Web-based processing of physiological noise in fMRI: addition of the PhysIO toolbox to CBRAIN
Neuroimaging research requires sophisticated tools for analyzing complex data, but efficiently leveraging these tools can be a major challenge, especially on large datasets. CBRAIN is a web-based platform designed to simplify the use and accessibility of neuroimaging research tools for large-scale,...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-09-01
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| Series: | Frontiers in Neuroinformatics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fninf.2023.1251023/full |
| _version_ | 1797671756393086976 |
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| author | Darius Valevicius Natacha Beck Lars Kasper Lars Kasper Sergiy Boroday Johanna Bayer Johanna Bayer Pierre Rioux Bryan Caron Reza Adalat Alan C. Evans Najmeh Khalili-Mahani Najmeh Khalili-Mahani |
| author_facet | Darius Valevicius Natacha Beck Lars Kasper Lars Kasper Sergiy Boroday Johanna Bayer Johanna Bayer Pierre Rioux Bryan Caron Reza Adalat Alan C. Evans Najmeh Khalili-Mahani Najmeh Khalili-Mahani |
| author_sort | Darius Valevicius |
| collection | DOAJ |
| description | Neuroimaging research requires sophisticated tools for analyzing complex data, but efficiently leveraging these tools can be a major challenge, especially on large datasets. CBRAIN is a web-based platform designed to simplify the use and accessibility of neuroimaging research tools for large-scale, collaborative studies. In this paper, we describe how CBRAIN’s unique features and infrastructure were leveraged to integrate TAPAS PhysIO, an open-source MATLAB toolbox for physiological noise modeling in fMRI data. This case study highlights three key elements of CBRAIN’s infrastructure that enable streamlined, multimodal tool integration: a user-friendly GUI, a Brain Imaging Data Structure (BIDS) data-entry schema, and convenient in-browser visualization of results. By incorporating PhysIO into CBRAIN, we achieved significant improvements in the speed, ease of use, and scalability of physiological preprocessing. Researchers now have access to a uniform and intuitive interface for analyzing data, which facilitates remote and collaborative evaluation of results. With these improvements, CBRAIN aims to become an essential open-science tool for integrative neuroimaging research, supporting FAIR principles and enabling efficient workflows for complex analysis pipelines. |
| first_indexed | 2024-03-11T21:20:09Z |
| format | Article |
| id | doaj.art-b2c82e2d8ff24cff9175a9687e1d1314 |
| institution | Directory Open Access Journal |
| issn | 1662-5196 |
| language | English |
| last_indexed | 2024-03-11T21:20:09Z |
| publishDate | 2023-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Neuroinformatics |
| spelling | doaj.art-b2c82e2d8ff24cff9175a9687e1d13142023-09-28T09:31:44ZengFrontiers Media S.A.Frontiers in Neuroinformatics1662-51962023-09-011710.3389/fninf.2023.12510231251023Web-based processing of physiological noise in fMRI: addition of the PhysIO toolbox to CBRAINDarius Valevicius0Natacha Beck1Lars Kasper2Lars Kasper3Sergiy Boroday4Johanna Bayer5Johanna Bayer6Pierre Rioux7Bryan Caron8Reza Adalat9Alan C. Evans10Najmeh Khalili-Mahani11Najmeh Khalili-Mahani12McGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montreal, QC, CanadaMcGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montreal, QC, CanadaBRAIN-TO Lab, Krembil Brain Institute, University Health Network, Toronto, ON, CanadaTranslational Neuromodeling Unit, Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, SwitzerlandMcGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montreal, QC, CanadaCenter for Youth Mental Health, The University of Melbourne, Melbourne, VIC, AustraliaOrygen Youth Health, Orygen, Melbourne, VIC, AustraliaMcGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montreal, QC, CanadaMcGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montreal, QC, CanadaMcGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montreal, QC, CanadaMcGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montreal, QC, CanadaMcGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montreal, QC, CanadaDepartment of Electrical and Computer Engineering, Concordia University, Montreal, QC, CanadaNeuroimaging research requires sophisticated tools for analyzing complex data, but efficiently leveraging these tools can be a major challenge, especially on large datasets. CBRAIN is a web-based platform designed to simplify the use and accessibility of neuroimaging research tools for large-scale, collaborative studies. In this paper, we describe how CBRAIN’s unique features and infrastructure were leveraged to integrate TAPAS PhysIO, an open-source MATLAB toolbox for physiological noise modeling in fMRI data. This case study highlights three key elements of CBRAIN’s infrastructure that enable streamlined, multimodal tool integration: a user-friendly GUI, a Brain Imaging Data Structure (BIDS) data-entry schema, and convenient in-browser visualization of results. By incorporating PhysIO into CBRAIN, we achieved significant improvements in the speed, ease of use, and scalability of physiological preprocessing. Researchers now have access to a uniform and intuitive interface for analyzing data, which facilitates remote and collaborative evaluation of results. With these improvements, CBRAIN aims to become an essential open-science tool for integrative neuroimaging research, supporting FAIR principles and enabling efficient workflows for complex analysis pipelines.https://www.frontiersin.org/articles/10.3389/fninf.2023.1251023/fullneuroimagingsoftwarefMRIbrain imaging data structure (BIDS)physiological noise correctionhigh performance computing (HPC) |
| spellingShingle | Darius Valevicius Natacha Beck Lars Kasper Lars Kasper Sergiy Boroday Johanna Bayer Johanna Bayer Pierre Rioux Bryan Caron Reza Adalat Alan C. Evans Najmeh Khalili-Mahani Najmeh Khalili-Mahani Web-based processing of physiological noise in fMRI: addition of the PhysIO toolbox to CBRAIN Frontiers in Neuroinformatics neuroimaging software fMRI brain imaging data structure (BIDS) physiological noise correction high performance computing (HPC) |
| title | Web-based processing of physiological noise in fMRI: addition of the PhysIO toolbox to CBRAIN |
| title_full | Web-based processing of physiological noise in fMRI: addition of the PhysIO toolbox to CBRAIN |
| title_fullStr | Web-based processing of physiological noise in fMRI: addition of the PhysIO toolbox to CBRAIN |
| title_full_unstemmed | Web-based processing of physiological noise in fMRI: addition of the PhysIO toolbox to CBRAIN |
| title_short | Web-based processing of physiological noise in fMRI: addition of the PhysIO toolbox to CBRAIN |
| title_sort | web based processing of physiological noise in fmri addition of the physio toolbox to cbrain |
| topic | neuroimaging software fMRI brain imaging data structure (BIDS) physiological noise correction high performance computing (HPC) |
| url | https://www.frontiersin.org/articles/10.3389/fninf.2023.1251023/full |
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