Your browser doesn't support javascript.
loading
Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging.
Renton, Angela I; Dao, Thuy T; Johnstone, Tom; Civier, Oren; Sullivan, Ryan P; White, David J; Lyons, Paris; Slade, Benjamin M; Abbott, David F; Amos, Toluwani J; Bollmann, Saskia; Botting, Andy; Campbell, Megan E J; Chang, Jeryn; Close, Thomas G; Eckstein, Korbinian; Egan, Gary F; Evas, Stefanie; Flandin, Guillaume; Garner, Kelly G; Garrido, Marta I; Ghosh, Satrajit S; Grignard, Martin; Hannan, Anthony J; Huber, Renzo; Kaczmarzyk, Jakub R; Kasper, Lars; Kuhlmann, Levin; Lou, Kexin; Mantilla-Ramos, Yorguin-Jose; Mattingley, Jason B; Morris, Jo; Narayanan, Akshaiy; Pestilli, Franco; Puce, Aina; Ribeiro, Fernanda L; Rogasch, Nigel C; Rorden, Chris; Schira, Mark; Shaw, Thomas B; Sowman, Paul F; Spitz, Gershon; Stewart, Ashley; Ye, Xincheng; Zhu, Judy D; Hughes, Matthew E; Narayanan, Aswin; Bollmann, Steffen.
Affiliation
  • Renton AI; The University of Queensland, Queensland Brain Institute, St Lucia 4072, Australia.
  • Dao TT; The University of Queensland, School of Information Technology and Electrical Engineering, St Lucia 4072, Australia.
  • Johnstone T; The University of Queensland, School of Information Technology and Electrical Engineering, St Lucia 4072, Australia.
  • Civier O; Centre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn 3122, Australia.
  • Sullivan RP; Centre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn 3122, Australia.
  • White DJ; The University of Sydney, School of Biomedical Engineering, Sydney, Australia.
  • Lyons P; Centre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn 3122, Australia.
  • Slade BM; Centre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn 3122, Australia.
  • Abbott DF; Centre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn 3122, Australia.
  • Amos TJ; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria, Australia.
  • Bollmann S; School of Life Science and Technology, University of Electronic Science and Technology, China.
  • Botting A; The University of Queensland, School of Information Technology and Electrical Engineering, St Lucia 4072, Australia.
  • Campbell MEJ; Australian Research Data Commons (ARDC), Australia.
  • Chang J; School of Psychological Sciences, University of Newcastle, Australia.
  • Close TG; Hunter Medical Research Institute Imaging Centre, Newcastle, Australia.
  • Eckstein K; The University of Queensland, School of Biomedical Sciences, St Lucia 4072, Australia.
  • Egan GF; The University of Sydney, School of Biomedical Engineering, Sydney, Australia.
  • Evas S; The University of Queensland, School of Information Technology and Electrical Engineering, St Lucia 4072, Australia.
  • Flandin G; The Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Victoria, Australia.
  • Garner KG; Monash Biomedical Imaging, Monash University, Victoria, Australia.
  • Garrido MI; School of Psychology, University of Adelaide, Adelaide, 5000, Australia.
  • Ghosh SS; Human Health, Health & Biosecurity, CSIRO, Adelaide, 5000, Australia.
  • Grignard M; Wellcome Centre for Human Neuroimaging, University College London, London, UK.
  • Hannan AJ; The University of Queensland, Queensland Brain Institute, St Lucia 4072, Australia.
  • Huber R; The University of Queensland, School of Psychology, St Lucia 4072, Australia.
  • Kaczmarzyk JR; Melbourne School of Psychological Sciences, The University of Melbourne.
  • Kasper L; Graeme Clark Institute for Biomedical Engineering, The University of Melbourne.
  • Kuhlmann L; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
  • Lou K; Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School, Boston, MA, USA.
  • Mantilla-Ramos YJ; GIGA CRC In-Vivo Imaging, University of Liege, Liege, Belgium.
  • Mattingley JB; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria, Australia.
  • Morris J; Functional Magnetic Resonance Imaging Core Facility (FMRIF), National Institute of Mental Health (NIMH), USA.
  • Narayanan A; Medical Scientist Training Program, Stony Brook University, Stony Brook, NY, United States of America.
  • Pestilli F; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America.
  • Puce A; Techna Institute, University Health Network, Toronto, Canada.
  • Ribeiro FL; Department of Data Science and AI, Faculty of Information Technology, Monash University, Clayton VIC 3800, Australia.
  • Rogasch NC; The University of Queensland, School of Information Technology and Electrical Engineering, St Lucia 4072, Australia.
  • Rorden C; Grupo Neuropsicología y Conducta (GRUNECO), Facultad de Medicina, Universidad de Antioquia, Colombia.
  • Schira M; The University of Queensland, Queensland Brain Institute, St Lucia 4072, Australia.
  • Shaw TB; The University of Queensland, School of Psychology, St Lucia 4072, Australia.
  • Sowman PF; Australian Research Data Commons (ARDC), Australia.
  • Spitz G; The University of Auckland, Auckland, 1010, New Zealand.
  • Stewart A; Department 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.
  • Ye X; Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405, USA.
  • Zhu JD; The University of Queensland, School of Information Technology and Electrical Engineering, St Lucia 4072, Australia.
  • Hughes ME; Discipline of Psychiatry, Adelaide Medical School, University of Adelaide, Australia.
  • Narayanan A; Hopwood Centre for Neurobiology, Lifelong Health Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.
  • Bollmann S; The Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Victoria, Australia.
Res Sq ; 2023 Mar 13.
Article in En | MEDLINE | ID: mdl-36993557
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.
Fulltext
Print
XML
PubMed Links
Search on Google

Full text: 1 Database: MEDLINE Language: En Year: 2023 Type: Article
Fulltext
Print
XML
PubMed Links
Search on Google

Full text: 1 Database: MEDLINE Language: En Year: 2023 Type: Article