Literature DB >> 23912507

Neuroinformatics Database (NiDB)--a modular, portable database for the storage, analysis, and sharing of neuroimaging data.

Gregory A Book1, Beth M Anderson, Michael C Stevens, David C Glahn, Michal Assaf, Godfrey D Pearlson.   

Abstract

We present a modular, high performance, open-source database system that incorporates popular neuroimaging database features with novel peer-to-peer sharing, and a simple installation. An increasing number of imaging centers have created a massive amount of neuroimaging data since fMRI became popular more than 20 years ago, with much of that data unshared. The Neuroinformatics Database (NiDB) provides a stable platform to store and manipulate neuroimaging data and addresses several of the impediments to data sharing presented by the INCF Task Force on Neuroimaging Datasharing, including 1) motivation to share data, 2) technical issues, and 3) standards development. NiDB solves these problems by 1) minimizing PHI use, providing a cost effective simple locally stored platform, 2) storing and associating all data (including genome) with a subject and creating a peer-to-peer sharing model, and 3) defining a sample, normalized definition of a data storage structure that is used in NiDB. NiDB not only simplifies the local storage and analysis of neuroimaging data, but also enables simple sharing of raw data and analysis methods, which may encourage further sharing.

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Year:  2013        PMID: 23912507      PMCID: PMC3864015          DOI: 10.1007/s12021-013-9194-1

Source DB:  PubMed          Journal:  Neuroinformatics        ISSN: 1539-2791


  13 in total

1.  Improved optimization for the robust and accurate linear registration and motion correction of brain images.

Authors:  Mark Jenkinson; Peter Bannister; Michael Brady; Stephen Smith
Journal:  Neuroimage       Date:  2002-10       Impact factor: 6.556

2.  The Extensible Neuroimaging Archive Toolkit: an informatics platform for managing, exploring, and sharing neuroimaging data.

Authors:  Daniel S Marcus; Timothy R Olsen; Mohana Ramaratnam; Randy L Buckner
Journal:  Neuroinformatics       Date:  2007

3.  PLINK: a tool set for whole-genome association and population-based linkage analyses.

Authors:  Shaun Purcell; Benjamin Neale; Kathe Todd-Brown; Lori Thomas; Manuel A R Ferreira; David Bender; Julian Maller; Pamela Sklar; Paul I W de Bakker; Mark J Daly; Pak C Sham
Journal:  Am J Hum Genet       Date:  2007-07-25       Impact factor: 11.025

4.  XCEDE: an extensible schema for biomedical data.

Authors:  Syam Gadde; Nicole Aucoin; Jeffrey S Grethe; David B Keator; Daniel S Marcus; Steve Pieper
Journal:  Neuroinformatics       Date:  2012-01

5.  Ways toward an early diagnosis in Alzheimer's disease: the Alzheimer's Disease Neuroimaging Initiative (ADNI).

Authors:  Susanne G Mueller; Michael W Weiner; Leon J Thal; Ronald C Petersen; Clifford R Jack; William Jagust; John Q Trojanowski; Arthur W Toga; Laurel Beckett
Journal:  Alzheimers Dement       Date:  2005-07       Impact factor: 21.566

6.  The Alzheimer's Disease Neuroimaging Initiative (ADNI): MRI methods.

Authors:  Clifford R Jack; Matt A Bernstein; Nick C Fox; Paul Thompson; Gene Alexander; Danielle Harvey; Bret Borowski; Paula J Britson; Jennifer L Whitwell; Chadwick Ward; Anders M Dale; Joel P Felmlee; Jeffrey L Gunter; Derek L G Hill; Ron Killiany; Norbert Schuff; Sabrina Fox-Bosetti; Chen Lin; Colin Studholme; Charles S DeCarli; Gunnar Krueger; Heidi A Ward; Gregory J Metzger; Katherine T Scott; Richard Mallozzi; Daniel Blezek; Joshua Levy; Josef P Debbins; Adam S Fleisher; Marilyn Albert; Robert Green; George Bartzokis; Gary Glover; John Mugler; Michael W Weiner
Journal:  J Magn Reson Imaging       Date:  2008-04       Impact factor: 4.813

Review 7.  FSL.

Authors:  Mark Jenkinson; Christian F Beckmann; Timothy E J Behrens; Mark W Woolrich; Stephen M Smith
Journal:  Neuroimage       Date:  2011-09-16       Impact factor: 6.556

8.  Data sharing in neuroimaging research.

Authors:  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; John Ashburner; David N Kennedy
Journal:  Front Neuroinform       Date:  2012-04-05       Impact factor: 4.081

9.  LORIS: a web-based data management system for multi-center studies.

Authors:  Samir Das; Alex P Zijdenbos; Jonathan Harlap; Dario Vins; Alan C Evans
Journal:  Front Neuroinform       Date:  2012-01-20       Impact factor: 4.081

10.  COINS: An Innovative Informatics and Neuroimaging Tool Suite Built for Large Heterogeneous Datasets.

Authors:  Adam Scott; Will Courtney; Dylan Wood; Raul de la Garza; Susan Lane; Margaret King; Runtang Wang; Jody Roberts; Jessica A Turner; Vince D Calhoun
Journal:  Front Neuroinform       Date:  2011-12-23       Impact factor: 4.081

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  14 in total

1.  A Comprehensive Framework to Capture the Arcana of Neuroimaging Analysis.

Authors:  Thomas G Close; Phillip G D Ward; Francesco Sforazzini; Wojtek Goscinski; Zhaolin Chen; Gary F Egan
Journal:  Neuroinformatics       Date:  2020-01

2.  CranialCloud: a cloud-based architecture to support trans-institutional collaborative efforts in neurodegenerative disorders.

Authors:  Pierre-François D'Haese; Peter E Konrad; Srivatsan Pallavaram; Rui Li; Priyanka Prassad; William Rodriguez; Benoit M Dawant
Journal:  Int J Comput Assist Radiol Surg       Date:  2015-04-11       Impact factor: 2.924

3.  Neuroimaging data sharing on the neuroinformatics database platform.

Authors:  Gregory A Book; Michael C Stevens; Michal Assaf; David C Glahn; Godfrey D Pearlson
Journal:  Neuroimage       Date:  2015-04-16       Impact factor: 6.556

4.  MIRMAID: A Content Management System for Medical Image Analysis Research.

Authors:  Panagiotis D Korfiatis; Timothy L Kline; Daniel J Blezek; Steve G Langer; William J Ryan; Bradley J Erickson
Journal:  Radiographics       Date:  2015-08-18       Impact factor: 5.333

Review 5.  Neuroinformatics Software Applications Supporting Electronic Data Capture, Management, and Sharing for the Neuroimaging Community.

Authors:  B Nolan Nichols; Kilian M Pohl
Journal:  Neuropsychol Rev       Date:  2015-08-13       Impact factor: 7.444

6.  Neuroanatomical domain of the foundational model of anatomy ontology.

Authors:  B Nolan Nichols; Jose Lv Mejino; Landon T Detwiler; Trond T Nilsen; Maryann E Martone; Jessica A Turner; Daniel L Rubin; James F Brinkley
Journal:  J Biomed Semantics       Date:  2014-01-08

7.  A simple tool for neuroimaging data sharing.

Authors:  Christian Haselgrove; Jean-Baptiste Poline; David N Kennedy
Journal:  Front Neuroinform       Date:  2014-05-21       Impact factor: 4.081

8.  The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments.

Authors:  Krzysztof J Gorgolewski; Tibor Auer; Vince D Calhoun; R Cameron Craddock; Samir Das; Eugene P Duff; Guillaume Flandin; Satrajit S Ghosh; Tristan Glatard; Yaroslav O Halchenko; Daniel A Handwerker; Michael Hanke; David Keator; Xiangrui Li; Zachary Michael; Camille Maumet; B Nolan Nichols; Thomas E Nichols; John Pellman; Jean-Baptiste Poline; Ariel Rokem; Gunnar Schaefer; Vanessa Sochat; William Triplett; Jessica A Turner; Gaël Varoquaux; Russell A Poldrack
Journal:  Sci Data       Date:  2016-06-21       Impact factor: 6.444

9.  Neuroimaging, Genetics, and Clinical Data Sharing in Python Using the CubicWeb Framework.

Authors:  Antoine Grigis; David Goyard; Robin Cherbonnier; Thomas Gareau; Dimitri Papadopoulos Orfanos; Nicolas Chauvat; Adrien Di Mascio; Gunter Schumann; Will Spooren; Declan Murphy; Vincent Frouin
Journal:  Front Neuroinform       Date:  2017-03-16       Impact factor: 4.081

10.  Common Data Elements, Scalable Data Management Infrastructure, and Analytics Workflows for Large-Scale Neuroimaging Studies.

Authors:  Rayus Kuplicki; James Touthang; Obada Al Zoubi; Ahmad Mayeli; Masaya Misaki; Robin L Aupperle; T Kent Teague; Brett A McKinney; Martin P Paulus; Jerzy Bodurka
Journal:  Front Psychiatry       Date:  2021-06-17       Impact factor: 5.435

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