Soma and neurite density MRI (SANDI) of the in‐vivo mouse brain and comparison with the Allen Brain Atlas
Open accessAbstract
Diffusion MRI (dMRI) provides unique insights into the neural tissue milieu by probing interactions between diffusing molecules and tissue microstructure. Most dMRI techniques focus on white matter (WM) tissues, nevertheless, interest in gray matter characterizations is growing. The Soma and Neurite Density MRI (SANDI) methodology harnesses a model incorporating water diffusion in spherical objects (assumed to be associated with cell bodies) and in impermeable "sticks" (assumed to represent neurites), which potentially enables the characterization of cellular and neurite densities. Recognising the importance of rodents in animal models of development, aging, plasticity, and disease, we here employ SANDI for in-vivo preclinical imaging and provide a first validation of the methodology by comparing SANDI metrics with cellular density reflected by the Allen mouse brain atlas. SANDI was implemented on a 9.4T scanner equipped with a cryogenic coil, and in-vivo experiments were carried out on N = 6 mice. Pixelwise, ROI-based, and atlas comparisons were performed, magnitude vs. real-valued analyses were compared, and shorter acquisitions with reduced the number of b-value shells were investigated. Our findings reveal good reproducibility of the SANDI parameters, including the sphere and stick fractions, as well as sphere size (CoV < 7%, 12% and 3%, respectively). Additionally, we find a very good rank correlation between SANDI-driven sphere fraction and Allen mouse brain atlas contrast that represents cellular density. We conclude that SANDI is a viable preclinical MRI technique that can greatly contribute to research on brain tissue microstructure.
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Exchange-sensitive NEXI and SMEX/SANDIX models suggest that inter-compartment water exchange and diffusion-time dependence substantially affect gray-matter diffusion signals but are not explicitly modeled by conventional SANDI.
“Although they correlate with the Allen Brain Atlas, 93 exchange‐sensitive NEXI 55 and SMEX/SANDIX 54 models suggest that inter‐compartment water exchange and diffusion‐time dependence substantially affect gray‐matter diffusion signals but are not explicitly modeled by conventional SANDI.”
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- Authors
- Ianuş, A., Carvalho, J., Fernandes, F. F., Cruz, R., Chavarrias, C., Palombo, M., & Shemesh, N.
- Affiliations
- Champalimaud Foundation (PT)
- University College London (GB)
- Corresponding author
- Shemesh, Noam
- Venue
- NeuroImage
- Publisher
- Elsevier BV
- Published
- 2022-07
- Volume
- 254
- Pages
- 119135
- ISSN
- 1053-8119 (ISSN-L)
- OpenAlex
- W4220805356
- Cited by
- 40
- References
- 52
- Citations by year
- 2026: 12 · 2025: 14 · 2024: 4 · 2023: 4 · 2022: 6
- FWCI
- 4.00
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- NeuroImage (publishedVersion, cc-by)
- PubMed (publishedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (acceptedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- European Research Council (679058)
- Horizon 2020 (100010434, CF/BQ/PI20/11760029, LISBOA01-0145-FEDER-022170)
- Fundación La Caixa
- UK Research and Innovation (MR/T020296/2)
- H2020 Marie Skłodowska-Curie Actions (101032056, 847648)
- 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
- Physical Sciences › Physics and Astronomy › Nuclear and High Energy Physics › NMR spectroscopy and applications
- Keywords
- diffusion MRI, neurite density, cell density, Allen Mouse Brain Atlas, tissue microstructure, preclinical MRI
- MeSH terms
- Animals, Brain, Humans, Magnetic Resonance Imaging, Reproducibility of Results, Neurites, Diffusion Magnetic Resonance Imaging, Mice, White Matter, Cell Body
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