Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging.
| Title: | Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging. |
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| Authors: | Renton AI; The University of Queensland, Queensland Brain Institute, St Lucia, Brisbane, Queensland, Australia. angie.renton23@gmail.com.; The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia. angie.renton23@gmail.com.; Dao TT; The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia.; Johnstone T; Centre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia.; Civier O; Centre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia.; Sullivan RP; The University of Sydney, School of Biomedical Engineering, Sydney, New South Wales, Australia.; White DJ; Centre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia.; Lyons P; Centre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia.; Slade BM; Centre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia.; Abbott DF; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Melbourne, Victoria, Australia.; Amos TJ; School of Life Science and Technology, University of Electronic Science and Technology, Chengdu, China.; Bollmann S; The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia.; Botting A; Australian Research Data Commons (ARDC), Sydney, New South Wales, Australia.; Campbell MEJ; School of Psychological Sciences, University of Newcastle, Newcastle, New South Wales, Australia.; Hunter Medical Research Institute Imaging Centre, Newcastle, New South Wales, Australia.; Chang J; The University of Queensland, School of Biomedical Sciences, St Lucia, Brisbane, Queensland, Australia.; Close TG; The University of Sydney, School of Biomedical Engineering, Sydney, New South Wales, Australia.; Dörig M; Integrative Spinal Research, Department of Chiropractic Medicine, Balgrist University Hospital, University of Zurich, Zurich, Switzerland.; Eckstein K; The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia.; Egan GF; The Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia.; Monash Biomedical Imaging, Monash University, Melbourne, Victoria, Australia.; Evas S; School of Psychology, University of Adelaide, Adelaide, South Australia, Australia.; Human Health, Health & Biosecurity, CSIRO, Adelaide, South Australia, Australia.; Flandin G; Wellcome Centre for Human Neuroimaging, University College London, London, UK.; Garner KG; School of Psychology, University of New South Wales, Sydney, New South Wales, Australia.; The University of Queensland, School of Psychology, St Lucia, Brisbane, Queensland, Australia.; Garrido MI; Melbourne School of Psychological Sciences, he University of Melbourne, Melbourne, Victoria, Australia.; Graeme Clark Institute for Biomedical Engineering, The University of Melbourne, Melbourne, Victoria, Australia.; Ghosh SS; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.; Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School, Boston, MA, USA.; Grignard M; GIGA CRC In-Vivo Imaging, University of Liège, Liège, Belgium.; Halchenko YO; Center for Open Neuroscience, Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USA.; Hannan AJ; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Melbourne, Victoria, Australia.; Heinsfeld AS; Department of Psychology, Center for Perceptual Systems, Institute for Neuroscience, Center For Learning and Memory, The University of Texas at Austin, Austin, TX, USA.; Huber L; National Institute of Mental Health (NIMH), National Institutes Health, Bethesda, MD, USA.; Hughes ME; Centre for Mental Health & Brain Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia.; Kaczmarzyk JR; Department of Biomedical Informatics, Stony Brook University, New York, NY, USA.; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, New York, NY, USA.; Kasper L; BRAIN-TO Lab, Krembil Brain Institute, University Health Network, Toronto, Ontario, Canada.; Translational Neuromodeling Unit, Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland.; Kuhlmann L; Department of Data Science and AI, Faculty of Information Technology, Monash University, Melbourne, Victoria, Australia.; Lou K; The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia.; Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China.; Mantilla-Ramos YJ; Grupo Neuropsicología y Conducta (GRUNECO), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.; Mattingley JB; The University of Queensland, Queensland Brain Institute, St Lucia, Brisbane, Queensland, Australia.; The University of Queensland, School of Psychology, St Lucia, Brisbane, Queensland, Australia.; Meier ML; Integrative Spinal Research, Department of Chiropractic Medicine, Balgrist University Hospital, University of Zurich, Zurich, Switzerland.; Morris J; Australian Research Data Commons (ARDC), Sydney, New South Wales, Australia.; Narayanan A; School of Computer Science, The University of Auckland, Auckland, New Zealand.; Pestilli F; Department of Psychology, Center for Perceptual Systems, Institute for Neuroscience, Center For Learning and Memory, The University of Texas at Austin, Austin, TX, USA.; Puce A; Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA.; Ribeiro FL; The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia.; Rogasch NC; The Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia.; Discipline of Psychiatry, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia.; Hopwood Centre for Neurobiology, Lifelong Health Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia.; Rorden C; McCausland Center for Brain Imaging, Department of Psychology, University of South Carolina, Columbia, SC, USA.; Schira MM; School of Psychology, University of Wollongong, Wollongong, New South Wales, Australia.; Shaw TB; The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia.; The University of Queensland, Centre for Advanced Imaging, St Lucia, Brisbane, Queensland, Australia.; Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia.; Sowman PF; Macquarie University, School of Psychological Sciences, Sydney, New South Wales, Australia.; Spitz G; Department of Neuroscience, Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia.; Monash-Epworth Rehabilitation Research Centre, Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia.; Stewart AW; The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia.; ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, Brisbane, Queensland, Australia.; Ye X; The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia.; Zhu JD; Macquarie University, School of Psychological Sciences, Sydney, New South Wales, Australia.; Narayanan A; The University of Queensland, Centre for Advanced Imaging, St Lucia, Brisbane, Queensland, Australia.; Bollmann S; The University of Queensland, School of Electrical Engineering and Computer Science, St Lucia, Brisbane, Queensland, Australia. s.bollmann@uq.edu.au.; The University of Queensland, Centre for Advanced Imaging, St Lucia, Brisbane, Queensland, Australia. s.bollmann@uq.edu.au.; ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, Brisbane, Queensland, Australia. s.bollmann@uq.edu.au.; Queensland Digital Health Centre, The University of Queensland, Brisbane, Queensland, Australia. s.bollmann@uq.edu.au. |
| Source: | Nature methods [Nat Methods] 2024 May; Vol. 21 (5), pp. 804-808. Date of Electronic Publication: 2024 Jan 08. |
| Publication Type: | Journal Article |
| Language: | English |
| Journal Info: | Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: New York, NY : Nature Pub. Group, c2004- |
| MeSH Terms: | Neuroimaging*/methods ; Software*; Brain/diagnostic imaging ; Humans ; User-Computer Interface ; Reproducibility of Results |
| Abstract: | Neuroimaging research requires purpose-built analysis software, which is challenging to install and may produce different results across computing environments. The community-oriented, open-source Neurodesk platform ( https://www.neurodesk.org/ ) harnesses a comprehensive and growing suite of neuroimaging software containers. Neurodesk includes a browser-accessible virtual desktop, command-line interface and computational notebook compatibility, allowing for accessible, flexible, portable and fully reproducible neuroimaging analysis on personal workstations, high-performance computers and the cloud.; (© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.) |
| Comments: | Update of: Res Sq. 2023 Mar 13:rs.3.rs-2649734. doi: 10.21203/rs.3.rs-2649734/v1.. (PMID: 36993557) |
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| Grant Information: | P41 EB019936 United States EB NIBIB NIH HHS; R01 EB030896 United States EB NIBIB NIH HHS; R01 MH126699 United States MH NIMH NIH HHS |
| Entry Date(s): | Date Created: 20240109 Date Completed: 20240514 Latest Revision: 20241126 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC11180540 |
| DOI: | 10.1038/s41592-023-02145-x |
| PMID: | 38191935 |
| Database: | MEDLINE |
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