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      Brainhack: a collaborative workshop for the open neuroscience community

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      GigaScience
      BioMed Central
      Hackathon, Unconference, Open science, Neuroscience, Data sharing, Collaboration, Networking

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          Abstract

          Brainhack events offer a novel workshop format with participant-generated content that caters to the rapidly growing open neuroscience community. Including components from hackathons and unconferences, as well as parallel educational sessions, Brainhack fosters novel collaborations around the interests of its attendees. Here we provide an overview of its structure, past events, and example projects. Additionally, we outline current innovations such as regional events and post-conference publications. Through introducing Brainhack to the wider neuroscience community, we hope to provide a unique conference format that promotes the features of collaborative, open science.

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          Most cited references12

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          Measuring the thickness of the human cerebral cortex from magnetic resonance images.

          Accurate and automated methods for measuring the thickness of human cerebral cortex could provide powerful tools for diagnosing and studying a variety of neurodegenerative and psychiatric disorders. Manual methods for estimating cortical thickness from neuroimaging data are labor intensive, requiring several days of effort by a trained anatomist. Furthermore, the highly folded nature of the cortex is problematic for manual techniques, frequently resulting in measurement errors in regions in which the cortical surface is not perpendicular to any of the cardinal axes. As a consequence, it has been impractical to obtain accurate thickness estimates for the entire cortex in individual subjects, or group statistics for patient or control populations. Here, we present an automated method for accurately measuring the thickness of the cerebral cortex across the entire brain and for generating cross-subject statistics in a coordinate system based on cortical anatomy. The intersubject standard deviation of the thickness measures is shown to be less than 0.5 mm, implying the ability to detect focal atrophy in small populations or even individual subjects. The reliability and accuracy of this new method are assessed by within-subject test-retest studies, as well as by comparison of cross-subject regional thickness measures with published values.
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            The Autism Brain Imaging Data Exchange: Towards Large-Scale Evaluation of the Intrinsic Brain Architecture in Autism

            Autism spectrum disorders (ASD) represent a formidable challenge for psychiatry and neuroscience because of their high prevalence, life-long nature, complexity and substantial heterogeneity. Facing these obstacles requires large-scale multidisciplinary efforts. While the field of genetics has pioneered data sharing for these reasons, neuroimaging had not kept pace. In response, we introduce the Autism Brain Imaging Data Exchange (ABIDE) – a grassroots consortium aggregating and openly sharing 1112 existing resting-state functional magnetic resonance imaging (R-fMRI) datasets with corresponding structural MRI and phenotypic information from 539 individuals with ASD and 573 age-matched typical controls (TC; 7–64 years) (http://fcon_1000.projects.nitrc.org/indi/abide/). Here, we present this resource and demonstrate its suitability for advancing knowledge of ASD neurobiology based on analyses of 360 males with ASD and 403 male age-matched TC. We focused on whole-brain intrinsic functional connectivity and also survey a range of voxel-wise measures of intrinsic functional brain architecture. Whole-brain analyses reconciled seemingly disparate themes of both hypo and hyperconnectivity in the ASD literature; both were detected, though hypoconnectivity dominated, particularly for cortico-cortical and interhemispheric functional connectivity. Exploratory analyses using an array of regional metrics of intrinsic brain function converged on common loci of dysfunction in ASD (mid and posterior insula, posterior cingulate cortex), and highlighted less commonly explored regions such as thalamus. The survey of the ABIDE R-fMRI datasets provides unprecedented demonstrations of both replication and novel discovery. By pooling multiple international datasets, ABIDE is expected to accelerate the pace of discovery setting the stage for the next generation of ASD studies.
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              Automatic "pipeline" analysis of 3-D MRI data for clinical trials: application to multiple sclerosis.

              The quantitative analysis of magnetic resonance imaging (MRI) data has become increasingly important in both research and clinical studies aiming at human brain development, function, and pathology. Inevitably, the role of quantitative image analysis in the evaluation of drug therapy will increase, driven in part by requirements imposed by regulatory agencies. However, the prohibitive length of time involved and the significant intraand inter-rater variability of the measurements obtained from manual analysis of large MRI databases represent major obstacles to the wider application of quantitative MRI analysis. We have developed a fully automatic "pipeline" image analysis framework and have successfully applied it to a number of large-scale, multicenter studies (more than 1,000 MRI scans). This pipeline system is based on robust image processing algorithms, executed in a parallel, distributed fashion. This paper describes the application of this system to the automatic quantification of multiple sclerosis lesion load in MRI, in the context of a phase III clinical trial. The pipeline results were evaluated through an extensive validation study, revealing that the obtained lesion measurements are statistically indistinguishable from those obtained by trained human observers. Given that intra- and inter-rater measurement variability is eliminated by automatic analysis, this system enhances the ability to detect small treatment effects not readily detectable through conventional analysis techniques. While useful for clinical trial analysis in multiple sclerosis, this system holds widespread potential for applications in other neurological disorders, as well as for the study of neurobiology in general.
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                Author and article information

                Contributors
                cameron.craddock@gmail.com
                margulies@cbs.mpg.de
                pierre.bellec@criugm.qc.ca
                nolan.nichols@gmail.com
                alcauter@gmail.com
                fbarrios@unam.mx
                yburnod@gmail.com
                Christopher.Cannistraci@mssm.edu
                jcohen@polymtl.ca
                benjamin.de-leener@polymtl.ca
                sderymail@gmail.com
                Jonathan.Downar@uhn.ca
                katharine.dunlop@gmail.com
                alexandre.franco@pucrs.br
                cfroehlich@nki.rfmh.org
                GerberA@nyspi.columbia.edu
                satra@mit.edu
                tgrabow@uw.edu
                sean.hill@incf.org
                anibal.heinsfeld@acad.pucrs.br
                rhutchison@fas.harvard.edu
                prantik.kundu@mssm.edu
                alaird@fiu.edu
                sliew@usc.edu
                danjlurie@gmail.com
                donald@biospective.com
                felipe.meneguzzi@pucrs.br
                mennes.maarten@gmail.com
                salma.mesmoudi@gmail.com
                david.oconnor@childmind.org
                pasayeric@hotmail.com
                spelt@umich.edu
                jbpoline@gmail.com
                gautam.prasad@loni.usc.edu
                ramon.pereira@acad.pucrs.br
                pioliqui@gmail.com
                arokem@gmail.com
                ziad.ss@gmail.com
                yonggang.shi@loni.usc.edu
                sstrother@research.baycrest.org
                rto@pasteur.fr
                l.uddin@miami.edu
                jvanhorn@usc.edu
                john.vanmeter.phd@gmail.com
                rcwelsh@umich.edu
                ting.xu@childmind.org
                Journal
                Gigascience
                Gigascience
                GigaScience
                BioMed Central (London )
                2047-217X
                31 March 2016
                31 March 2016
                2016
                : 5
                : 16
                Affiliations
                [ ]The Neuro Bureau, Leipzig, 04317 Germany
                [ ]Computational Neuroimaging Lab, Center for Biomedical Imaging and Neuromodulation, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, New York, 10962 USA
                [ ]Center for the Developing Brain, Child Mind Institute, New York, New York, 10022 USA
                [ ]Max Planck Research Group for Neuroanatomy & Connectivity, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, 04103 Germany
                [ ]Département d’Informatique et de Recherche Opérationnelle, Université de Montréal, Montréal, Québec H3W 1W5, Canada
                [ ]Functional Neuroimaging Unit, Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal, Montréal, Québec H3W 1W5, Canada
                [ ]Center for Health Sciences, SRI International, Menlo Park, California, 94025 USA
                [ ]Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California, 94305 USA
                [ ]Instituto De Neurobiología, Universidad Nacional Autónoma de México, Querétaro, 76203 México
                [ ]Laboratoire d’Imagerie Biomédicale, Sorbonne Universités, UPMC Université Paris 06, Paris, 75005 France
                [ ]Institut des Systèmes Complexes de Paris-Île-de-France, Paris, 75013 France
                [ ]Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 10029 USA
                [ ]Institute of Biomedical Engineering, Ecole Polytechnique de Montréal, Montréal, Québec H3T 1J4, Canada
                [ ]McConnell Brain Imaging Center, Montreal Neurological Institute, Montreal, Quebec H3A 2B4, Canada
                [ ]MRI-Guided rTMS Clinic, University Health Network, Toronto, Ontario M5T 2S8, Canada
                [ ]Department of Psychiatry, University Health Network, University of Toronto, Toronto, Ontario M5T 2S8, Canada
                [ ]Institute of Medical Sciences, University of Toronto, Toronto, Ontario M5S 1A8, Canada
                [ ]Faculdade de Engenharia, PUCRS, Porto Alegre, 90619 Brazil
                [ ]Instituto do Cérebro do Rio Grande do Sul, PUCRS, Porto Alegre, 90610 Brazil
                [ ]Faculdade de Medicina, PUCRS, Porto Alegre, 90619 Brazil
                [ ]New York State Psychiatric Institute, New York, New York, 10032 USA
                [ ]Division of Child and Adolescent Psychiatry, Department of Psychiatry, Columbia University, New York, New York, 10032 USA
                [ ]McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
                [ ]Department of Otology and Laryngology, Harvard Medical School, Boston, Massachusetts, 02115 USA
                [ ]Department of Radiology, University of Washington, Seattle, Washington, 98105 USA
                [ ]Department of Neurology, University of Washington, Seattle, Washington, 98105 USA
                [ ]International Neuroinformatics Coordinating Facility, Stockholm, 171 77 Sweden
                [ ]Karolinska Institutet, Stockholm, 171 77 Sweden
                [ ]Faculdade de Informática, PUCRS, Porto Alegre, 90619 Brazil
                [ ]Center for Brain Science, Harvard University, Cambridge, Massachusetts, 02138 USA
                [ ]Department of Physics, Florida International University, Miami, Florida, 33199 USA
                [ ]Chan Division of Occupational Science and Occupational Therapy, Division of Physical Therapy and Biokinesiology, Department of Neurology, University of Southern California, Los Angeles, California, 90033 USA
                [ ]USC Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Los Angeles, Canada, 90033 USA
                [ ]Department of Psychology,, University of California, Berkeley, California, 94720 USA
                [ ]Biospective, Inc., Montréal,, Québec H4P 1K6, Canada
                [ ]Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA
                [ ]Radboud University Nijmegen, Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Nijmegen, 6525 EN The Netherlands
                [ ]Sorbonne Universités, Paris-1 Université, Equipement d’Excellence MATRICE, Paris, 75005, France
                [ ]Functional MRI Laboratory, University of Michigan, Ann Arbor, Michigan, 48109 USA
                [ ]Helen Wills Neuroscience Institute, University of California, Berkeley, California, 94720 USA
                [ ]Henry H. Wheeler Jr. Brain Imaging Center, University of California, Berkeley, California, 94709 USA
                [ ]Laboratory of Neuro Imaging, Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of University of Southern California, Los Angeles, California, 90033 USA
                [ ]The University of Washington eScience Institute, Seattle, Washington, 98195 USA
                [ ]Scientific and Statistical Computing Core, National Institute of Mental Health, Bethesda, Maryland, 20892 USA
                [ ]Rotman Research Institute, Baycrest Hospital, Toronto, Ontario M6A 2E1, Canada
                [ ]Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
                [ ]Human Genetics and Cognitive Functions Unit, Institut Pasteur, Paris, 75015 France
                [ ]Unité Mixte de Recherche 3571, Genes, Synapses and Cognition, Centre National de la Recherche Scientifique, Institut Pasteur, Paris, 75015 France
                [ ]Department of Psychology, University of Miami, Coral Gables, Florida, 33124 USA
                [ ]Neuroscience Program, University of Miami Miller School of Medicine, Miami, Florida, 33136 USA
                [ ]Center for Functional and Molecular Imaging, Georgetown University Medical Center, Washington,, 20007 DC USA
                [ ]Department of Psychiatry, University of Michigan, Ann Arbor, Michigan, 48109 USA
                [ ]Department of Radiology,, University of Michigan, Ann Arbor, Michigan, 48109 USA
                Article
                121
                10.1186/s13742-016-0121-x
                4818387
                27042293
                18a1ee2d-eb33-46ad-a24d-5014d6163d71
                © Craddock et al. 2016

                Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 8 February 2016
                : 15 March 2016
                Funding
                Funded by: Allen Institute for Brain Science
                Funded by: FundRef http://dx.doi.org/10.13039/100008536, Amazon Web Services;
                Funded by: Athinoula A. Martinos Center for Biomedical Imaging
                Funded by: Child Mind Institute, Inc
                Funded by: FIU Division of Research
                Funded by: Frontiers
                Funded by: Frontiers in Neuroscience
                Funded by: International Neuroinformatics Coordinating Facility
                Funded by: MATRICE
                Funded by: Max Planck Institute for Cognitive and Brain Sciences
                Funded by: Microsoft Azure
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Funded by: Organization for Human Brain Mapping
                Funded by: FundRef http://dx.doi.org/10.13039/100008914, Ontario Brain Institute;
                Funded by: Quebec Bio-Imaging Network
                Funded by: Siemens Medical Systems
                Funded by: University of Miami Flipse Funds
                Funded by: FundRef http://dx.doi.org/10.13039/100004440, Wellcome Trust;
                Funded by: OpenfMRI
                Categories
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                © The Author(s) 2016

                hackathon,unconference,open science,neuroscience,data sharing,collaboration,networking

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