Literature DB >> 30792636

Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging.

David N Kennedy1, Sanu A Abraham2, Julianna F Bates1, Albert Crowley3, Satrajit Ghosh2, Tom Gillespie4, Mathias Goncalves2, Jeffrey S Grethe4, Yaroslav O Halchenko5, Michael Hanke6, Christian Haselgrove1, Steven M Hodge1, Dorota Jarecka2, Jakub Kaczmarzyk2, David B Keator7, Kyle Meyer5, Maryann E Martone4, Smruti Padhy2, Jean-Baptiste Poline8, Nina Preuss3, Troy Sincomb4, Matt Travers3.   

Abstract

There has been a recent major upsurge in the concerns about reproducibility in many areas of science. Within the neuroimaging domain, one approach is to promote reproducibility is to target the re-executability of the publication. The information supporting such re-executability can enable the detailed examination of how an initial finding generalizes across changes in the processing approach, and sampled population, in a controlled scientific fashion. ReproNim: A Center for Reproducible Neuroimaging Computation is a recently funded initiative that seeks to facilitate the "last mile" implementations of core re-executability tools in order to reduce the accessibility barrier and increase adoption of standards and best practices at the neuroimaging research laboratory level. In this report, we summarize the overall approach and tools we have developed in this domain.

Entities:  

Keywords:  data model; neuroimaging; publication; re-executability; reproducibility

Year:  2019        PMID: 30792636      PMCID: PMC6374302          DOI: 10.3389/fninf.2019.00001

Source DB:  PubMed          Journal:  Front Neuroinform        ISSN: 1662-5196            Impact factor:   4.081


  28 in total

1.  Reproducible research in computational science.

Authors:  Roger D Peng
Journal:  Science       Date:  2011-12-02       Impact factor: 47.728

2.  An open source multivariate framework for n-tissue segmentation with evaluation on public data.

Authors:  Brian B Avants; Nicholas J Tustison; Jue Wu; Philip A Cook; James C Gee
Journal:  Neuroinformatics       Date:  2011-12

3.  Toward standard practices for sharing computer code and programs in neuroscience.

Authors:  Stephen J Eglen; Ben Marwick; Yaroslav O Halchenko; Michael Hanke; Shoaib Sufi; Padraig Gleeson; R Angus Silver; Andrew P Davison; Linda Lanyon; Mathew Abrams; Thomas Wachtler; David J Willshaw; Christophe Pouzat; Jean-Baptiste Poline
Journal:  Nat Neurosci       Date:  2017-05-25       Impact factor: 24.884

Review 4.  Power failure: why small sample size undermines the reliability of neuroscience.

Authors:  Katherine S Button; John P A Ioannidis; Claire Mokrysz; Brian A Nosek; Jonathan Flint; Emma S J Robinson; Marcus R Munafò
Journal:  Nat Rev Neurosci       Date:  2013-04-10       Impact factor: 34.870

5.  A very simple, re-executable neuroimaging publication.

Authors:  Satrajit S Ghosh; Jean-Baptiste Poline; David B Keator; Yaroslav O Halchenko; Adam G Thomas; Daniel A Kessler; David N Kennedy
Journal:  F1000Res       Date:  2017-02-10

6.  Achieving human and machine accessibility of cited data in scholarly publications.

Authors:  Joan Starr; Eleni Castro; Mercè Crosas; Michel Dumontier; Robert R Downs; Ruth Duerr; Laurel L Haak; Melissa Haendel; Ivan Herman; Simon Hodson; Joe Hourclé; John Ernest Kratz; Jennifer Lin; Lars Holm Nielsen; Amy Nurnberger; Stefan Proell; Andreas Rauber; Simone Sacchi; Arthur Smith; Mike Taylor; Tim Clark
Journal:  PeerJ Comput Sci       Date:  2015

7.  Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in python.

Authors:  Krzysztof Gorgolewski; Christopher D Burns; Cindee Madison; Dav Clark; Yaroslav O Halchenko; Michael L Waskom; Satrajit S Ghosh
Journal:  Front Neuroinform       Date:  2011-08-22       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.  101 labeled brain images and a consistent human cortical labeling protocol.

Authors:  Arno Klein; Jason Tourville
Journal:  Front Neurosci       Date:  2012-12-05       Impact factor: 4.677

10.  Why most published research findings are false.

Authors:  John P A Ioannidis
Journal:  PLoS Med       Date:  2005-08-30       Impact factor: 11.613

View more
  18 in total

1.  File-based localization of numerical perturbations in data analysis pipelines.

Authors:  Ali Salari; Gregory Kiar; Lindsay Lewis; Alan C Evans; Tristan Glatard
Journal:  Gigascience       Date:  2020-12-02       Impact factor: 6.524

2.  Understanding the impact of preprocessing pipelines on neuroimaging cortical surface analyses.

Authors:  Nikhil Bhagwat; Amadou Barry; Erin W Dickie; Shawn T Brown; Gabriel A Devenyi; Koji Hatano; Elizabeth DuPre; Alain Dagher; Mallar Chakravarty; Celia M T Greenwood; Bratislav Misic; David N Kennedy; Jean-Baptiste Poline
Journal:  Gigascience       Date:  2021-01-22       Impact factor: 6.524

3.  NEURO-LEARN: a Solution for Collaborative Pattern Analysis of Neuroimaging Data.

Authors:  Bingye Lei; Fengchun Wu; Jing Zhou; Dongsheng Xiong; Kaixi Wang; Lingyin Kong; Pengfei Ke; Jun Chen; Yuping Ning; Xiaobo Li; Zhiming Xiang; Kai Wu
Journal:  Neuroinformatics       Date:  2021-01

4.  Analysis of task-based functional MRI data preprocessed with fMRIPrep.

Authors:  Oscar Esteban; Rastko Ciric; Karolina Finc; Ross W Blair; Christopher J Markiewicz; Craig A Moodie; James D Kent; Mathias Goncalves; Elizabeth DuPre; Daniel E P Gomez; Zhifang Ye; Taylor Salo; Romain Valabregue; Inge K Amlien; Franziskus Liem; Nir Jacoby; Hrvoje Stojić; Matthew Cieslak; Sebastian Urchs; Yaroslav O Halchenko; Satrajit S Ghosh; Alejandro De La Vega; Tal Yarkoni; Jessey Wright; William H Thompson; Russell A Poldrack; Krzysztof J Gorgolewski
Journal:  Nat Protoc       Date:  2020-06-08       Impact factor: 13.491

5.  Preliminary Minimum Reporting Requirements for In-Vivo Neural Interface Research: I. Implantable Neural Interfaces.

Authors:  Calvin D Eiber; Jean Delbeke; Jorge Cardoso; Martijn de Neeling; Sam E John; Chang Won Lee; Jerry Skefos; Argus Sun; Dimiter Prodanov; Zach McKinney
Journal:  IEEE Open J Eng Med Biol       Date:  2021-02-22

6.  Brainhack: Developing a culture of open, inclusive, community-driven neuroscience.

Authors:  Rémi Gau; Stephanie Noble; Katja Heuer; Katherine L Bottenhorn; Isil P Bilgin; Yu-Fang Yang; Julia M Huntenburg; Johanna M M Bayer; Richard A I Bethlehem; Shawn A Rhoads; Christoph Vogelbacher; Valentina Borghesani; Elizabeth Levitis; Hao-Ting Wang; Sofie Van Den Bossche; Xenia Kobeleva; Jon Haitz Legarreta; Samuel Guay; Selim Melvin Atay; Gael P Varoquaux; Dorien C Huijser; Malin S Sandström; Peer Herholz; Samuel A Nastase; AmanPreet Badhwar; Guillaume Dumas; Simon Schwab; Stefano Moia; Michael Dayan; Yasmine Bassil; Paula P Brooks; Matteo Mancini; James M Shine; David O'Connor; Xihe Xie; Davide Poggiali; Patrick Friedrich; Anibal S Heinsfeld; Lydia Riedl; Roberto Toro; César Caballero-Gaudes; Anders Eklund; Kelly G Garner; Christopher R Nolan; Damion V Demeter; Fernando A Barrios; Junaid S Merchant; Elizabeth A McDevitt; Robert Oostenveld; R Cameron Craddock; Ariel Rokem; Andrew Doyle; Satrajit S Ghosh; Aki Nikolaidis; Olivia W Stanley; Eneko Uruñuela
Journal:  Neuron       Date:  2021-04-30       Impact factor: 18.688

7.  Management and Quality Control of Large Neuroimaging Datasets: Developments From the Barcelonaβeta Brain Research Center.

Authors:  Jordi Huguet; Carles Falcon; David Fusté; Sergi Girona; David Vicente; José Luis Molinuevo; Juan Domingo Gispert; Grégory Operto
Journal:  Front Neurosci       Date:  2021-04-15       Impact factor: 4.677

8.  Brain markers predicting response to cognitive-behavioral therapy for social anxiety disorder: an independent replication of Whitfield-Gabrieli et al. 2015.

Authors:  Yoni K Ashar; Joseph Clark; Faith M Gunning; Philippe Goldin; James J Gross; Tor D Wager
Journal:  Transl Psychiatry       Date:  2021-05-01       Impact factor: 7.989

9.  Scan Once, Analyse Many: Using Large Open-Access Neuroimaging Datasets to Understand the Brain.

Authors:  Christopher R Madan
Journal:  Neuroinformatics       Date:  2021-05-11

10.  Current Challenges in Translational and Clinical fMRI and Future Directions.

Authors:  Karsten Specht
Journal:  Front Psychiatry       Date:  2020-01-08       Impact factor: 4.157

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.