Three-dimensional encoding methods like multi-shot 3D-EPI are increasingly being explored as alternatives to multi-slice 2D acquisitions in functional MRI, particularly in cases where high isotropic resolution is needed. However, multi-shot 3D methods can suffer from artifacts and reduction of temporal SNR (tSNR) due to inter-shot variability from motion or physiological fluctuations. Here, we present a method for reconstruction of multi-shot 3D EPI data, that is insensitive to smooth inter-shot phase inconsistencies due to physiologically-induced B0 variations. This approach is based on annihilating filter Hankel structured low-rank matrix completion, illustrating improved tSNR compared to conventional multi-shot reconstruction.
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