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      Non-Cartesian 3D-SPARKLING vs Cartesian 3D-EPI encoding schemes for functional Magnetic Resonance Imaging at 7 Tesla

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          Abstract

          The quest for higher spatial and/or temporal resolution in functional MRI (fMRI) while preserving a sufficient temporal signal-to-noise ratio (tSNR) has generated a tremendous amount of methodological contributions in the last decade ranging from Cartesian vs. non-Cartesian readouts, 2D vs. 3D acquisition strategies, parallel imaging and/or compressed sensing (CS) accelerations and simultaneous multi-slice acquisitions to cite a few. In this paper, we investigate the use of a finely tuned version of 3D-SPARKLING. This is a non-Cartesian CS-based acquisition technique for high spatial resolution whole-brain fMRI. We compare it to state-of-the-art Cartesian 3D-EPI during both a retinotopic mapping paradigm and resting-state acquisitions at 1mm 3 (isotropic spatial resolution). This study involves six healthy volunteers and both acquisition sequences were run on each individual in a randomly-balanced order across subjects. The performances of both acquisition techniques are compared to each other in regards to tSNR, sensitivity to the BOLD effect and spatial specificity. Our findings reveal that 3D-SPARKLING has a higher tSNR than 3D-EPI, an improved sensitivity to detect the BOLD contrast in the gray matter, and an improved spatial specificity. Compared to 3D-EPI, 3D-SPARKLING yields, on average, 7% more activated voxels in the gray matter relative to the total number of activated voxels.

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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: InvestigationRole: MethodologyRole: ValidationRole: VisualizationRole: Writing – original draft
                Role: Formal analysisRole: Funding acquisitionRole: MethodologyRole: SupervisionRole: ValidationRole: Writing – review & editing
                Role: SoftwareRole: Writing – review & editing
                Role: SoftwareRole: Writing – review & editing
                Role: SoftwareRole: Writing – review & editing
                Role: SoftwareRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: SupervisionRole: ValidationRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                PLOS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                2024
                13 May 2024
                : 19
                : 5
                : e0299925
                Affiliations
                [1 ] CEA, Joliot, NeuroSpin, Université Paris-Saclay, Gif-sur-Yvette, France
                [2 ] Inria, MIND team, Université Paris-Saclay, Palaiseau, France
                [3 ] Siemens Heathineers, Courbevoie, France
                King’s College London, UNITED KINGDOM
                Author notes

                Competing Interests: Guillaume Daval-Frérot was employed by Siemens Healthineers at the time this work was performed. This does not alter our adherence to PLOS ONE policies on sharing data and materials. The other authors have declared that no competing interests exist.

                Author information
                https://orcid.org/0000-0002-7776-790X
                https://orcid.org/0000-0002-0128-061X
                https://orcid.org/0000-0001-5018-7895
                Article
                PONE-D-23-03044
                10.1371/journal.pone.0299925
                11090341
                38739571
                c6e97a12-ff83-46d6-8b21-ddf026e9e741
                © 2024 Amor et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 2 February 2023
                : 16 February 2024
                Page count
                Figures: 9, Tables: 6, Pages: 30
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100010665, H2020 Marie Skłodowska-Curie Actions;
                Award ID: 800945
                Award Recipient :
                Funded by: Fondation Leducq
                Chaithya G R was supported by the CEA NUMERICS program, which has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 800945. This work has received financial support from the Leducq Foundation (Large Equipment de Recherche et Plateformes Technologiques program). Finally, this work was granted access to the HPC resources of IDRIS under the allocation 2021-AD011011153 made by GENCI. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
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                Custom metadata
                The GitHub links of the different python packages used for this work, namely the pysap-mri plugin from the pySAP package for MR image reconstruction and the Nilearn package for fMRI data statistical analysis and visualization, were included within the text of the manuscript. Additional author-generated code can be found in https://github.com/Zaineb18/code_plosone. The clinical protocol approved by the national ethics committee for our experiments and our research center policies prohibits sharing medical data in an open-source fashion. Therefore, we do not publicly share our data. It can, however, be shared with specific organizations and researchers upon special written request at projets.neurospin@ 123456cea.fr . This email address targets NeuroSpin’s representatives for clinical projects management. Additionally, the corresponding author, Alexandre Vignaud should be contacted at: alexandre.vignaud@ 123456cea.fr .

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