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Improving robustness of 3D multi-shot EPI by structured low-rank reconstruction of segmented CAIPI sampling for fMRI at 7T

View ORCID ProfileXi Chen, Wenchuan Wu, Mark Chiew
doi: https://doi.org/10.1101/2021.08.19.457024
Xi Chen
1Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
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  • For correspondence: xi.chen@ndcn.ox.ac.uk
Wenchuan Wu
1Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
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Mark Chiew
1Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
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Abstract

Three-dimensional (3D) encoding methods are increasingly being explored as alternatives to multi-slice two-dimensional (2D) acquisitions in fMRI, particularly in cases where high isotropic resolution is needed. 3D multi-shot EPI is the most popular 3D fMRI acquisition method, but is susceptible to physiological fluctuations which can induce inter-shot phase variations, and thus reducing the achievable tSNR, negating some of the benefit of 3D encoding. This issue can be particularly problematic at ultra-high fields like 7T, which have more severe off-resonance effects. In this work, we aim to improve the temporal stability of 3D multi-shot EPI at 7T by improving its robustness to inter-shot phase variations. We presented a 3D segmented CAIPI sampling trajectory (“seg-CAIPI”) and an improved reconstruction method based on Hankel structured low-rank matrix recovery. Simulation and in-vivo results demonstrate that the combination of the seg-CAIPI sampling scheme and the proposed structured low-rank reconstruction is a promising way to effectively reduce the unwanted temporal variance induced by inter-shot physiological fluctuations, and thus improve the robustness of 3D multi-shot EPI for fMRI.

Highlights

  • A 3D multi-shot EPI sampling trajectory using interleaved ordering along kz and a CAIPI blipping pattern improves robustness to inter-shot phase variations

  • Reconstruction based on Hankel structured low-rank matrix completion can significantly improve the temporal stability of 3D multi-shot acquisitions at 7T

  • 1.5mm resolution brain fMRI data show that ~60% improvement in mean tSNR can be obtained using the proposed method compared to the conventional method

  • 1.8mm resolution brain fMRI data demonstrate that the proposed method allows for 4-fold acceleration without loss of tSNR compared to conventional 3D EPI

  • Preliminary brainstem fMRI data show that ~40% improvement in mean tSNR can be obtained using the proposed sampling and reconstruction

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted August 19, 2021.
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Improving robustness of 3D multi-shot EPI by structured low-rank reconstruction of segmented CAIPI sampling for fMRI at 7T
Xi Chen, Wenchuan Wu, Mark Chiew
bioRxiv 2021.08.19.457024; doi: https://doi.org/10.1101/2021.08.19.457024
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Improving robustness of 3D multi-shot EPI by structured low-rank reconstruction of segmented CAIPI sampling for fMRI at 7T
Xi Chen, Wenchuan Wu, Mark Chiew
bioRxiv 2021.08.19.457024; doi: https://doi.org/10.1101/2021.08.19.457024

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