The Reproducibility Working Group Bibliography
The Reproducibility Working Group Bibliography
Bibliography
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2024
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2022
2021
2020
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2017
2013
Heterogenous brain activations across individuals localize to a common network
Shaoling Peng
,
Zaixu Cui
,
Suyu Zhong
,
Yanyang Zhang
,
Alexander L. Cohen
,
Michael D. Fox
,
Gaolang Gong
Cite
DOI
URL
Prédire l'évolution de la maladie de Parkinson à l'aide de données cliniques et d'IRM fonctionnelles: reproduction et robustesse d'une étude
Elodie Germani
,
Nikhil Baghwat
,
Mathieu Dugré
,
Remi Gau
,
Andrzej Sokolowski
,
Elisa Fromont
,
Camille Maumet
,
Madeleine Sharp
,
Jean-Baptiste Poline
,
Tristan Glatard
Cite
Hype, Sustainability, and the Price of the Bigger-is-Better Paradigm in AI
With the growing attention and investment in recent AI approaches such as large language models, the narrative that the larger the AI …
Gaël Varoquaux
,
Alexandra Sasha Luccioni
,
Meredith Whittaker
Cite
DOI
URL
ENCORE: a practical implementation to improve reproducibility and transparency of computational research
Antoine H. C. Van Kampen
,
Utkarsh Mahamune
,
Aldo Jongejan
,
Barbera D. C. Van Schaik
,
Daria Balashova
,
Danial Lashgari
,
Mia Pras-Raves
,
Eric J. M. Wever
,
Adrie D. Dane
,
Rodrigo García-Valiente
,
Perry D. Moerland
Cite
DOI
URL
Confidence intervals uncovered: Are we ready for real-world medical imaging AI?
Medical imaging is spearheading the AI transformation of healthcare. Performance reporting is key to determine which methods should be …
Evangelia Christodoulou
,
Annika Reinke
,
Rola Houhou
,
Piotr Kalinowski
,
Selen Erkan
,
Carole H. Sudre
,
Ninon Burgos
,
Sofiène Boutaj
,
Sophie Loizillon
,
Maëlys Solal
,
Nicola Rieke
,
Veronika Cheplygina
,
Michela Antonelli
,
Leon D. Mayer
,
Minu D. Tizabi
,
M. Jorge Cardoso
,
Amber Simpson
,
Paul F. Jäger
,
Annette Kopp-Schneider
,
Gaël Varoquaux
,
Olivier Colliot
,
Lena Maier-Hein
Cite
URL
Garden of forking paths in ERP research – Effects of varying pre-processing and analysis steps in an N400 experiment
Abstract This study tackles the Garden of Forking Paths, as a challenge for replicability and reproducibility of ERP studies. Here, we …
Anđela Šoškić
,
Suzy J. Styles
,
Emily S. Kappenman
,
Vanja Ković
Cite
DOI
URL
Nonlinear latent representations of high-dimensional task-fMRI data: Unveiling cognitive and behavioral insights in heterogeneous spatial maps
Finding an interpretable and compact representation of complex neuroimaging data is extremely useful for understanding brain behavioral …
Mariam Zabihi
,
Seyed Mostafa Kia
,
Thomas Wolfers
,
Stijn De Boer
,
Charlotte Fraza
,
Richard Dinga
,
Alberto Llera Arenas
,
Danilo Bzdok
,
Christian F. Beckmann
,
Andre Marquand
Cite
DOI
URL
Moving beyond processing- and analysis-related variation in resting-state functional brain imaging
Xinhui Li
,
Nathalia Bianchini Esper
,
Lei Ai
,
Steve Giavasis
,
Hecheng Jin
,
Eric Feczko
,
Ting Xu
,
Jon Clucas
,
Alexandre Franco
,
Anibal Sólon Heinsfeld
,
Azeez Adebimpe
,
Joshua T. Vogelstein
,
Chao-Gan Yan
,
Oscar Esteban
,
Russell A. Poldrack
,
Cameron Craddock
,
Damien Fair
,
Theodore Satterthwaite
,
Gregory Kiar
,
Michael P. Milham
Cite
DOI
URL
From Maps to Models: A Survey on the Reliability of Small Studies of Task-Based fMRI
Task-based functional magnetic resonance imaging is a powerful tool for studying brain function, but neuroimaging research produces …
Patrick Sadil
,
Martin A. Lindquist
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DOI
URL
A standardized image processing and data quality platform for rodent fMRI
Abstract Functional magnetic resonance imaging in rodents holds great potential for advancing our understanding of brain networks. …
Gabriel Desrosiers-Grégoire
,
Gabriel A. Devenyi
,
Joanes Grandjean
,
M. Mallar Chakravarty
Cite
DOI
URL
A Set of FMRI Quality Control Tools in AFNI: Systematic, in-depth, and interactive QC with afni_proc.py and more
Abstract Quality control (QC) assessment is a vital part of FMRI processing and analysis, and a typically underdiscussed aspect of …
Paul A. Taylor
,
Daniel R. Glen
,
Gang Chen
,
Robert W. Cox
,
Taylor Hanayik
,
Chris Rorden
,
Dylan M. Nielson
,
Justin K. Rajendra
,
Richard C. Reynolds
Cite
DOI
URL
Towards reusable derived data in neuroimaging
Camille Maumet
Cite
Towards reproducible neuroimaging: Solutions for sharing and re-using brain imaging data
Camille Maumet
Cite
The best of both worlds: using semantic web with JSON-LD. An example with NIDM-Results & Datalad
Camille Maumet
,
Satrajit Ghosh
,
Yaroslav O Halchenko
,
Dorota Jarecka
,
Nolan B Nichols
,
Jean-Baptiste Poline
,
Michael Hanke
Cite
Open-source tools and platforms to investigate analytical variability in neuroimaging
Jacob Sanz-Robinson
,
Michelle Wang
,
Brent McPherson
,
Tristan Glatard
,
Jean-Baptiste Poline
Cite
DataLad extension module for neuroimaging studies — Datalad for Hirnis 0.0.8 documentation
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URL
Computational basis and ReproIn/DataLad: A complete portable and reproducible fMRI study from scratch
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URL
BIDS Extension Proposal (BEP028): Provenance
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URL
XCP-D: A Robust Pipeline for the Post-Processing of fMRI data
Abstract Functional neuroimaging is an essential tool for neuroscience research. Pre-processing pipelines produce standardized, …
Kahini Mehta
,
Taylor Salo
,
Thomas J. Madison
,
Azeez Adebimpe
,
Danielle S. Bassett
,
Max Bertolero
,
Matthew Cieslak
,
Sydney Covitz
,
Audrey Houghton
,
Arielle S. Keller
,
Jacob T. Lundquist
,
Audrey Luo
,
Oscar Miranda-Dominguez
,
Steve M. Nelson
,
Golia Shafiei
,
Sheila Shanmugan
,
Russell T. Shinohara
,
Christopher D. Smyser
,
Valerie J. Sydnor
,
Kimberly B. Weldon
,
Eric Feczko
,
Damien A. Fair
,
Theodore D. Satterthwaite
Cite
DOI
URL
Sharing brain imaging data in the Open Science era: how and why?
Kathrin Giehl
,
Henk-Jan Mutsaerts
,
Kristien Aarts
,
Frederik Barkhof
,
Svenja Caspers
,
Gaël Chetelat
,
Marie-Elisabeth Colin
,
Emrah Düzel
,
Giovanni B Frisoni
,
M Arfan Ikram
,
Jorge Jovicich
,
Silvia Morbelli
,
Wolfgang Oertel
,
Christian Paret
,
Daniela Perani
,
Petra Ritter
,
Bàrbara Segura
,
Laura E M Wisse
,
Elke De Witte
,
Stefano F Cappa
,
Thilo Van Eimeren
Cite
DOI
URL
Garden of forking paths in ERP research – Effects of varying pre-processing and analysis steps in an N400 experiment
Abstract This study tackles the Garden of Forking Paths, as a challenge for replicability and reproducibility of ERP studies. Here, we …
Anđela Šoškić
,
Suzy J. Styles
,
Emily S. Kappenman
,
Vanja Ković
Cite
DOI
URL
Flexible adaptation of task-positive brain networks predicts efficiency of evidence accumulation
Abstract Efficiency of evidence accumulation (EEA), an individual’s ability to selectively gather goal-relevant information to make …
Alexander Weigard
,
Mike Angstadt
,
Aman Taxali
,
Andrew Heathcote
,
Mary M. Heitzeg
,
Chandra Sripada
Cite
DOI
URL
Beyond Increasing Sample Sizes: Optimizing Effect Sizes in Neuroimaging Research on Individual Differences
Linking neurobiology to relatively stable individual differences in cognition, emotion, motivation, and behavior can require large …
Colin G. DeYoung
,
Kirsten Hilger
,
Jamie L. Hanson
,
Rany Abend
,
Timothy Allen
,
Roger Beaty
,
Scott D. Blain
,
Robert Chavez
,
Stephen A. Engel
,
Feilong Ma
,
Alex Fornito
,
Erhan Genç
,
Vina Goghari
,
Rachael G. Grazioplene
,
Philipp Homan
,
Keenan Joyner
,
Antonia N. Kaczkurkin
,
Robert D Latzman
,
Elizabeth a Martin
,
Aki Nikolaidis
,
Alan Pickering
,
Adam Safron
,
Tyler Sassenberg
,
Michelle Servaas
,
Luke D. Smillie
,
R. Nathan Spreng
,
Essi Viding
,
Jan Wacker
Cite
DOI
URL
Addressing researcher degrees of freedom through minP adjustment
Abstract When different researchers study the same research question using the same dataset they may obtain different and potentially …
Maximilian M. Mandl
,
Andrea S. Becker-Pennrich
,
Ludwig C. Hinske
,
Sabine Hoffmann
,
Anne-Laure Boulesteix
Cite
DOI
URL
Systematic evaluation of fMRI data-processing pipelines for consistent functional connectomics
Abstract Functional interactions between brain regions can be viewed as a network, enabling neuroscientists to investigate brain …
Andrea I. Luppi
,
Helena M. Gellersen
,
Zhen-Qi Liu
,
Alexander R. D. Peattie
,
Anne E. Manktelow
,
Ram Adapa
,
Adrian M. Owen
,
Lorina Naci
,
David K. Menon
,
Stavros I. Dimitriadis
,
Emmanuel A. Stamatakis
Cite
DOI
URL
Quality over quantity: powering neuroimaging samples in psychiatry
Carolina Makowski
,
Thomas E. Nichols
,
Anders M. Dale
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DOI
URL
Embracing variability in the search for biological mechanisms of psychiatric illness
Despite decades of research, we lack objective diagnostic or prognostic biomarkers of mental health problems. A key reason for this …
Ashlea Segal
,
Jeggan Tiego
,
Avram J Holmes
,
Andre
,
Alex Fornito
Cite
DOI
URL
demidenm/PyReliMRI: v2.1.0
Several changes and additions are made: A more comprehensive docstring is used to enhance information on PyReliMRI readthedocs The …
Michael Demidenko
,
Russ Poldrack
,
Chris Markiewicz
,
Elizabeth DuPre
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DOI
URL
Open Source in Lab Management
This document explores the advantages of integrating open source software and practices in managing a scientific lab, emphasizing …
Julien Cohen-Adad
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URL
Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging
Angela I. Renton
,
Thuy T. Dao
,
Tom Johnstone
,
Oren Civier
,
Ryan P. Sullivan
,
David J. White
,
Paris Lyons
,
Benjamin M. Slade
,
David F. Abbott
,
Toluwani J. Amos
,
Saskia Bollmann
,
Andy Botting
,
Megan E. J. Campbell
,
Jeryn Chang
,
Thomas G. Close
,
Monika Dörig
,
Korbinian Eckstein
,
Gary F. Egan
,
Stefanie Evas
,
Guillaume Flandin
,
Kelly G. Garner
,
Marta I. Garrido
,
Satrajit S. Ghosh
,
Martin Grignard
,
Yaroslav O. Halchenko
,
Anthony J. Hannan
,
Anibal S. Heinsfeld
,
Laurentius Huber
,
Matthew E. Hughes
,
Jakub R. Kaczmarzyk
,
Lars Kasper
,
Levin Kuhlmann
,
Kexin Lou
,
Yorguin-Jose Mantilla-Ramos
,
Jason B. Mattingley
,
Michael L. Meier
,
Jo Morris
,
Akshaiy Narayanan
,
Franco Pestilli
,
Aina Puce
,
Fernanda L. Ribeiro
,
Nigel C. Rogasch
,
Chris Rorden
,
Mark M. Schira
,
Thomas B. Shaw
,
Paul F. Sowman
,
Gershon Spitz
,
Ashley W. Stewart
,
Xincheng Ye
,
Judy D. Zhu
,
Aswin Narayanan
,
Steffen Bollmann
Cite
DOI
URL
Consequences of the Scientific Reform Movement
Sarahanne M. Field
,
Noah Van Dongen
,
Leo Tiokhin
,
Aoife 0'Mahony
,
Rebecca Kaplan
,
Alex Visser
,
Meike Robaard
,
Jip Prinsen
,
Thomas F.K. Korna
Cite
DOI
The past, present, and future of the brain imaging data structure (BIDS)
Abstract The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a …
Russell A. Poldrack
,
Christopher J. Markiewicz
,
Stefan Appelhoff
,
Yoni K. Ashar
,
Tibor Auer
,
Sylvain Baillet
,
Shashank Bansal
,
Leandro Beltrachini
,
Christian G. Benar
,
Giacomo Bertazzoli
,
Suyash Bhogawar
,
Ross W. Blair
,
Marta Bortoletto
,
Mathieu Boudreau
,
Teon L. Brooks
,
Vince D. Calhoun
,
Filippo Maria Castelli
,
Patricia Clement
,
Alexander L. Cohen
,
Julien Cohen-Adad
,
Sasha D’Ambrosio
,
Gilles De Hollander
,
María De La Iglesia-Vayá
,
Alejandro De La Vega
,
Arnaud Delorme
,
Orrin Devinsky
,
Dejan Draschkow
,
Eugene Paul Duff
,
Elizabeth DuPre
,
Eric Earl
,
Oscar Esteban
,
Franklin W. Feingold
,
Guillaume Flandin
,
Anthony Galassi
,
Giuseppe Gallitto
,
Melanie Ganz
,
Rémi Gau
,
James Gholam
,
Satrajit S. Ghosh
,
Alessio Giacomel
,
Ashley G. Gillman
,
Padraig Gleeson
,
Alexandre Gramfort
,
Samuel Guay
,
Giacomo Guidali
,
Yaroslav O. Halchenko
,
Daniel A. Handwerker
,
Nell Hardcastle
,
Peer Herholz
,
Dora Hermes
,
Christopher J. Honey
,
Robert B. Innis
,
Horea-Ioan Ioanas
,
Andrew Jahn
,
Agah Karakuzu
,
David B. Keator
,
Gregory Kiar
,
Balint Kincses
,
Angela R. Laird
,
Jonathan C. Lau
,
Alberto Lazari
,
Jon Haitz Legarreta
,
Adam Li
,
Xiangrui Li
,
Bradley C. Love
,
Hanzhang Lu
,
Eleonora Marcantoni
,
Camille Maumet
,
Giacomo Mazzamuto
,
Steven L. Meisler
,
Mark Mikkelsen
,
Henk Mutsaerts
,
Thomas E. Nichols
,
Aki Nikolaidis
,
Gustav Nilsonne
,
Guiomar Niso
,
Martin Norgaard
,
Thomas W. Okell
,
Robert Oostenveld
,
Eduard Ort
,
Patrick J. Park
,
Mateusz Pawlik
,
Cyril R. Pernet
,
Franco Pestilli
,
Jan Petr
,
Christophe Phillips
,
Jean-Baptiste Poline
,
Luca Pollonini
,
Pradeep Reddy Raamana
,
Petra Ritter
,
Gaia Rizzo
,
Kay A. Robbins
,
Alexander P. Rockhill
,
Christine Rogers
,
Ariel Rokem
,
Chris Rorden
,
Alexandre Routier
,
Jose Manuel Saborit-Torres
,
Taylor Salo
,
Michael Schirner
,
Robert E. Smith
,
Tamas Spisak
,
Julia Sprenger
,
Nicole C. Swann
,
Martin Szinte
,
Sylvain Takerkart
,
Bertrand Thirion
,
Adam G. Thomas
,
Sajjad Torabian
,
Gael Varoquaux
,
Bradley Voytek
,
Julius Welzel
,
Martin Wilson
,
Tal Yarkoni
,
Krzysztof J. Gorgolewski
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DOI
URL
Impact of analytic decisions on test-retest reliability of individual and group estimates in functional magnetic resonance imaging: a multiverse analysis using the monetary incentive delay task
Abstract Empirical studies reporting low test-retest reliability of individual blood oxygen-level dependent (BOLD) signal estimates in …
Michael I. Demidenko
,
Jeanette A. Mumford
,
Russell A. Poldrack
Cite
DOI
URL
The Impact of Hardware Variability on Applications Packaged with Docker and Guix: a Case Study in Neuroimaging
The reproducibility of neuroimaging analyses across computational environments has gained significant attention over the last few …
Gaël Vila
,
Emmanuel Medernach
,
Inés Gonzalez
,
Axel Bonnet
,
Yohan Chatelain
,
Michaël Sdika
,
Tristan Glatard
,
Sorina Camarasu-Pop
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URL
Exploring a formal approach to selecting studies for replication: A feasibility study in social neuroscience
Peder M. Isager
,
Daniël Lakens
,
Thed Van Leeuwen
,
Anna E. Van 'T Veer
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DOI
URL
Data leakage inflates prediction performance in connectome-based machine learning models
Abstract Predictive modeling is a central technique in neuroimaging to identify brain-behavior relationships and test their …
Matthew Rosenblatt
,
Link Tejavibulya
,
Rongtao Jiang
,
Stephanie Noble
,
Dustin Scheinost
Cite
DOI
URL
Data leakage inflates prediction performance in connectome-based machine learning models
Abstract Predictive modeling is a central technique in neuroimaging to identify brain-behavior relationships and test their …
Matthew Rosenblatt
,
Link Tejavibulya
,
Rongtao Jiang
,
Stephanie Noble
,
Dustin Scheinost
Cite
DOI
URL
Vers une recherche reproductible
Livre d’introduction à la recherche reproductible rédigé lors d’un booksprint.
Sabrina Granger, Boris Hejblum, Arnaud Legrand, Pascal Pernot, Nicolas Rougier Facilitatrice :, Loïc Desquilbet Elisa de Castro Guerra
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URL
The value of replications goes beyond replicability and is tied to the value of the research it replicates: Commentary on Isager et al. (2024)
Gilad Feldman
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DOI
URL
The past, present and future of neuroscience data sharing: a perspective on the state of practices and infrastructure for FAIR
Neuroscience has made significant strides over the past decade in moving from a largely closed science characterized by anemic data …
Maryann E. Martone
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DOI
URL
Reproducibility in medical image computing: what is it and how is it assessed?
Medical image computing (MIC) is devoted to computational methods for analysis of medical imaging data and their assessment through …
Olivier Colliot
,
Elina Thibeau-Sutre
,
Camille Brianceau
,
Ninon Burgos
Cite
Illusory generalizability of clinical prediction models
It is widely hoped that statistical models can improve decision-making related to medical treatments. Because of the cost and scarcity …
Adam M. Chekroud
,
Matt Hawrilenko
,
Hieronimus Loho
,
Julia Bondar
,
Ralitza Gueorguieva
,
Alkomiet Hasan
,
Joseph Kambeitz
,
Philip R. Corlett
,
Nikolaos Koutsouleris
,
Harlan M. Krumholz
,
John H. Krystal
,
Martin Paulus
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DOI
URL
ENIGMA’s simple seven: Recommendations to enhance the reproducibility of resting-state fMRI in traumatic brain injury
Karen Caeyenberghs
,
Phoebe Imms
,
Andrei Irimia
,
Martin M. Monti
,
Carrie Esopenko
,
Nicola L. De Souza
,
Juan F. Dominguez D
,
Mary R. Newsome
,
Ekaterina Dobryakova
,
Andrew Cwiek
,
Hollie A.C. Mullin
,
Nicholas J. Kim
,
Andrew R. Mayer
,
Maheen M. Adamson
,
Kevin Bickart
,
Katherine M. Breedlove
,
Emily L. Dennis
,
Seth G. Disner
,
Courtney Haswell
,
Cooper B. Hodges
,
Kristen R. Hoskinson
,
Paula K. Johnson
,
Marsh Königs
,
Lucia M. Li
,
Spencer W. Liebel
,
Abigail Livny
,
Rajendra A. Morey
,
Alexandra M. Muir
,
Alexander Olsen
,
Adeel Razi
,
Matthew Su
,
David F. Tate
,
Carmen Velez
,
Elisabeth A. Wilde
,
Brandon A. Zielinski
,
Paul M. Thompson
,
Frank G. Hillary
Cite
DOI
URL
bids-standard/BEP028_BIDSprov
Organizing and coordinating BIDS extension proposal 28 : BIDS Provenance
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URL
A reproducible and generalizable software workflow for analysis of large-scale neuroimaging data collections using BIDS Apps
Abstract Neuroimaging research faces a crisis of reproducibility. With massive sample sizes and greater data complexity, this problem …
Chenying Zhao
,
Dorota Jarecka
,
Sydney Covitz
,
Yibei Chen
,
Simon B. Eickhoff
,
Damien A. Fair
,
Alexandre R. Franco
,
Yaroslav O. Halchenko
,
Timothy J. Hendrickson
,
Felix Hoffstaedter
,
Audrey Houghton
,
Gregory Kiar
,
Austin Macdonald
,
Kahini Mehta
,
Michael P. Milham
,
Taylor Salo
,
Michael Hanke
,
Satrajit S. Ghosh
,
Matthew Cieslak
,
Theodore D. Satterthwaite
Cite
DOI
URL
nipy/heudiconv: v1.0.0
💥 Breaking Change gh-actions: Bump actions/checkout from 3 to 4 #703 (@dependabot[bot]) 🚀 Enhancement Fix inconsistent behavior of …
Yaroslav Halchenko
,
Mathias Goncalves
,
Pablo Velasco
,
Matteo Visconti Di Oleggio Castello
,
Satrajit Ghosh
,
Taylor Salo
,
John T. Wodder
,
Michael Hanke
,
Patrick Sadil
,
Horea Christian
,
Dae
,
Steven Tilley
,
James Kent
,
Isaac To
,
Matthew Brett
,
Inge Amlien
,
Chris Gorgolewski
,
Chris Markiewicz
,
Darren Christopher Lukas
,
Keith Callenberg
,
Aksoo
,
Ari Kahn
,
Austin Macdonald
,
Benjamin Poldrack
,
Bruno Melo
,
Henry Braun
,
John Lee
,
John Pellman
,
Michael
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DOI
URL
Reproducibility in Neuroimaging Analysis: Challenges and Solutions
Recent years have marked a renaissance in efforts to increase research reproducibility in psychology, neuroscience, and related fields. …
Rotem Botvinik-Nezer
,
Tor D. Wager
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DOI
URL
Editorial: Reproducibility in neuroscience
Nafisa M. Jadavji
,
Nele A. Haelterman
,
Reeteka Sud
,
Alberto Antonietti
Cite
DOI
URL
Why every lab needs a handbook
A lab handbook is a flexible document that outlines the ethos of a research lab or group. A good handbook will outline the different …
Benjamin C Tendler
,
Maddie Welland
,
Karla L Miller
,
The WIN Handbook Team
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DOI
URL
Sampling inequalities affect generalization of neuroimaging-based diagnostic classifiers in psychiatry
Abstract Background The development of machine learning models for aiding in the diagnosis of mental disorder is recognized as a …
Zhiyi Chen
,
Bowen Hu
,
Xuerong Liu
,
Benjamin Becker
,
Simon B. Eickhoff
,
Kuan Miao
,
Xingmei Gu
,
Yancheng Tang
,
Xin Dai
,
Chao Li
,
Artemiy Leonov
,
Zhibing Xiao
,
Zhengzhi Feng
,
Ji Chen
,
Hu Chuan-Peng
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DOI
URL
Containers for computational reproducibility
This PrimeView highlights the range of applications benefiting from the use of containers for reproducibility of computational data …
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DOI
URL
Reprohackathons: promoting reproducibility in bioinformatics through training
The reproducibility crisis has highlighted the importance of improving the way bioinformatics data analyses are implemented, executed, …
Thomas Cokelaer
,
Sarah Cohen-Boulakia
,
Frédéric Lemoine
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DOI
URL
A reproducible benchmark of resting-state fMRIdenoising strategies using fMRIPrep and Nilearn
Reducing contributions from non-neuronal sources is a crucial step in functional magnetic resonance imaging (fMRI) connectivity …
Hao-Ting Wang
,
Steven L Meisler
,
Hanad Sharmarke
,
Natasha Clarke
,
François Paugam
,
Nicolas Gensollen
,
Christopher J Markiewicz
,
Bertrand Thirion
,
Pierre Bellec
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Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging
Abstract Neuroimaging data analysis often requires purpose-built software, which can be challenging to install and may produce …
Steffen Bollmann
,
Angela Renton
,
Thuy Dao
,
Tom Johnstone
,
Oren Civier
,
Ryan Sullivan
,
David White
,
Paris Lyons
,
Benjamin Slade
,
David Abbott
,
Toluwani Amos
,
Saskia Bollmann
,
Andy Botting
,
Megan Campbell
,
Jeryn Chang
,
Thomas Close
,
Korbinian Eckstein
,
Gary Egan
,
Stefanie Evas
,
Guillaume Flandin
,
Kelly Garner
,
Marta Garrido
,
Satrajit Ghosh
,
Martin Grignard
,
Anthony Hannan
,
Laurentius (Renzo) Huber
,
Jakub Kaczmarzyk
,
Lars Kasper
,
Levin Kuhlmann
,
Kexin Lou
,
Yorguin-Jose Mantilla-Ramos
,
Jason Mattingley
,
Jo Morris
,
Akshaiy Narayanan
,
Franco Pestilli
,
Aina Puce
,
Fernanda Ribeiro
,
Nigel Rogasch
,
Chris Rorden
,
Mark Schira
,
Thomas Shaw
,
Paul Sowman
,
Gershon Spitz
,
Ashley Stewart
,
Xincheng Ye
,
Judy Zhu
,
Matthew Hughes
,
Aswin Narayanan
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Multivariate BWAS can be replicable with moderate sample sizes
Tamas Spisak
,
Ulrike Bingel
,
Tor D. Wager
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The Software Heritage Open Science Ecosystem
Software Heritage is the largest public archive of software source code and associated development history, as captured by modern …
Roberto Di Cosmo
,
Stefano Zacchiroli
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Reproducibility in MRI
Nina Vogt
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Integrating the BIDS Neuroimaging Data Format and Workflow Optimization for Large-Scale Medical Image Analysis
A robust medical image computing infrastructure must host massive multimodal archives, perform extensive analysis pipelines, and …
Shunxing Bao
,
Brian D. Boyd
,
Praitayini Kanakaraj
,
Karthik Ramadass
,
Francisco A. C. Meyer
,
Yuqian Liu
,
William E. Duett
,
Yuankai Huo
,
Ilwoo Lyu
,
David H. Zald
,
Seth A. Smith
,
Baxter P. Rogers
,
Bennett A. Landman
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Open and reproducible neuroimaging: From study inception to publication
Guiomar Niso
,
Rotem Botvinik-Nezer
,
Stefan Appelhoff
,
Alejandro De La Vega
,
Oscar Esteban
,
Joset A. Etzel
,
Karolina Finc
,
Melanie Ganz
,
Rémi Gau
,
Yaroslav O. Halchenko
,
Peer Herholz
,
Agah Karakuzu
,
David B. Keator
,
Christopher J. Markiewicz
,
Camille Maumet
,
Cyril R. Pernet
,
Franco Pestilli
,
Nazek Queder
,
Tina Schmitt
,
Weronika Sójka
,
Adina S. Wagner
,
Kirstie J. Whitaker
,
Jochem W. Rieger
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Toward practical transparent verifiable and long-term reproducible research using Guix
Abstract Reproducibility crisis urge scientists to promote transparency which allows peers to draw same conclusions after performing …
Nicolas Vallet
,
David Michonneau
,
Simon Tournier
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qMRI-BIDS: An extension to the brain imaging data structure for quantitative magnetic resonance imaging data
Abstract The Brain Imaging Data Structure (BIDS) established community consensus on the organization of data and metadata for several …
Agah Karakuzu
,
Stefan Appelhoff
,
Tibor Auer
,
Mathieu Boudreau
,
Franklin Feingold
,
Ali R. Khan
,
Alberto Lazari
,
Chris Markiewicz
,
Martijn Mulder
,
Christophe Phillips
,
Taylor Salo
,
Nikola Stikov
,
Kirstie Whitaker
,
Gilles De Hollander
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Reproducing FSL's fMRI data analysis via Nipype: Relevance, challenges, and solutions
The “replication crisis” in neuroscientific research has led to calls for improving reproducibility. In traditional neuroscience …
Yibei Chen
,
Frederic R. Hopp
,
Musa Malik
,
Paula T. Wang
,
Kylie Woodman
,
Sungbin Youk
,
René Weber
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A guided multiverse study of neuroimaging analyses
Abstract For most neuroimaging questions the range of possible analytic choices makes it unclear how to evaluate conclusions from any …
Jessica Dafflon
,
Pedro F. Da Costa
,
František Váša
,
Ricardo Pio Monti
,
Danilo Bzdok
,
Peter J. Hellyer
,
Federico Turkheimer
,
Jonathan Smallwood
,
Emily Jones
,
Robert Leech
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The replication crisis is not a crisis of false positives
Efforts to replicate portions of the scientific literature have lead to widely varying and often low rates of replicability. This has …
Joseph B Bak-Coleman
,
Richard P. Mann
,
Carl T. Bergstrom
,
Kevin Gross
,
Jevin West
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Reproducible brain-wide association studies require thousands of individuals
Magnetic resonance imaging (MRI) has transformed our understanding of the human brain through well-replicated mapping of abilities to …
Scott Marek
,
Brenden Tervo-Clemmens
,
Finnegan J. Calabro
,
David F. Montez
,
Benjamin P. Kay
,
Alexander S. Hatoum
,
Meghan Rose Donohue
,
William Foran
,
Ryland L. Miller
,
Timothy J. Hendrickson
,
Stephen M. Malone
,
Sridhar Kandala
,
Eric Feczko
,
Oscar Miranda-Dominguez
,
Alice M. Graham
,
Eric A. Earl
,
Anders J. Perrone
,
Michaela Cordova
,
Olivia Doyle
,
Lucille A. Moore
,
Gregory M. Conan
,
Johnny Uriarte
,
Kathy Snider
,
Benjamin J. Lynch
,
James C. Wilgenbusch
,
Thomas Pengo
,
Angela Tam
,
Jianzhong Chen
,
Dillan J. Newbold
,
Annie Zheng
,
Nicole A. Seider
,
Andrew N. Van
,
Athanasia Metoki
,
Roselyne J. Chauvin
,
Timothy O. Laumann
,
Deanna J. Greene
,
Steven E. Petersen
,
Hugh Garavan
,
Wesley K. Thompson
,
Thomas E. Nichols
,
B. T. Thomas Yeo
,
Deanna M. Barch
,
Beatriz Luna
,
Damien A. Fair
,
Nico U. F. Dosenbach
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FAIRly big: A framework for computationally reproducible processing of large-scale data
Abstract Large-scale datasets present unique opportunities to perform scientific investigations with unprecedented breadth. However, …
Adina S. Wagner
,
Laura K. Waite
,
Małgorzata Wierzba
,
Felix Hoffstaedter
,
Alexander Q. Waite
,
Benjamin Poldrack
,
Simon B. Eickhoff
,
Michael Hanke
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Data sharing and privacy issues in neuroimaging research: Opportunities, obstacles, challenges, and monsters under the bed
Collaborative networks and data sharing initiatives are broadening the opportunities for the advancement of science. These initiatives …
Tonya White
,
Elisabet Blok
,
Vince D. Calhoun
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DataLad: distributed system for joint management of code, data, and their relationship
Yaroslav Halchenko
,
Kyle Meyer
,
Benjamin Poldrack
,
Debanjum Solanky
,
Adina Wagner
,
Jason Gors
,
Dave MacFarlane
,
Dorian Pustina
,
Vanessa Sochat
,
Satrajit Ghosh
,
Christian Mönch
,
Christopher Markiewicz
,
Laura Waite
,
Ilya Shlyakhter
,
Alejandro De La Vega
,
Soichi Hayashi
,
Christian Häusler
,
Jean-Baptiste Poline
,
Tobias Kadelka
,
Kusti Skytén
,
Dorota Jarecka
,
David Kennedy
,
Ted Strauss
,
Matt Cieslak
,
Peter Vavra
,
Horea-Ioan Ioanas
,
Robin Schneider
,
Mika Pflüger
,
James Haxby
,
Simon Eickhoff
,
Michael Hanke
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A hitchhiker’s guide to working with large, open-source neuroimaging datasets
Corey Horien
,
Stephanie Noble
,
Abigail S. Greene
,
Kangjoo Lee
,
Daniel S. Barron
,
Siyuan Gao
,
David O’Connor
,
Mehraveh Salehi
,
Javid Dadashkarimi
,
Xilin Shen
,
Evelyn M. R. Lake
,
R. Todd Constable
,
Dustin Scheinost
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Influence of sample size and analytic approach on stability and interpretation of brain‐behavior correlations in task‐related fMRI data
Limited statistical power due to small sample sizes is a problem in fMRI research. Most of the work to date has examined the impact of …
Cheryl L. Grady
,
Jenny R. Rieck
,
Daniel Nichol
,
Karen M. Rodrigue
,
Kristen M. Kennedy
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FAIR Computational Workflows
Computational workflows describe the complex multi-step methods that are used for data collection, data preparation, analytics, …
Carole Goble
,
Sarah Cohen-Boulakia
,
Stian Soiland-Reyes
,
Daniel Garijo
,
Yolanda Gil
,
Michael R. Crusoe
,
Kristian Peters
,
Daniel Schober
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fMRI data of mixed gambles from the Neuroimaging Analysis Replication and Prediction Study
Abstract There is an ongoing debate about the replicability of neuroimaging research. It was suggested that one of the main reasons for …
Rotem Botvinik-Nezer
,
Roni Iwanir
,
Felix Holzmeister
,
Jürgen Huber
,
Magnus Johannesson
,
Michael Kirchler
,
Anna Dreber
,
Colin F. Camerer
,
Russell A. Poldrack
,
Tom Schonberg
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Scrutinizing the EU General Data Protection Regulation
How will new decentralized governance impact research? , On 25 May 2018, the European Union (EU) regulation 2016/679 on data …
Luca Marelli
,
Giuseppe Testa
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Best practices in data analysis and sharing in neuroimaging using MRI
Thomas E Nichols
,
Samir Das
,
Simon B Eickhoff
,
Alan C Evans
,
Tristan Glatard
,
Michael Hanke
,
Nikolaus Kriegeskorte
,
Michael P Milham
,
Russell a Poldrack
,
Jean-Baptiste Poline
,
Erika Proal
,
Bertrand Thirion
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Making data sharing work: The FCP/INDI experience
Over a decade ago, the fMRI Data Center (fMRIDC) pioneered open-access data sharing in the task-based functional neuroimaging …
Maarten Mennes
,
Bharat B. Biswal
,
F. Xavier Castellanos
,
Michael P. Milham
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