Scattered slice shard reconstruction for motion correction in multi-shell diffusion MRI
Open accessAbstract
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.
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In vivo tractography on the fetal brain has become available and exhibits high agreement with ex vivo and neuroanatomical studies.
“Due to recent advances in methodological progress such as motion correction algorithms, in vivo tractography on the fetal brain has become available and exhibit highly agreement with ex vivo and neuroanatomical studies (Christiaens et al., 2021; Khan et al., 2019), which indicates strong potential for future prenatal brain investigations.”
From Quantitative mapping of the brain’s structural connectivity using diffusion MRI tractography: A review (2022) · cites this paper as Christiaens et al., 2021
The Discussion reports that the motion-correction framework has proved effective in fetal data, supporting the methodological-progress part of the attribution. But this paper analyzes scans acquired after birth (Data and preprocessing) and does not report in vivo fetal tractography or compare it with ex vivo or neuroanatomical studies. (LLM, conf=0.85)
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1 of the 44 references couldn’t be matched to a known paper.
Research works printed but not linked: 3
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“roanatomical studies [260, 97], which indicates strong potential for future prenatal brain investigations.”
BackgroundMaternal depressive symptoms, neonatal white matter, and toddler social-emotional development
Lautarescu, A., Bonthrone, A. F., Pietsch, M., Batalle, D., Cordero-Grande, L., Tournier, J.-D., Christiaens, D., Hajnal, J. V., Chew, A., Falconer, S., et al. (2022) · Translational Psychiatry · doi:10.1038/s41398-022-02073-y · Cited by 29 · see citing works
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Self-citationPremature birth changes wiring constraints in neonatal structural brain networks
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Self-citationDiffusion tensor driven image registration: a deep learning approachPreprint
Grigorescu, I., Uus, A. U., Christiaens, D., Cordero‐Grande, L., Hutter, J. M., Edwards, A. D., Hajnal, J. V., Marc Modat, A., & Deprez, M. (2020) · arXiv (Cornell University) · doi:10.48550/arxiv.2005.06926
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- Authors
- Christiaens, D., Cordero-Grande, L., Pietsch, M., Hutter, J., Price, A. N., Hughes, E. J., Vecchiato, K., Deprez, M., Edwards, A. D., Hajnal, J. V., & Tournier, J.-D.
- Affiliations
- King's College London (GB)
- Corresponding author
- Christiaens, Daan
- ORCID
- Venue
- NeuroImage
- Publisher
- Elsevier BV
- Published
- 2021-01
- Volume
- 225
- Pages
- 117437
- ISSN
- 1053-8119 (ISSN-L)
- PMC
- PMC7779423
- OpenAlex
- W3019456751
- Cited by
- 4
- References
- 44
- Citations by year
- 2025: 3 · 2020: 1
- FWCI
- 0.12
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- NeuroImage (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- arXiv (Cornell University) (submittedVersion)
- Lirias (KU Leuven) (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- arXiv (Cornell University)
- Zenodo (CERN European Organization for Nuclear Research) (cc-by)
- Funders
- Fonds Wetenschappelijk Onderzoek (12ZV420N)
- Wellcome Trust (WT/201374/Z/16/Z)
- European Research Council (FP7/20072013, 319456)
- King’s College London (WT/203148/Z/16/Z)
- Seventh Framework Programme
- NIHR Biomedical Research Centre, Royal Marsden NHS Foundation Trust/Institute of Cancer Research
- King's College London
- Medical Research Council (MR/K006355/1)
- Guy's and St Thomas' NHS Foundation Trust
- National Institute for Health and Care Research
- Topics
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced Neuroimaging Techniques and Applications
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced MRI Techniques and Applications
- Life Sciences › Neuroscience › Cognitive Neuroscience › Functional Brain Connectivity Studies
- Keywords
- motion correction, multi-shell diffusion MRI, high angular resolution diffusion imaging, neonatal brain imaging, orientation distribution function, brain microstructure, Human Connectome Project
- MeSH terms
- Brain, Humans, Image Processing, Computer-Assisted, Infant, Newborn, Movement, Diffusion Magnetic Resonance Imaging, Connectome
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