently, the heightened risks to data privacy posed by the rapid advances in artificial intelligence and machine learning techniques have made data sharing more challenging; the regulatory landscape around data sharing has also been evolving rapidly. Here we present an in-depth ethical and regulatory analysis that examines how neuroimaging data are currently shared against the backdrop of the relevant regulations and policies in the United States and how advanced software tools and algorithms might undermine subjects' privacy in neuroimaging data sharing. The implications of these novel technological threats to privacy in neuroimaging data sharing practices and policies will also be discussed. We then conclude with a proposal for a legal prohibition against malicious use of neuroscience data as a regulatory mechanism to address privacy risks associated with the data while maximizing the benefits of data sharing and open science practice in the field of neuroscience.
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Affiliation(s)
- Anita S. Jwa
- Department of PsychologyStanford UniversityStanfordCaliforniaUSA
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13
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Paret C, Unverhau N, Feingold F, Poldrack RA, Stirner M, Schmahl C, Sicorello M. Survey on Open Science Practices in Functional Neuroimaging. Neuroimage 2022; 257:119306. [PMID: 35595201 DOI: 10.1016/j.neuroimage.2022.119306] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 05/03/2022] [Accepted: 05/10/2022] [Indexed: 12/12/2022] Open
Abstract
Replicability and reproducibility of scientific findings is paramount for sustainable progress in neuroscience. Preregistration of the hypotheses and methods of an empirical study before analysis, the sharing of primary research data, and compliance with data standards such as the Brain Imaging Data Structure (BIDS), are considered effective practices to secure progress and to substantiate quality of research. We investigated the current level of adoption of open science practices in neuroimaging and the difficulties that prevent researchers from using them. Email invitations to participate in the survey were sent to addresses received through a PubMed search of human functional magnetic resonance imaging studies that were published between 2010 and 2020. 283 persons completed the questionnaire. Although half of the participants were experienced with preregistration, the willingness to preregister studies in the future was modest. The majority of participants had experience with the sharing of primary neuroimaging data. Most of the participants were interested in implementing a standardized data structure such as BIDS in their labs. Based on demographic variables, we compared participants on seven subscales, which had been generated through factor analysis. Exploratory analyses found that experienced researchers at lower career level had higher fear of being transparent and researchers with residence in the EU had a higher need for data governance. Additionally, researchers at medical faculties as compared to other university faculties reported a more unsupportive supervisor with regards to open science practices and a higher need for data governance. The results suggest growing adoption of open science practices but also highlight a number of important impediments.
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Affiliation(s)
- Christian Paret
- Department of Psychosomatic Medicine and Psychotherapy, Central Institute of Mental Health Mannheim, Medical Faculty Mannheim / Heidelberg University, Germany; Sagol Brain Institute, Wohl Institute for Advanced Imaging, Tel-Aviv Sourasky Medical Center and School of Psychological Sciences, Tel-Aviv University, Israel.
| | - Nike Unverhau
- Department of Psychosomatic Medicine and Psychotherapy, Central Institute of Mental Health Mannheim, Medical Faculty Mannheim / Heidelberg University, Germany
| | | | | | - Madita Stirner
- Department of Psychosomatic Medicine and Psychotherapy, Central Institute of Mental Health Mannheim, Medical Faculty Mannheim / Heidelberg University, Germany
| | - Christian Schmahl
- Department of Psychosomatic Medicine and Psychotherapy, Central Institute of Mental Health Mannheim, Medical Faculty Mannheim / Heidelberg University, Germany
| | - Maurizio Sicorello
- Department of Psychosomatic Medicine and Psychotherapy, Central Institute of Mental Health Mannheim, Medical Faculty Mannheim / Heidelberg University, Germany
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14
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Rousi AM. Using current research information systems to investigate data acquisition and data sharing practices of computer scientists. JOURNAL OF LIBRARIANSHIP AND INFORMATION SCIENCE 2022. [DOI: 10.1177/09610006221093049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Without sufficient information about research data practices occurring in a particular research organisation, there is a risk of mismatching research data service efforts with the needs of its researchers. This study describes how data acquiring and data sharing occurring within a particular research organisation can be investigated by using current research information system publication data. The case study organisation’s current research information system was used to identify the sample of investigated articles. A sample of 193 journal articles published by researchers in the computer science department of the case study’s university during 2019 were extracted for scrutiny from the current research information system. For these 193 articles, a classification of the main study types was developed to accommodate the multidisciplinary nature of the case department’s research agenda. Furthermore, a coding framework was developed to capture the key elements of data acquiring and data sharing. The articles representing life sciences and computational research relatively frequently reused open data, whereas data acquisition of experimental research, human interaction studies and human intervention studies often relied on collecting original data. Data sharing also differed between the computationally intensive study types of life sciences and computational research and the study types relying on collection of original data. Research data were not available for reuse in only a minority of life science ( n = 2; 7%) and computational research ( n = 15; 14%) studies. The study types of experimental research, human interaction studies and human intervention studies less frequently made their data available for reuse. The findings suggest that research organisations representing computer sciences may include different subfields that have their own cultures of data sharing. This study demonstrates that analyses of publications listed in current research information systems provide detailed descriptions how the affiliated researchers acquire and share research data.
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15
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Kossen T, Hirzel MA, Madai VI, Boenisch F, Hennemuth A, Hildebrand K, Pokutta S, Sharma K, Hilbert A, Sobesky J, Galinovic I, Khalil AA, Fiebach JB, Frey D. Toward Sharing Brain Images: Differentially Private TOF-MRA Images With Segmentation Labels Using Generative Adversarial Networks. Front Artif Intell 2022; 5:813842. [PMID: 35586223 PMCID: PMC9108458 DOI: 10.3389/frai.2022.813842] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/31/2022] [Indexed: 12/03/2022] Open
Abstract
Sharing labeled data is crucial to acquire large datasets for various Deep Learning applications. In medical imaging, this is often not feasible due to privacy regulations. Whereas anonymization would be a solution, standard techniques have been shown to be partially reversible. Here, synthetic data using a Generative Adversarial Network (GAN) with differential privacy guarantees could be a solution to ensure the patient's privacy while maintaining the predictive properties of the data. In this study, we implemented a Wasserstein GAN (WGAN) with and without differential privacy guarantees to generate privacy-preserving labeled Time-of-Flight Magnetic Resonance Angiography (TOF-MRA) image patches for brain vessel segmentation. The synthesized image-label pairs were used to train a U-net which was evaluated in terms of the segmentation performance on real patient images from two different datasets. Additionally, the Fréchet Inception Distance (FID) was calculated between the generated images and the real images to assess their similarity. During the evaluation using the U-Net and the FID, we explored the effect of different levels of privacy which was represented by the parameter ϵ. With stricter privacy guarantees, the segmentation performance and the similarity to the real patient images in terms of FID decreased. Our best segmentation model, trained on synthetic and private data, achieved a Dice Similarity Coefficient (DSC) of 0.75 for ϵ = 7.4 compared to 0.84 for ϵ = ∞ in a brain vessel segmentation paradigm (DSC of 0.69 and 0.88 on the second test set, respectively). We identified a threshold of ϵ <5 for which the performance (DSC <0.61) became unstable and not usable. Our synthesized labeled TOF-MRA images with strict privacy guarantees retained predictive properties necessary for segmenting the brain vessels. Although further research is warranted regarding generalizability to other imaging modalities and performance improvement, our results mark an encouraging first step for privacy-preserving data sharing in medical imaging.
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Affiliation(s)
- Tabea Kossen
- CLAIM-Charité Lab for AI in Medicine, Charité Universitätsmedizin Berlin, Berlin, Germany
- Department of Computer Engineering and Microelectronics, Computer Vision & Remote Sensing, Technical University Berlin, Berlin, Germany
| | - Manuel A. Hirzel
- CLAIM-Charité Lab for AI in Medicine, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Vince I. Madai
- CLAIM-Charité Lab for AI in Medicine, Charité Universitätsmedizin Berlin, Berlin, Germany
- QUEST Center for Responsible Research, Berlin Institute of Health (BIH), Charité-Universitätsmedizin Berlin, Berlin, Germany
- Faculty of Computing, Engineering and the Built Environment, School of Computing and Digital Technology, Birmingham City University, Birmingham, United Kingdom
| | | | - Anja Hennemuth
- Department of Computer Engineering and Microelectronics, Computer Vision & Remote Sensing, Technical University Berlin, Berlin, Germany
- Institute for Imaging Science and Computational Modelling in Cardiovascular Medicine, Charité Universitätsmedizin Berlin, Berlin, Germany
- Fraunhofer MEVIS, Bremen, Germany
| | - Kristian Hildebrand
- Department VI Computer Science and Media, Berlin University of Applied Sciences and Technology, Berlin, Germany
| | - Sebastian Pokutta
- Department for AI in Society, Science, and Technology, Zuse Institute Berlin, Berlin, Germany
- Institute of Mathematics, Technical University Berlin, Berlin, Germany
| | - Kartikey Sharma
- Department for AI in Society, Science, and Technology, Zuse Institute Berlin, Berlin, Germany
| | - Adam Hilbert
- CLAIM-Charité Lab for AI in Medicine, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Jan Sobesky
- Johanna-Etienne-Hospital, Neuss, Germany
- Centre for Stroke Research Berlin, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Ivana Galinovic
- Centre for Stroke Research Berlin, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Ahmed A. Khalil
- Centre for Stroke Research Berlin, Charité Universitätsmedizin Berlin, Berlin, Germany
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Mind, Brain, Body Institute, Berlin School of Mind and Brain, Humboldt-Universität Berlin, Berlin, Germany
| | - Jochen B. Fiebach
- Centre for Stroke Research Berlin, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Dietmar Frey
- CLAIM-Charité Lab for AI in Medicine, Charité Universitätsmedizin Berlin, Berlin, Germany
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16
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Eke DO, Bernard A, Bjaalie JG, Chavarriaga R, Hanakawa T, Hannan AJ, Hill SL, Martone ME, McMahon A, Ruebel O, Crook S, Thiels E, Pestilli F. International data governance for neuroscience. Neuron 2022; 110:600-612. [PMID: 34914921 PMCID: PMC8857067 DOI: 10.1016/j.neuron.2021.11.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/16/2021] [Accepted: 11/15/2021] [Indexed: 12/19/2022]
Abstract
As neuroscience projects increase in scale and cross international borders, different ethical principles, national and international laws, regulations, and policies for data sharing must be considered. These concerns are part of what is collectively called data governance. Whereas neuroscience data transcend borders, data governance is typically constrained within geopolitical boundaries. An international data governance framework and accompanying infrastructure can assist investigators, institutions, data repositories, and funders with navigating disparate policies. Here, we propose principles and operational considerations for how data governance in neuroscience can be navigated at an international scale and highlight gaps, challenges, and opportunities in a global brain data ecosystem. We consider how to approach data governance in a way that balances data protection requirements and the need for open science, so as to promote international collaboration through federated constructs such as the International Brain Initiative (IBI).
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Affiliation(s)
- Damian O Eke
- Centre for Computing and Social Responsibility, De Montfort University, Leicester, UK; Human Brain Project
| | | | | | - Ricardo Chavarriaga
- Center for Artificial Intelligence, School of Engineering, Zurich University of Applied Sciences, Zurich, Switzerland
| | | | - Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Australia
| | - Sean L Hill
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | | | | | - Oliver Ruebel
- Scientific Data Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sharon Crook
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ, USA
| | - Edda Thiels
- National Science Foundation, Alexandria, VA, USA
| | - Franco Pestilli
- Department of Psychology, Center for Perceptual Systems, Center for Theoretical and Computational Neuroscience, and Institute for Neuroscience, University of Texas, Austin, TX, USA.
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17
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Petr J, Hogeboom L, Nikulin P, Wiegers E, Schroyen G, Kallehauge J, Chmelík M, Clement P, Nechifor RE, Fodor LA, De Witt Hamer PC, Barkhof F, Pernet C, Lequin M, Deprez S, Jančálek R, Mutsaerts HJMM, Pizzini FB, Emblem KE, Keil VC. A systematic review on the use of quantitative imaging to detect cancer therapy adverse effects in normal-appearing brain tissue. MAGMA (NEW YORK, N.Y.) 2022; 35:163-186. [PMID: 34919195 PMCID: PMC8901489 DOI: 10.1007/s10334-021-00985-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 11/09/2021] [Accepted: 12/03/2021] [Indexed: 12/17/2022]
Abstract
Cancer therapy for both central nervous system (CNS) and non-CNS tumors has been previously associated with transient and long-term cognitive deterioration, commonly referred to as 'chemo fog'. This therapy-related damage to otherwise normal-appearing brain tissue is reported using post-mortem neuropathological analysis. Although the literature on monitoring therapy effects on structural magnetic resonance imaging (MRI) is well established, such macroscopic structural changes appear relatively late and irreversible. Early quantitative MRI biomarkers of therapy-induced damage would potentially permit taking these treatment side effects into account, paving the way towards a more personalized treatment planning.This systematic review (PROSPERO number 224196) provides an overview of quantitative tomographic imaging methods, potentially identifying the adverse side effects of cancer therapy in normal-appearing brain tissue. Seventy studies were obtained from the MEDLINE and Web of Science databases. Studies reporting changes in normal-appearing brain tissue using MRI, PET, or SPECT quantitative biomarkers, related to radio-, chemo-, immuno-, or hormone therapy for any kind of solid, cystic, or liquid tumor were included. The main findings of the reviewed studies were summarized, providing also the risk of bias of each study assessed using a modified QUADAS-2 tool. For each imaging method, this review provides the methodological background, and the benefits and shortcomings of each method from the imaging perspective. Finally, a set of recommendations is proposed to support future research.
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Affiliation(s)
- Jan Petr
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany.
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam, The Netherlands.
| | - Louise Hogeboom
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Pavel Nikulin
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
| | - Evita Wiegers
- Department of Radiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gwen Schroyen
- Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Jesper Kallehauge
- Danish Center for Particle Therapy, Aarhus University Hospital, Aarhus, Denmark
| | - Marek Chmelík
- Department of Technical Disciplines in Medicine, Faculty of Health Care, University of Prešov, Prešov, Slovakia
| | - Patricia Clement
- Ghent Institute for Functional and Metabolic Imaging (GIfMI), Ghent University, Ghent, Belgium
| | - Ruben E Nechifor
- International Institute for the Advanced Studies of Psychotherapy and Applied Mental Health, Department of Clinical Psychology and Psychotherapy, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Liviu-Andrei Fodor
- International Institute for the Advanced Studies of Psychotherapy and Applied Mental Health, Evidence Based Psychological Assessment and Interventions Doctoral School, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Philip C De Witt Hamer
- Department of Neurosurgery, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Frederik Barkhof
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam, The Netherlands
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Cyril Pernet
- Neurobiology Research Unit, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Maarten Lequin
- Department of Radiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sabine Deprez
- Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Radim Jančálek
- St. Anne's University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Henk J M M Mutsaerts
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Ghent Institute for Functional and Metabolic Imaging (GIfMI), Ghent University, Ghent, Belgium
| | - Francesca B Pizzini
- Radiology, Deptartment of Diagnostic and Public Health, Verona University, Verona, Italy
| | - Kyrre E Emblem
- Department of Diagnostic Physics, Division of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway
| | - Vera C Keil
- Department of Radiology and Nuclear Medicine, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam, The Netherlands
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18
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Scan Once, Analyse Many: Using Large Open-Access Neuroimaging Datasets to Understand the Brain. Neuroinformatics 2022; 20:109-137. [PMID: 33974213 PMCID: PMC8111663 DOI: 10.1007/s12021-021-09519-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2021] [Indexed: 02/06/2023]
Abstract
We are now in a time of readily available brain imaging data. Not only are researchers now sharing data more than ever before, but additionally large-scale data collecting initiatives are underway with the vision that many future researchers will use the data for secondary analyses. Here I provide an overview of available datasets and some example use cases. Example use cases include examining individual differences, more robust findings, reproducibility-both in public input data and availability as a replication sample, and methods development. I further discuss a variety of considerations associated with using existing data and the opportunities associated with large datasets. Suggestions for further readings on general neuroimaging and topic-specific discussions are also provided.
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19
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Elam JS, Glasser MF, Harms MP, Sotiropoulos SN, Andersson JLR, Burgess GC, Curtiss SW, Oostenveld R, Larson-Prior LJ, Schoffelen JM, Hodge MR, Cler EA, Marcus DM, Barch DM, Yacoub E, Smith SM, Ugurbil K, Van Essen DC. The Human Connectome Project: A retrospective. Neuroimage 2021; 244:118543. [PMID: 34508893 PMCID: PMC9387634 DOI: 10.1016/j.neuroimage.2021.118543] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/13/2021] [Accepted: 08/30/2021] [Indexed: 01/21/2023] Open
Abstract
The Human Connectome Project (HCP) was launched in 2010 as an ambitious effort to accelerate advances in human neuroimaging, particularly for measures of brain connectivity; apply these advances to study a large number of healthy young adults; and freely share the data and tools with the scientific community. NIH awarded grants to two consortia; this retrospective focuses on the "WU-Minn-Ox" HCP consortium centered at Washington University, the University of Minnesota, and University of Oxford. In just over 6 years, the WU-Minn-Ox consortium succeeded in its core objectives by: 1) improving MR scanner hardware, pulse sequence design, and image reconstruction methods, 2) acquiring and analyzing multimodal MRI and MEG data of unprecedented quality together with behavioral measures from more than 1100 HCP participants, and 3) freely sharing the data (via the ConnectomeDB database) and associated analysis and visualization tools. To date, more than 27 Petabytes of data have been shared, and 1538 papers acknowledging HCP data use have been published. The "HCP-style" neuroimaging paradigm has emerged as a set of best-practice strategies for optimizing data acquisition and analysis. This article reviews the history of the HCP, including comments on key events and decisions associated with major project components. We discuss several scientific advances using HCP data, including improved cortical parcellations, analyses of connectivity based on functional and diffusion MRI, and analyses of brain-behavior relationships. We also touch upon our efforts to develop and share a variety of associated data processing and analysis tools along with detailed documentation, tutorials, and an educational course to train the next generation of neuroimagers. We conclude with a look forward at opportunities and challenges facing the human neuroimaging field from the perspective of the HCP consortium.
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Affiliation(s)
| | | | - Michael P Harms
- Washington University School of Medicine, St. Louis, MO, USA
| | - Stamatios N Sotiropoulos
- Sir Peter Mansfield Imaging Centre & NIHR Nottingham Biomedical Research Centre, Queen's Medical Centre, School of Medicine, University of Nottingham, UK; Wellcome Centre for Integrative Neuroimaging, University of Oxford, UK
| | | | | | | | - Robert Oostenveld
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, the Netherlands
| | | | - Jan-Mathijs Schoffelen
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, the Netherlands
| | - Michael R Hodge
- Washington University School of Medicine, St. Louis, MO, USA
| | - Eileen A Cler
- Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel M Marcus
- Washington University School of Medicine, St. Louis, MO, USA
| | - Deanna M Barch
- Washington University School of Medicine, St. Louis, MO, USA
| | - Essa Yacoub
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, USA
| | - Stephen M Smith
- Wellcome Centre for Integrative Neuroimaging, University of Oxford, UK
| | - Kamil Ugurbil
- Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN, USA
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20
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Large, open datasets for human connectomics research: Considerations for reproducible and responsible data use. Neuroimage 2021; 244:118579. [PMID: 34536537 DOI: 10.1016/j.neuroimage.2021.118579] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 08/27/2021] [Accepted: 09/14/2021] [Indexed: 12/19/2022] Open
Abstract
Large, open datasets have emerged as important resources in the field of human connectomics. In this review, the evolution of data sharing involving magnetic resonance imaging is described. A summary of the challenges and progress in conducting reproducible data analyses is provided, including description of recent progress made in the development of community guidelines and recommendations, software and data management tools, and initiatives to enhance training and education. Finally, this review concludes with a discussion of ethical conduct relevant to analyses of large, open datasets and a researcher's responsibility to prevent further stigmatization of historically marginalized racial and ethnic groups. Moving forward, future work should include an enhanced emphasis on the social determinants of health, which may further contextualize findings among diverse population-based samples. Leveraging the progress to date and guided by interdisciplinary collaborations, the future of connectomics promises to be an impressive era of innovative research, yielding a more inclusive understanding of brain structure and function.
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21
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Multiple sclerosis lesions segmentation from multiple experts: The MICCAI 2016 challenge dataset. Neuroimage 2021; 244:118589. [PMID: 34563682 DOI: 10.1016/j.neuroimage.2021.118589] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/03/2021] [Accepted: 09/16/2021] [Indexed: 11/23/2022] Open
Abstract
MRI plays a crucial role in multiple sclerosis diagnostic and patient follow-up. In particular, the delineation of T2-FLAIR hyperintense lesions is crucial although mostly performed manually - a tedious task. Many methods have thus been proposed to automate this task. However, sufficiently large datasets with a thorough expert manual segmentation are still lacking to evaluate these methods. We present a unique dataset for MS lesions segmentation evaluation. It consists of 53 patients acquired on 4 different scanners with a harmonized protocol. Hyperintense lesions on FLAIR were manually delineated on each patient by 7 experts with control on T2 sequence, and gathered in a consensus segmentation for evaluation. We provide raw and preprocessed data and a split of the dataset into training and testing data, the latter including data from a scanner not present in the training dataset. We strongly believe that this dataset will become a reference in MS lesions segmentation evaluation, allowing to evaluate many aspects: evaluation of performance on unseen scanner, comparison to individual experts performance, comparison to other challengers who already used this dataset, etc.
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22
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Markiewicz CJ, Gorgolewski KJ, Feingold F, Blair R, Halchenko YO, Miller E, Hardcastle N, Wexler J, Esteban O, Goncavles M, Jwa A, Poldrack R. The OpenNeuro resource for sharing of neuroscience data. eLife 2021; 10:e71774. [PMID: 34658334 PMCID: PMC8550750 DOI: 10.7554/elife.71774] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/15/2021] [Indexed: 11/25/2022] Open
Abstract
The sharing of research data is essential to ensure reproducibility and maximize the impact of public investments in scientific research. Here, we describe OpenNeuro, a BRAIN Initiative data archive that provides the ability to openly share data from a broad range of brain imaging data types following the FAIR principles for data sharing. We highlight the importance of the Brain Imaging Data Structure standard for enabling effective curation, sharing, and reuse of data. The archive presently shares more than 600 datasets including data from more than 20,000 participants, comprising multiple species and measurement modalities and a broad range of phenotypes. The impact of the shared data is evident in a growing number of published reuses, currently totalling more than 150 publications. We conclude by describing plans for future development and integration with other ongoing open science efforts.
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Affiliation(s)
| | | | | | - Ross Blair
- Department of Psychology, Stanford UniversityStanfordUnited States
| | - Yaroslav O Halchenko
- Department of Psychological & Brain Sciences, Dartmouth CollegeHanoverUnited States
| | | | | | - Joe Wexler
- Department of Psychology, Stanford UniversityStanfordUnited States
| | - Oscar Esteban
- Department of Psychology, Stanford UniversityStanfordUnited States
- Lausanne University Hospital and University of LausanneLausanneSwitzerland
| | | | - Anita Jwa
- Department of Psychology, Stanford UniversityStanfordUnited States
| | - Russell Poldrack
- Department of Psychology, Stanford UniversityStanfordUnited States
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23
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Gau R, Noble S, Heuer K, Bottenhorn KL, Bilgin IP, Yang YF, Huntenburg JM, Bayer JMM, Bethlehem RAI, Rhoads SA, Vogelbacher C, Borghesani V, Levitis E, Wang HT, Van Den Bossche S, Kobeleva X, Legarreta JH, Guay S, Atay SM, Varoquaux GP, Huijser DC, Sandström MS, Herholz P, Nastase SA, Badhwar A, Dumas G, Schwab S, Moia S, Dayan M, Bassil Y, Brooks PP, Mancini M, Shine JM, O'Connor D, Xie X, Poggiali D, Friedrich P, Heinsfeld AS, Riedl L, Toro R, Caballero-Gaudes C, Eklund A, Garner KG, Nolan CR, Demeter DV, Barrios FA, Merchant JS, McDevitt EA, Oostenveld R, Craddock RC, Rokem A, Doyle A, Ghosh SS, Nikolaidis A, Stanley OW, Uruñuela E. Brainhack: Developing a culture of open, inclusive, community-driven neuroscience. Neuron 2021; 109:1769-1775. [PMID: 33932337 DOI: 10.1016/j.neuron.2021.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/23/2021] [Accepted: 04/01/2021] [Indexed: 11/25/2022]
Abstract
Brainhack is an innovative meeting format that promotes scientific collaboration and education in an open, inclusive environment. This NeuroView describes the myriad benefits for participants and the research community and how Brainhacks complement conventional formats to augment scientific progress.
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Affiliation(s)
- Rémi Gau
- Institute of Psychology, Université Catholique de Louvain, Louvain la Neuve, Belgium.
| | - Stephanie Noble
- Radiology & Biomedical Imaging, Yale University, New Haven CT, USA
| | - Katja Heuer
- Center for Research and Interdisciplinarity, Université of Paris, Paris, France; Department of Neuropsychology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | | | - Isil P Bilgin
- Biomedical Engineering, Cybernetics, University of Reading, Reading, UK; Allied Health Professions Institute, University of the West of England, Bristol, UK
| | - Yu-Fang Yang
- Department of Psychology, University of Würzburg, Würzburg, Germany
| | | | - Johanna M M Bayer
- Centre for Youth Mental Health, University of Melbourne, Melbourne, Australia; Orygen Youth Health, Melbourne, Australia
| | - Richard A I Bethlehem
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK; Brain Mapping Unit, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Shawn A Rhoads
- Department of Psychology, Georgetown University, Washington DC, USA
| | - Christoph Vogelbacher
- Laboratory for Multimodal Neuroimaging, Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany
| | - Valentina Borghesani
- Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, Université de Montréal, Montréal, QC, Canada
| | - Elizabeth Levitis
- Section on Developmental Neurogenomics, National Institute of Mental Health, Bethesda, MD, USA; Centre for Medical Image Computing, Department of Computer Science, University College London, London, UK
| | - Hao-Ting Wang
- Sackler Centre for Consciousness Science, University of Sussex, Brighton, UK; Department of Neuroscience, Brighton and Sussex Medical School, University of Sussex, Brighton, UK; Sussex Neuroscience, University of Sussex, Brighton, UK
| | - Sofie Van Den Bossche
- Department of Data Analysis, Faculty of Psychology and Educational Sciences, Ghent University, Ghent, Belgium
| | - Xenia Kobeleva
- Department of Neurology, University of Bonn, Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Samuel Guay
- Université de Montréal, Montréal, QC, Canada
| | - Selim Melvin Atay
- Neuroscience and Neurotechnology, Middle East Technical University, Ankara, Turkey
| | - Gael P Varoquaux
- Parietal, INRIA, Saclay, France; Montréal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Dorien C Huijser
- Erasmus School of Social and Behavioural Sciences, Erasmus University Rotterdam, Rotterdam, the Netherlands; Developmental and Educational Psychology, Leiden University, Leiden, the Netherlands
| | | | - Peer Herholz
- NeuroDataScience - ORIGAMI laboratory, Faculty of Medicine and Health Sciences McGill University Montréal, QC Canada
| | - Samuel A Nastase
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - AmanPreet Badhwar
- Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, Université de Montréal, Montréal, QC, Canada; Multiomics Investigation of Neurodegenerative Diseases (MIND) Lab, Université de Montréal, Montréal, QC, Canada; Département de Pharmacologie et Physiologie, Université de Montréal, Montréal, QC, Canada
| | - Guillaume Dumas
- Department of Psychiatry, Université de Montréal, Montréal, QC, Canada; Mila, Université de Montréal, Montréal, QC, Canada
| | - Simon Schwab
- Department of Biostatistics & Center for Reproducible Science, University of Zurich, Zurich, Switzerland
| | - Stefano Moia
- Basque Center on Cognition, Brain and Language, San Sebastián-Donostia, Spain; University of the Basque Country (EHU UPV), San Sebastián-Donostia, Spain
| | - Michael Dayan
- Human Neuroscience Platform, Fondation Campus Biotech Geneva, Geneva, Switzerland
| | - Yasmine Bassil
- Graduate Division of Biological & Biomedical Sciences, Emory University, Atlanta, GA, USA
| | - Paula P Brooks
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Matteo Mancini
- Department of Neuroscience, Brighton and Sussex Medical School, University of Sussex, Brighton, UK; Cardiff University Brain Research Imaging Centre, Cardiff University, Cardiff, UK; NeuroPoly Lab, Polytechnique Montréal, Montréal, QC, Canada
| | - James M Shine
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - David O'Connor
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Xihe Xie
- Department of Neuroscience, Weill Cornell Medicine, New York City, NY, USA
| | - Davide Poggiali
- Padova Neuroscience Center, University of Padova, Padova, Italy
| | - Patrick Friedrich
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich, Jülich, Germany
| | - Anibal S Heinsfeld
- Computational Neuroimaging Lab, University of Texas at Austin, Austin, TX, USA; Department of Computer Science, University of Texas at Austin, Austin, TX, USA
| | - Lydia Riedl
- Department of Psychiatry and Psychotherapy, Philipps Universität, Marburg, Germany
| | - Roberto Toro
- Center for Research and Interdisciplinarity, Université of Paris, Paris, France; Neuroscience Department, Institut Pasteur, Paris, France
| | | | - Anders Eklund
- Department of Biomedical Engineering, Linköping University, Linköping, Sweden; Department of Computer and Information Science, Linköping University, Linköping, Sweden; Center for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden
| | - Kelly G Garner
- Queensland Brain Institute, The University of Queensland, St Lucia, Australia; School of Psychology, University of Birmingham, Birmingham, UK; School of Psychology, The University of Queensland, St Lucia, Australia
| | | | - Damion V Demeter
- Psychology Department, The University of Texas at Austin, Austin, TX, USA
| | - Fernando A Barrios
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Junaid S Merchant
- Neuroscience and Cognitive Science Program, University of Maryland, College Park, MD, USA; Department of Psychology, University of Maryland, College Park, MD, USA
| | | | - Robert Oostenveld
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands; NatMEG, Karolinska Institutet, Stockholm, Sweden
| | - R Cameron Craddock
- Department of Diagnostic Medicine, The University of Texas at Austin Dell Medical School, Austin, TX, USA
| | - Ariel Rokem
- Psychology and eScience Institute, University of Washington, Seattle, WA, USA
| | - Andrew Doyle
- McGill Centre for Integrative Neuroscience, McGill University, Montréal, QC, Canada
| | - Satrajit S Ghosh
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA; Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School, Boston, MA, USA
| | - Aki Nikolaidis
- Center for the Developing Brain, Child Mind Institute, New York City, NY, USA
| | - Olivia W Stanley
- Centre for Functional and Metabolic Mapping, University of Western Ontario, London, ON, Canada; Department of Medical Biophysics, University of Western Ontario, London, ON, Canada
| | - Eneko Uruñuela
- Basque Center on Cognition, Brain and Language, San Sebastián-Donostia, Spain; University of the Basque Country (EHU UPV), San Sebastián-Donostia, Spain
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24
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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: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [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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25
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Bannier E, Barker G, Borghesani V, Broeckx N, Clement P, Emblem KE, Ghosh S, Glerean E, Gorgolewski KJ, Havu M, Halchenko YO, Herholz P, Hespel A, Heunis S, Hu Y, Hu CP, Huijser D, de la Iglesia Vayá M, Jancalek R, Katsaros VK, Kieseler ML, Maumet C, Moreau CA, Mutsaerts HJ, Oostenveld R, Ozturk-Isik E, Pascual Leone Espinosa N, Pellman J, Pernet CR, Pizzini FB, Trbalić AŠ, Toussaint PJ, Visconti di Oleggio Castello M, Wang F, Wang C, Zhu H. The Open Brain Consent: Informing research participants and obtaining consent to share brain imaging data. Hum Brain Mapp 2021; 42:1945-1951. [PMID: 33522661 PMCID: PMC8046140 DOI: 10.1002/hbm.25351] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 02/06/2023] Open
Abstract
Having the means to share research data openly is essential to modern science. For human research, a key aspect in this endeavor is obtaining consent from participants, not just to take part in a study, which is a basic ethical principle, but also to share their data with the scientific community. To ensure that the participants' privacy is respected, national and/or supranational regulations and laws are in place. It is, however, not always clear to researchers what the implications of those are, nor how to comply with them. The Open Brain Consent (https://open-brain-consent.readthedocs.io) is an international initiative that aims to provide researchers in the brain imaging community with information about data sharing options and tools. We present here a short history of this project and its latest developments, and share pointers to consent forms, including a template consent form that is compliant with the EU general data protection regulation. We also share pointers to an associated data user agreement that is not only useful in the EU context, but also for any researchers dealing with personal (clinical) data elsewhere.
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Affiliation(s)
- Elise Bannier
- Radiology Department, CHU Rennes, Rennes, France.,Inria, CNRS, Inserm, IRISA UMR 6074, Empenn ERL, University of Rennes, Rennes, France
| | - Gareth Barker
- Department of Neuroimaging, King's College London, London, United Kingdom
| | - Valentina Borghesani
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, California, USA
| | - Nils Broeckx
- Dewallens & partners law firm, Leuven, Belgium & Antwerp Health Law and Ethics Chair (AHLEC) and P2 research group, Faculty of law, University of Antwerp, Antwerp, Belgium
| | - Patricia Clement
- Ghent Institute for functional and Metabolic Imaging, Ghent University, Ghent, Belgium
| | | | - Satrajit Ghosh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School, Boston, Massachusetts, USA.,Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School, Boston, Massachusetts, USA
| | - Enrico Glerean
- Aalto University, Espoo, Finland.,International Laboratory of Social Neurobiology, Institute of Cognitive Neuroscience, National Research University Higher School of Economics, Moscow, Russia
| | | | - Marko Havu
- Department of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland
| | | | - Peer Herholz
- NeuroDataScience - ORIGAMI laboratory, McConnell Brain Imaging Centre, The Neuro (Montreal Neurological Institute-Hospital), Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | | | - Stephan Heunis
- Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Yue Hu
- Institute for Experimental Psychology, Heinrich-Heine-University of Düsseldorf, Düsseldorf, Germany
| | - Chuan-Peng Hu
- School of Psychology, Nanjing Normal University, Nanjing, China
| | - Dorien Huijser
- Erasmus University Rotterdam, Rotterdam, The Netherlands
| | - María de la Iglesia Vayá
- Biomedical Imaging Unit FISABIO-CIPF, Foundation for the Promotion of Health and Biomedical Research of the Valencian Community, Valencia, Spain
| | - Radim Jancalek
- Department of Neurosurgery, St. Anne's University Hospital, Masaryk University, Brno, Czech Republic
| | - Vasileios K Katsaros
- Department of Advanced Imaging Modalities, MRI Unit, General Anti-Cancer and Oncological Hospital of Athens"St. Savvas", National and Kapodistrian University of Athens, Athens, Greece.,Department of Neurosurgery and Neurology, National and Kapodistrian University of Athens, Athens, Greece
| | - Marie-Luise Kieseler
- Department of Psychological and Brain Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Camille Maumet
- Inria, University of Rennes, CNRS, Inserm, IRISA UMR 6074, Empenn ERL U 1228, Rennes, France
| | | | - Henk-Jan Mutsaerts
- Department of Radiology and Nuclear Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands.,Department of Radiology and Nuclear Medicine, University Hospital Ghent, Ghent, Belgium
| | - Robert Oostenveld
- Donders Institute for Brain, Cognition and Behaviour; Radboud University, Nijmegen, The Netherlands
| | | | - Nicolas Pascual Leone Espinosa
- Biomedical Imaging Unit, FISABIO-CIPF, Foundation for the Promotion of Health and Biomedical Research of the Valencian Community, Valencia, Spain
| | - John Pellman
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, New York, USA
| | - Cyril R Pernet
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | | | - Paule-Joanne Toussaint
- McGill University, Montreal Neurological Institute and Hospital, Montreal, Quebec, Canada
| | | | - Fengjuan Wang
- National Institute of Education, Nanyang Technological University, Singapore, Singapore
| | - Cheng Wang
- School of Health, Fujian Medical University, Fuzhou, China
| | - Hua Zhu
- Department of Biological Medicine and Engineering, BUAA, Beihang University, Beijing, China
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