Literature DB >> 28781753

A very simple, re-executable neuroimaging publication.

Satrajit S Ghosh1,2, Jean-Baptiste Poline3, David B Keator4, Yaroslav O Halchenko5, Adam G Thomas6, Daniel A Kessler7, David N Kennedy8.   

Abstract

Reproducible research is a key element of the scientific process. Re-executability of neuroimaging workflows that lead to the conclusions arrived at in the literature has not yet been sufficiently addressed and adopted by the neuroimaging community. In this paper, we document a set of procedures, which include supplemental additions to a manuscript, that unambiguously define the data, workflow, execution environment and results of a neuroimaging analysis, in order to generate a verifiable re-executable publication. Re-executability provides a starting point for examination of the generalizability and reproducibility of a given finding.

Entities:  

Keywords:  Neuroimaging analysis; re-executable publication; reproducibility

Year:  2017        PMID: 28781753      PMCID: PMC5516225          DOI: 10.12688/f1000research.10783.2

Source DB:  PubMed          Journal:  F1000Res        ISSN: 2046-1402


  19 in total

1.  Provenance in neuroimaging.

Authors:  Allan J Mackenzie-Graham; John D Van Horn; Roger P Woods; Karen L Crawford; Arthur W Toga
Journal:  Neuroimage       Date:  2008-04-25       Impact factor: 6.556

2.  Toward discovery science of human brain function.

Authors:  Bharat B Biswal; Maarten Mennes; Xi-Nian Zuo; Suril Gohel; Clare Kelly; Steve M Smith; Christian F Beckmann; Jonathan S Adelstein; Randy L Buckner; Stan Colcombe; Anne-Marie Dogonowski; Monique Ernst; Damien Fair; Michelle Hampson; Matthew J Hoptman; James S Hyde; Vesa J Kiviniemi; Rolf Kötter; Shi-Jiang Li; Ching-Po Lin; Mark J Lowe; Clare Mackay; David J Madden; Kristoffer H Madsen; Daniel S Margulies; Helen S Mayberg; Katie McMahon; Christopher S Monk; Stewart H Mostofsky; Bonnie J Nagel; James J Pekar; Scott J Peltier; Steven E Petersen; Valentin Riedl; Serge A R B Rombouts; Bart Rypma; Bradley L Schlaggar; Sein Schmidt; Rachael D Seidler; Greg J Siegle; Christian Sorg; Gao-Jun Teng; Juha Veijola; Arno Villringer; Martin Walter; Lihong Wang; Xu-Chu Weng; Susan Whitfield-Gabrieli; Peter Williamson; Christian Windischberger; Yu-Feng Zang; Hong-Ying Zhang; F Xavier Castellanos; Michael P Milham
Journal:  Proc Natl Acad Sci U S A       Date:  2010-02-22       Impact factor: 11.205

Review 3.  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

4.  Cluster failure: Why fMRI inferences for spatial extent have inflated false-positive rates.

Authors:  Anders Eklund; Thomas E Nichols; Hans Knutsson
Journal:  Proc Natl Acad Sci U S A       Date:  2016-06-28       Impact factor: 11.205

5.  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

6.  Towards structured sharing of raw and derived neuroimaging data across existing resources.

Authors:  D B Keator; K Helmer; J Steffener; J A Turner; T G M Van Erp; S Gadde; N Ashish; G A Burns; B N Nichols
Journal:  Neuroimage       Date:  2013-05-30       Impact factor: 6.556

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.  The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements.

Authors:  Ed H B M Gronenschild; Petra Habets; Heidi I L Jacobs; Ron Mengelers; Nico Rozendaal; Jim van Os; Machteld Marcelis
Journal:  PLoS One       Date:  2012-06-01       Impact factor: 3.240

9.  Reproducibility of neuroimaging analyses across operating systems.

Authors:  Tristan Glatard; Lindsay B Lewis; Rafael Ferreira da Silva; Reza Adalat; Natacha Beck; Claude Lepage; Pierre Rioux; Marc-Etienne Rousseau; Tarek Sherif; Ewa Deelman; Najmeh Khalili-Mahani; Alan C Evans
Journal:  Front Neuroinform       Date:  2015-04-24       Impact factor: 4.081

10.  Data Citation in Neuroimaging: Proposed Best Practices for Data Identification and Attribution.

Authors:  Leah B Honor; Christian Haselgrove; Jean A Frazier; David N Kennedy
Journal:  Front Neuroinform       Date:  2016-08-12       Impact factor: 4.081

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  8 in total

1.  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

2.  A new virtue of phantom MRI data: explaining variance in human participant data.

Authors:  Christopher P Cheng; Yaroslav O Halchenko
Journal:  F1000Res       Date:  2020-09-14

3.  Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging.

Authors:  David N Kennedy; Sanu A Abraham; Julianna F Bates; Albert Crowley; Satrajit Ghosh; Tom Gillespie; Mathias Goncalves; Jeffrey S Grethe; Yaroslav O Halchenko; Michael Hanke; Christian Haselgrove; Steven M Hodge; Dorota Jarecka; Jakub Kaczmarzyk; David B Keator; Kyle Meyer; Maryann E Martone; Smruti Padhy; Jean-Baptiste Poline; Nina Preuss; Troy Sincomb; Matt Travers
Journal:  Front Neuroinform       Date:  2019-02-07       Impact factor: 4.081

4.  Neuroscience Cloud Analysis As a Service: An open-source platform for scalable, reproducible data analysis.

Authors:  Taiga Abe; Ian Kinsella; Shreya Saxena; E Kelly Buchanan; Joao Couto; John Briggs; Sian Lee Kitt; Ryan Glassman; John Zhou; Liam Paninski; John P Cunningham
Journal:  Neuron       Date:  2022-07-22       Impact factor: 18.688

5.  Reproducing Polychronization: A Guide to Maximizing the Reproducibility of Spiking Network Models.

Authors:  Robin Pauli; Philipp Weidel; Susanne Kunkel; Abigail Morrison
Journal:  Front Neuroinform       Date:  2018-08-03       Impact factor: 4.081

6.  Evaluating the Reliability of Human Brain White Matter Tractometry.

Authors:  John Kruper; Jason D Yeatman; Adam Richie-Halford; David Bloom; Mareike Grotheer; Sendy Caffarra; Gregory Kiar; Iliana I Karipidis; Ethan Roy; Bramsh Q Chandio; Eleftherios Garyfallidis; Ariel Rokem
Journal:  Apert Neuro       Date:  2021-11-17

7.  Neuroscout, a unified platform for generalizable and reproducible fMRI research.

Authors:  Alejandro de la Vega; Roberta Rocca; Ross W Blair; Christopher J Markiewicz; Jeff Mentch; James D Kent; Peer Herholz; Satrajit S Ghosh; Russell A Poldrack; Tal Yarkoni
Journal:  Elife       Date:  2022-08-30       Impact factor: 8.713

8.  Knowledge and Attitudes Among Life Scientists Toward Reproducibility Within Journal Articles: A Research Survey.

Authors:  Evanthia Kaimaklioti Samota; Robert P Davey
Journal:  Front Res Metr Anal       Date:  2021-06-29
  8 in total

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