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Meeting Curation Challenges in a Neuroimaging Group

Angus Whyte, Dominic Job, Stephen Giles, Stephen Lawrie
2008 International Journal of Digital Curation  
The study summarised here is of the Neuroimaging Group in the University of Edinburgh's Division of Psychiatry, which plays a leading role in eScience collaborations to improve the infrastructure for neuroimaging  ...  The study briefly reviews the policy context and current challenges to data integration and sharing in the neuroimaging field.  ...  Acknowledgements The study would not have been possible without the generosity and patience of colleagues in the Neuroimaging Group, Division of Psychiatry, University of Edinburgh.  ... 
doi:10.2218/ijdc.v3i1.53 fatcat:l5dgxmj52vdwnhstvs4p27tauu

Challenges in Preserving Neuroimaging Research Data

Angus Whyte
2020 Zenodo  
These are exemplified in a case study of a psychiatry research group.  ...  Preserving neuroimaging research data for sharing and re-use involves practical challenges for those concerned in its use and curation.  ...  Action Research •Preservation challenges •Risk assessment •Route map Participant review Neuroimaging Group Edinburgh Dept of Psychiatry • Backgrounds in psychiatry, image processing, psychology  ... 
doi:10.5281/zenodo.3782128 fatcat:h5xeeevonfftxnbcgybious5zq

Open Neuroimaging Laboratory

Roberto Toro, Katja Heuer, Satrajit Ghosh, Amy Robinson Sterling
2016 Research Ideas and Outcomes  
Neuroimaging data requires a substantial amount of human curation, visual quality assessment and manual editing.  ...  All too often, the inability of small research groups, individual researchers or citizen scientists to meet these requirements will prevent/ discourage them to explore the data or will force them to discard  ...  Neuroimaging data processing requires a substantial amount of human curation, visual quality assessment and manual editing.  ... 
doi:10.3897/rio.2.e9113 fatcat:zrxjmejtpneehlqwz5xpz5i7gu

Challenges and solutions in data sharing: Technical Perspectives

Stephan Heunis, Adina S. Wagner
2021 Zenodo  
Slides from the round-table discussion "Challenges and solutions in data sharing", held at the virtual ESMRMB 38th Annual Scientific Meeting, 7-9 October 2021.  ...  Data standard with near universal level of acceptance among medical imaging equipment vendors and healthcare IT organizations NIfTI1 The Data Format Working Group (DFWG) introduces NIfTI as a standard  ...  10.5281/zenodo.5557242 2006- An incomplete timeline for technological milestones for data sharing in neuroimaging fMRI Data Center (fMRIDC) (Van Horn et al.) 2000-2007 and Reusable DICOM  ... 
doi:10.5281/zenodo.5557242 fatcat:pythwwjihrfdnnu2u5kmb3k2lu

Data Curation Program Development in U.S. Universities: The Georgia Institute of Technology Example

Tyler O. Walters
2009 International Journal of Digital Curation  
However, and in spite of the challenges, some U.S. research universities are beginning to establish perceptible data curation programs.  ...  The Georgia Institute of Technology (GT) has had a similar development path toward a data curation program based in its library.  ...  for developing data curation programs at the institutional level is proving to be a challenge.  ... 
doi:10.2218/ijdc.v4i3.116 fatcat:7e7jedyzezcz7iffigngpnhtzu

Data sharing in neuroimaging research

Jean-Baptiste Poline, Janis L. Breeze, Satrajit Ghosh, Krzysztof Gorgolewski, Yaroslav O. Halchenko, Michael Hanke, Christian Haselgrove, Karl G. Helmer, David B. Keator, Daniel S. Marcus, Russell A. Poldrack, Yannick Schwartz (+2 others)
2012 Frontiers in Neuroinformatics  
A trend toward increased sharing of neuroimaging data has emerged in recent years. Nevertheless, a number of barriers continue to impede momentum.  ...  The INCF Task Force on Neuroimaging Datasharing, in conjunction with several collaborative groups around the world, has started work on several tools to ease and eventually automate the practice of data  ...  The lack of consistent metadata standards makes it difficult to curate data across research labs and for neuroimaging software to capture metadata and provenance in a systematic manner.  ... 
doi:10.3389/fninf.2012.00009 pmid:22493576 pmcid:PMC3319918 fatcat:f4cgaldeuraavmcnxqrsisdebe

Why share data? Lessons learned from the fMRIDC

John Darrell Van Horn, Michael S. Gazzaniga
2013 NeuroImage  
In this article, we discuss our own experience in the development of the fMRI Data Center (fMRIDC) -a large-scale effort to gather, curate, and openly share the complete data sets from published research  ...  However successful neuroimaging and the examination of cognitive processes may seem today, the culture of data sharing in these fields remains underdeveloped.  ...  each group.  ... 
doi:10.1016/j.neuroimage.2012.11.010 pmid:23160115 pmcid:PMC3807237 fatcat:z43vjx6cefbcbkzjfq7hkec7di

Data management and sharing in neuroimaging: Practices and perceptions of MRI researchers [article]

John A. Borghi, Ana E. Van Gulick
2018 bioRxiv   pre-print
Our results demonstrate that neuroimaging data is acquired in multifarious forms, transformed and analyzed using a wide variety of software tools, and that RDM practices and perceptions vary considerably  ...  Survey questions addressed the type(s) of data collected, tools used for data storage, organization, and analysis, and the degree to which practices are defined and standardized within a research group  ...  While conducting the work described in this publication, J.B. was funded as both a CLIR Software Curation Fellow (Alfred P. Sloan Foundation #G-2015-14112) and an RDA Data Share Fellow (Alfred P.  ... 
doi:10.1101/266627 fatcat:yux5zf3dsffxjfxl3plbpamvta

Data management and sharing in neuroimaging: Practices and perceptions of MRI researchers

John A. Borghi, Ana E. Van Gulick, Dzung Pham
2018 PLoS ONE  
Our results demonstrate that neuroimaging data is acquired in multifarious forms, transformed and analyzed using a wide variety of software tools, and that RDM practices and perceptions vary considerably  ...  OPEN ACCESS Citation: Borghi JA, Van Gulick AE (2018) Data management and sharing in neuroimaging: Practices and perceptions of MRI researchers. PLoS ONE 13(7): e0200562. https://doi.org/ 10.  ...  Neuroimaging is not unique in facing challenges related to rigor and reproducibility.  ... 
doi:10.1371/journal.pone.0200562 pmid:30011302 pmcid:PMC6047789 fatcat:56gz4ltzpfcsbldeidcyuqu6xa

A collaborative resource platform for non-human primate neuroimaging

Adam Messinger, Nikoloz Sirmpilatze, Katja Heuer, Kep Kee Loh, Rogier B. Mars, Julien Sein, Ting Xu, Daniel Glen, Benjamin Jung, Jakob Seidlitz, Paul Taylor, Roberto Toro (+20 others)
2021 NeuroImage  
Neuroimaging non-human primates (NHPs) is a growing, yet highly specialized field of neuroscience.  ...  Here we present the PRIMatE Resource Exchange (PRIME-RE), a new collaborative online platform for NHP neuroimaging.  ...  It can serve both as a starting point for researchers that are new to the field of NHP neuroimaging and as a meeting ground for more experienced researchers in the field.  ... 
doi:10.1016/j.neuroimage.2020.117519 pmid:33227425 pmcid:PMC9272762 fatcat:67ng3nt3uvbg3l4n4prlshuuwi

Developing a Neuroimaging Biomarker for Amyotrophic Lateral Sclerosis: Multi-Center Data Sharing and the Road to a "Global Cohort"

Robert Steinbach, Nayana Gaur, Beatrice Stubendorff, Otto W. Witte, Julian Grosskreutz
2018 Frontiers in Neurology  
Nevertheless, significant challenges need to be addressed for the translation of neuroimaging as a robust outcome-metric and biomarker in quality-of-care assessments and pharmaceutical trials.  ...  Neuroimaging in Amyotrophic Lateral Sclerosis (ALS) has steadily evolved from an academic exercise to a powerful clinical tool for detecting and following pathological change.  ...  Annual meetings have since cemented NiSALS' role as an international consortium fostering neuroimaging as a key tool for understanding ALS.  ... 
doi:10.3389/fneur.2018.01055 pmid:30564187 pmcid:PMC6288231 fatcat:bnh7ty4ygbdytbew6rj7xdmd44

tranSMART Foundation Datathon 1.0: The cross neurodegenerative diseases challenge

Carol Isaacson Barash, Keith Elliston, Rudy Potenzone
2015 Applied and Translational Genomics  
The group explored GEO studies of whole blood and post mortem brain samples in search of a shared biomarkers that could differential PD from healthy subjects.  ...  In doing so, the Platform proved to be a powerful tool in expediting research in a cost efficient way.  ... 
doi:10.1016/j.atg.2015.08.004 pmid:27054077 pmcid:PMC4803781 fatcat:hzmq7op3bjchzdx2c6wnggn2fe

Is it time to re-prioritize neuroimaging databases and digital repositories?

John Darrell Van Horn, Arthur W. Toga
2009 NeuroImage  
A range of neuroimaging databasing approaches has streamlined the transmission, storage, and dissemination of data from such brain imaging studies.  ...  In this article, we review the progress made in neuroimaging databases, their role in data sharing, data management, potential for the construction of brain atlases, recording data provenance, and value  ...  Acknowledgments The authors express their gratitude to our colleagues in the Laboratory of Neuro Imaging (LONI) and those collaborators at our partner laboratories who utilize LONI database and computational  ... 
doi:10.1016/j.neuroimage.2009.03.086 pmid:19371790 pmcid:PMC2754579 fatcat:qxjviytffrexbf7wrn2xfkrns4

A collaborative resource platform for non-human primate neuroimaging [article]

Adam Messinger, Nikoloz Sirmpilatze, Katja Heuer, Kep Kee Loh, Rogier Mars, Julien Sein, Ting Xu, Daniel Glen, Benjamin Jung, Jakob Seidlitz, Paul Taylor, Roberto Toro (+20 others)
2020 biorxiv/medrxiv   pre-print
Neuroimaging non-human primates (NHPs) is a growing, yet highly specialized field of neuroscience.  ...  Here we present the PRIMatE Resource Exchange (PRIME-RE), a new collaborative online platform for NHP neuroimaging.  ...  It can serve both as a starting point for researchers that are new to the field of NHP neuroimaging and as a meeting ground for more experienced researchers in the field.  ... 
doi:10.1101/2020.07.31.230185 fatcat:6vpogby2ezhu3jgxnpjlkbt3ai

From the Wet Lab to the Web Lab: A Paradigm Shift in Brain Imaging Research

Anisha Keshavan, Jean-Baptiste Poline
2019 Frontiers in Neuroinformatics  
Web technology has transformed our lives, and has led to a paradigm shift in the computational sciences.  ...  Here, we review the landscape of web technologies used in neuroimaging research, and discuss future applications, areas for improvement, and the limitations of using web technology in research.  ...  A curated list of biomedical image challenges can be found at https://grand-challenge.org/ challenges/.  ... 
doi:10.3389/fninf.2019.00003 pmid:30881299 pmcid:PMC6405692 fatcat:k7x2llfff5hfrhr6igrt7hwhu4
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