Scattered slice SHARD reconstruction for motion correction in multi-shell diffusion MRI

TY - JOUR

T1 - Scattered slice SHARD reconstruction for motion correction in multi-shell diffusion MRI

AU - Christiaens, Daan

AU - Cordero-Grande, Lucilio

AU - Pietsch, Maximilian

AU - Hutter, Jana

AU - Price, Anthony N

AU - Hughes, Emer J

AU - Vecchiato, Katy

AU - Deprez, Maria

AU - Edwards, A David

AU - Hajnal, Joseph V

AU - Tournier, J-Donald

N1 - Funding Information: This work received funding from the European Research Council under the European Union's Seventh Framework Programme [FP7/20072013], ERC grant agreement no. [319456] (developing Human Connectome Project) and MRC strategic funds [MR/K006355/1]. D.C. is supported by the Flemish Research Foundation (FWO), fellowship no. [12ZV420N]. J.H. is supported by Wellcome Trust Fellowship [WT/201374/Z/16/Z]. This work was also supported by the Wellcome/EPSRC Centre for Medical Engineering at King's College London [WT/203148/Z/16/Z] and by the National Institute for Health Research (NIHR) Biomedical Research Centre at Guy's and St Thomas? NHS Foundation Trust and King's College London. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health. Funding Information: This work received funding from the European Research Council under the European Union’s Seventh Framework Programme [ FP7/20072013 ], ERC grant agreement no. [ 319456 ] (developing Human Connectome Project) and MRC strategic funds [ MR/K006355/1 ]. D.C. is supported by the Flemish Research Foundation (FWO), fellowship no. [ 12ZV420N ]. J.H. is supported by Wellcome Trust Fellowship [WT/201374/Z/16/Z]. This work was also supported by the Wellcome/EPSRC Centre for Medical Engineering at King’s College London [WT/203148/Z/16/Z] and by the National Institute for Health Research (NIHR) Biomedical Research Centre at Guy’s and St Thomas’ NHS Foundation Trust and King’s College London. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health. Publisher Copyright: © 2020 The Author(s) Copyright: Copyright 2020 Elsevier B.V., All rights reserved.

PY - 2021/1/15

Y1 - 2021/1/15

N2 - Diffusion MRI offers a unique probe into neural microstructure and connectivity in the developing brain. However, analysis of neonatal brain imaging data is complicated by inevitable subject motion, leading to a series of scattered slices that need to be aligned within and across diffusion-weighted contrasts. Here, we develop a reconstruction method for scattered slice multi-shell high angular resolution diffusion imaging (HARDI) data, jointly estimating an uncorrupted data representation and motion parameters at the slice or multiband excitation level. The reconstruction relies on data-driven representation of multi-shell HARDI data using a bespoke spherical harmonics and radial decomposition (SHARD), which avoids imposing model assumptions, thus facilitating to compare various microstructure imaging methods in the reconstructed output. Furthermore, the proposed framework integrates slice-level outlier rejection, distortion correction, and slice profile correction. We evaluate the method in the neonatal cohort of the developing Human Connectome Project (650 scans). Validation experiments demonstrate accurate slice-level motion correction across the age range and across the range of motion in the population. Results in the neonatal data show successful reconstruction even in severely motion-corrupted subjects. In addition, we illustrate how local tissue modelling can extract advanced microstructure features such as orientation distribution functions from the motion-corrected reconstructions.

AB - Diffusion MRI offers a unique probe into neural microstructure and connectivity in the developing brain. However, analysis of neonatal brain imaging data is complicated by inevitable subject motion, leading to a series of scattered slices that need to be aligned within and across diffusion-weighted contrasts. Here, we develop a reconstruction method for scattered slice multi-shell high angular resolution diffusion imaging (HARDI) data, jointly estimating an uncorrupted data representation and motion parameters at the slice or multiband excitation level. The reconstruction relies on data-driven representation of multi-shell HARDI data using a bespoke spherical harmonics and radial decomposition (SHARD), which avoids imposing model assumptions, thus facilitating to compare various microstructure imaging methods in the reconstructed output. Furthermore, the proposed framework integrates slice-level outlier rejection, distortion correction, and slice profile correction. We evaluate the method in the neonatal cohort of the developing Human Connectome Project (650 scans). Validation experiments demonstrate accurate slice-level motion correction across the age range and across the range of motion in the population. Results in the neonatal data show successful reconstruction even in severely motion-corrupted subjects. In addition, we illustrate how local tissue modelling can extract advanced microstructure features such as orientation distribution functions from the motion-corrected reconstructions.

KW - Diffusion MRI

KW - Motion correction

KW - Multi-shell

KW - Neonatal imaging

KW - Slice-to-volume reconstruction

UR - http://www.scopus.com/inward/record.url?scp=85093941942&partnerID=8YFLogxK

U2 - 10.1016/j.neuroimage.2020.117437

DO - 10.1016/j.neuroimage.2020.117437

M3 - Article

C2 - 33068713

SN - 1053-8119

VL - 225

SP - 117437

JO - NeuroImage

JF - NeuroImage

M1 - 117437

ER -