Evidence map›Paper›PMID 36993557›Full record

ArticleResearch square2023

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 and 38 more

Abstract readPreprint
In one paragraph

Article in Research square, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

48 authors.

Angela I RentonThe University of Queensland, Queensland Brain Institute, St Lucia 4072, Australia.ORCID 0000-0003-4815-9056
Thuy T DaoThe University of Queensland, School of Information Technology and Electrical Engineering, St Lucia 4072, Australia.ORCID 0000-0003-0715-3555
Tom JohnstoneCentre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn 3122, Australia.
Oren CivierCentre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn 3122, Australia.
Ryan P SullivanThe University of Sydney, School of Biomedical Engineering, Sydney, Australia.ORCID 0000-0001-5554-7378
David J WhiteCentre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn 3122, Australia.
Paris LyonsCentre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn 3122, Australia.
Benjamin M SladeCentre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn 3122, Australia.
David F AbbottThe Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria, Australia.
Toluwani J AmosSchool of Life Science and Technology, University of Electronic Science and Technology, China.
Saskia BollmannThe University of Queensland, School of Information Technology and Electrical Engineering, St Lucia 4072, Australia.
Andy BottingAustralian Research Data Commons (ARDC), Australia.
Megan E J CampbellSchool of Psychological Sciences, University of Newcastle, Australia.
Jeryn ChangThe University of Queensland, School of Biomedical Sciences, St Lucia 4072, Australia.
Thomas G CloseThe University of Sydney, School of Biomedical Engineering, Sydney, Australia.
Korbinian EcksteinThe University of Queensland, School of Information Technology and Electrical Engineering, St Lucia 4072, Australia.
Gary F EganThe Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Victoria, Australia.
Stefanie EvasSchool of Psychology, University of Adelaide, Adelaide, 5000, Australia.ORCID 0000-0002-2090-2074
Guillaume FlandinWellcome Centre for Human Neuroimaging, University College London, London, UK.
Kelly G GarnerThe University of Queensland, Queensland Brain Institute, St Lucia 4072, Australia.
Marta I GarridoMelbourne School of Psychological Sciences, The University of Melbourne.ORCID 0000-0003-0679-4959
Satrajit S GhoshMcGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.ORCID 0000-0002-5312-6729
Martin GrignardGIGA CRC In-Vivo Imaging, University of Liege, Liege, Belgium.
Anthony J HannanThe Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria, Australia.ORCID 0000-0001-7532-8922
Renzo HuberFunctional Magnetic Resonance Imaging Core Facility (FMRIF), National Institute of Mental Health (NIMH), USA.
Jakub R KaczmarzykMedical Scientist Training Program, Stony Brook University, Stony Brook, NY, United States of America.
Lars KasperTechna Institute, University Health Network, Toronto, Canada.ORCID 0000-0001-7667-603X
Levin KuhlmannDepartment of Data Science and AI, Faculty of Information Technology, Monash University, Clayton VIC 3800, Australia.
Kexin LouThe University of Queensland, School of Information Technology and Electrical Engineering, St Lucia 4072, Australia.
Yorguin-Jose Mantilla-RamosGrupo Neuropsicología y Conducta (GRUNECO), Facultad de Medicina, Universidad de Antioquia, Colombia.ORCID 0000-0003-4473-0876
Jason B MattingleyThe University of Queensland, Queensland Brain Institute, St Lucia 4072, Australia.ORCID 0000-0003-0929-9216
Jo MorrisAustralian Research Data Commons (ARDC), Australia.
Akshaiy NarayananThe University of Auckland, Auckland, 1010, New Zealand.
Franco PestilliDepartment of Psychology, Center for Perceptual Systems, Center for Theoretical and Computational Neuroscience, Center on Aging and Population Sciences, Center for Learning and Memory, The University of Texas at Austin, 108 E Dean Keeton St, Austin, TX 78712, USA.
Aina PuceDepartment of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405, USA.
Fernanda L RibeiroThe University of Queensland, School of Information Technology and Electrical Engineering, St Lucia 4072, Australia.
Nigel C RogaschDiscipline of Psychiatry, Adelaide Medical School, University of Adelaide, Australia.
Chris RordenMcCausland Center for Brain Imaging, Department of Psychology, University of South Carolina, Columbia SC, 29208, USA.
Mark SchiraSchool of Psychology, University of Wollongong, Wollongong, 2522, Australia.
Thomas B ShawThe University of Queensland, School of Information Technology and Electrical Engineering, St Lucia 4072, Australia.
Paul F SowmanMacquarie University, School of Psychological Sciences, North Ryde 2112, Australia.
Gershon SpitzDepartment of Neuroscience, Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Australia.
Ashley StewartThe University of Queensland, School of Information Technology and Electrical Engineering, St Lucia 4072, Australia.
Xincheng YeThe University of Queensland, School of Information Technology and Electrical Engineering, St Lucia 4072, Australia.
Judy D ZhuMacquarie University, School of Psychological Sciences, North Ryde 2112, Australia.
Matthew E HughesCentre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn 3122, Australia.
Aswin NarayananThe University of Queensland, Centre for Advanced Imaging, St Lucia 4072, Australia.
Steffen BollmannThe University of Queensland, School of Information Technology and Electrical Engineering, St Lucia 4072, Australia.

Funding

Resource DiscoveryP41EB019936 · NIBIB · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI David Nelson Kennedy · 2016 to 2026
$15.2M
CRCNS: US-France Data Sharing Proposal: Open science & cloud computing of MEEGR01EB030896 · NIBIB · TRUSTEES OF INDIANA UNIVERSITY · PI PESTILLI, FRANCO, PUCE, AINA · 2020 to 2022
$651k
NIBIB NIH HHS P41 EB019936NIBIB NIH HHS R01 EB030896
6 · The paper itself

Abstract

Neuroimaging data analysis often requires purpose-built software, which can be challenging to install and may produce different results across computing environments. Beyond being a roadblock to neuroscientists, these issues of accessibility and portability can hamper the reproducibility of neuroimaging data analysis pipelines. Here, we introduce the Neurodesk platform, which harnesses software containers to support a comprehensive and growing suite of neuroimaging software (https://www.neurodesk.org/). Neurodesk includes a browser-accessible virtual desktop environment and a command line interface, mediating access to containerized neuroimaging software libraries on various computing platforms, including personal and high-performance computers, cloud computing and Jupyter Notebooks. This community-oriented, open-source platform enables a paradigm shift for neuroimaging data analysis, allowing for accessible, flexible, fully reproducible, and portable data analysis pipelines.

Identifiers

PMID36993557
PMCPMC10055538

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.