Optimisation and Pre-clinical Demonstration of Temporal Diffusion Ratio for Imaging Restricted Diffusion DOI Creative Commons

William Warner,

Marco Palombo, Renata Cruz

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: July 27, 2022

Abstract Temporal Diffusion Ratio (TDR) is a recently proposed dMRI technique (Dell’Acqua, 2019) which provides contrast between areas with restricted diffusion and either without or length scales too small for characterisation. Hence, it has potential mapping pore sizes, in particular large axon diameters other cellular structures. TDR employs the signal from two acquisitions obtained same, large, b-value but different times gradient settings. advantageous as standard acquisition sequences, does not make any assumptions on underlying tissue structure require model fitting, avoiding issues related to degeneracy. This work first time optimises sequences simulation range of tissues scanner constraints. We extend original (which considers substrates containing cylinders) by additionally considering spherical structures, representing cell soma tissue. Our results show that contrasting an short duration long improves wide configurations. Additionally, presence Rician noise, computing subset (50% fewer) acquired gradients rather than entire shell originally further contrast. In last part are demonstrated experimentally rat spinal cord. line simulations, experimental data shows optimised compared non-optimised TDR. Furthermore, we find strong correlation histology measurements diameter. conclusion, great very promising alternative (or potentially complement) model-based approaches sizes general. Highlights 2-seq approach maps Optimised waveform pair is: δ + low G high If noisy calculating using HARDI subsets increases accuracy demonstrate pre-clinically cord Pre-clinical values strongly correlated diameter

Language: Английский

Tensor denoising of multidimensional MRI data DOI
Jonas L. Olesen, Andrada Ianuş, Leif Østergaard

et al.

Magnetic Resonance in Medicine, Journal Year: 2022, Volume and Issue: 89(3), P. 1160 - 1172

Published: Oct. 11, 2022

To develop a denoising strategy leveraging redundancy in high-dimensional data.The SNR fundamentally limits the information accessible by MRI. This limitation has been addressed host of techniques, recently including so-called MPPCA: principal component analysis signal followed automated rank estimation, exploiting Marchenko-Pastur distribution noise singular values. Operating on matrices comprised data patches, this popular approach objectively identifies components and, ideally, allows to be removed without introducing artifacts such as image blurring, or nonlocal averaging. The MPPCA however, relies large number values relative avoid ill effects. condition is unlikely met when patches and therefore are small, for example due spatially varying noise. Here, we introduce tensor (tMPPCA) purpose multidimensional data, from multicontrast acquisitions. Rather than combining dimensions matrices, tMPPCA uses each dimension data's inherent tensor-structure better characterize noise, recursively estimate components.Relative matrix-based MPPCA, requires no additional assumptions, comparing two numerical phantom multi-TE diffusion MRI set, dramatically improves performance. particularly true small suggesting that can especially beneficial cases.The technique extended with improved performance smaller patch sizes.

Language: Английский

Citations

45
Soma and neurite density abnormalities of paramagnetic rim lesions and core-sign lesions in multiple sclerosis DOI
Paolo Preziosa, Elisabetta Pagani, Alessandro Meani

et al.

Journal of Neurology, Journal Year: 2025, Volume and Issue: 272(2)

Published: Jan. 15, 2025

Language: Английский

Citations

1
Considerations and recommendations from the ISMRM diffusion study group for preclinical diffusion MRI: Part 1: In vivo small‐animal imaging DOI Creative Commons
Ileana Jelescu, Francesco Grussu, Andrada Ianuş

et al.

Magnetic Resonance in Medicine, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 26, 2025

Abstract Small‐animal diffusion MRI (dMRI) has been used for methodological development and validation, characterizing the biological basis of phenomena, comparative anatomy. The steps from animal setup monitoring, to acquisition, analysis, interpretation are complex, with many decisions that may ultimately affect what questions can be answered using resultant data. This work aims present selected considerations recommendations community on best practices preclinical dMRI in vivo animals. We describe general foundational knowledge must considered when designing experiments. briefly differences species disease models discuss why some more or less appropriate different studies. We, then, give acquisition protocols, including hardware, preparation, imaging sequences, followed by advice data processing preprocessing, model‐fitting, tractography. Finally, we provide an online resource lists publicly available datasets software packages promote responsible reproducible research. In each section, attempt guides recommendations, but also highlight areas which no guidelines exist (and why), where future should focus. Although mainly cover central nervous system (on most studies focused), provide, possible applicable, other organs interest. An overarching goal is enhance rigor reproducibility small acquisitions analyses, thereby advance biomedical knowledge.

Language: Английский

Citations

1
A novel imaging marker of cortical “cellularity” in multiple sclerosis patients DOI Creative Commons
Muhamed Baraković, Matthias Weigel, Alessandro Cagol

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: April 29, 2024

Abstract Pathological data showed focal inflammation and regions of diffuse neuronal loss in the cortex people with multiple sclerosis (MS). In this work, we applied a novel model (“soma neurite density imaging (SANDI)”) to multishell diffusion-weighted MRI acquired healthy subjects (pwMS), order investigate degeneration-related changes cortical tissue pwMS. We aimed (i) establish whether SANDI is applicable vivo clinical data; (ii) inflammatory degenerative using soma fraction ( f )—a marker cellularity—in both lesions normal-appearing-cortex (iii) correlate biological measures simplified version scanners. then provided evidence that pwMS exhibited an overall decrease compared subjects, suggesting global processes compatible loss. On other hand, have found progressive higher outer part relapsing–remitting pwMS, possibly supporting current pathological knowledge increased innate cells these regions. A similar finding was obtained subpial patients, reflecting existing lesion types. significant correlation between serum neurofilament light chain—a biomarker axonal damage—suggesting relationship again. Overall, our show promising monitor cellularity neurodegeneration neuroinflammation MS patients.

Language: Английский

Citations

8
Mapping tissue microstructure across the human brain on a clinical scanner with soma and neurite density image metrics DOI Creative Commons
Simona Schiavi, Marco Palombo,

Domenico Zacà

et al.

Human Brain Mapping, Journal Year: 2023, Volume and Issue: 44(13), P. 4792 - 4811

Published: July 17, 2023

Abstract Soma and neurite density image (SANDI) is an advanced diffusion magnetic resonance imaging biophysical signal model devised to probe in vivo microstructural information the gray matter (GM). This requires acquisitions that include b values are at least six times higher than those used clinical practice. Such high required disentangle contribution of water diffusing soma from neurites extracellular space, while keeping time as short possible minimize potential bias due exchange. These requirements have limited use SANDI only preclinical or cutting‐edge human scanners. Here, we investigate impact neglecting exchange present a 10‐min acquisition protocol enables characterize both GM white (WM) on 3 T We implemented analytical simulations (i) evaluate stability fitting parameters when diminishing number shells; (ii) estimate between space such reduced scheme, comparing it with experimental noise. Then, demonstrated feasibility assessed repeatability reproducibility our approach by computing metrics AMICO toolbox other state‐of‐the‐art models five healthy subjects. Finally, applied multiple sclerosis patients. Results suggest practical method WM tissues performant

Language: Английский

Citations

14
Age‐related alterations in human cortical microstructure across the lifespan: Insights from high‐gradient diffusion MRI DOI Creative Commons
Hansol Lee, Hong‐Hsi Lee, Yixin Ma

et al.

Aging Cell, Journal Year: 2024, Volume and Issue: 23(11)

Published: Aug. 8, 2024

Abstract The human brain undergoes age‐related microstructural alterations across the lifespan. Soma and Neurite Density Imaging (SANDI), a novel biophysical model of diffusion MRI, provides estimates cell body (soma) radius density, neurite density in gray matter. goal this cross‐sectional study was to assess sensitivity high‐gradient MRI toward cortical microstructure adult lifespan using SANDI. Seventy‐two cognitively unimpaired healthy subjects (ages 19–85 years; 40 females) were scanned on 3T Connectome scanner with maximum gradient strength 300mT/m multi‐shell protocol incorporating 8 b ‐values time 19 ms. Intra‐soma signal fraction obtained from SANDI model‐fitting data strongly correlated age all major lobes ( r = −0.69 −0.60, FDR‐ p < 0.001). 0.48–0.63, 0.001) soma 0.28–0.40, 0.04) significantly volume prefrontal cortex, frontal, parietal, temporal lobes. relationship between metrics greater than or comparable regions, particularly occipital lobe anterior cingulate gyrus. In contrast metrics, associations tensor imaging (DTI) kurtosis low moderate. These results suggest that may be more sensitive underlying substrates neurodegeneration aging DTI traditional macroscopic measures such as thickness.

Language: Английский

Citations

4
Temporal Diffusion Ratio (TDR) for imaging restricted diffusion: Optimisation and pre-clinical demonstration DOI Creative Commons

William Warner,

Marco Palombo, Renata Cruz

et al.

NeuroImage, Journal Year: 2023, Volume and Issue: 269, P. 119930 - 119930

Published: Feb. 5, 2023

Temporal Diffusion Ratio (TDR) is a recently proposed dMRI technique (Dell'Acqua et al., proc. ISMRM 2019) which provides contrast between areas with restricted diffusion and either without or length scales too small for characterisation. Hence, it has potential informing on pore sizes, in particular the presence of large axon diameters other cellular structures. TDR employs signal from two acquisitions obtained same, large, b-value but different gradient waveforms. advantageous as standard acquisition sequences, does not make any assumptions underlying tissue structure require model fitting, avoiding issues related to degeneracy. This work first time introduces optimises method simulation range tissues scanner constraints validates pre-clinical demonstration. We consider both substrates containing cylinders spherical structures, representing cell soma tissue. Our results show that contrasting an short duration, high strength long low strength, maximises wide configurations. Additionally, Rician noise, computing subset (50% fewer) acquired gradients rather than entire shell originally further improves contrast. In last part are demonstrated experimentally rat spinal cord. line simulations, experimental data shows optimised compared non-optimised TDR. Furthermore, we find strong correlation histology measurements diameter. conclusion, great very promising alternative (or potentially complement) model-based approaches sizes general.

Language: Английский

Citations

11
Soma and neurite density imaging detects brain microstructural impairments in amyotrophic lateral sclerosis DOI
J. Y. Zeng, Hui‐Wei Huang,

Shao-Peng Zhuang

et al.

European Journal of Radiology, Journal Year: 2025, Volume and Issue: 184, P. 111981 - 111981

Published: Feb. 5, 2025

Language: Английский

Citations

0
MRI signatures of cortical microstructure in human development align with oligodendrocyte cell-type expression DOI Creative Commons
Sila Genc, Gareth Ball, Maxime Chamberland

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: April 7, 2025

Language: Английский

Citations

0
The Duke Mouse Brain Atlas: MRI and light sheet microscopy stereotaxic atlas of the mouse brain DOI Creative Commons

Harrison Mansour,

Ryan Azrak,

James J. Cook

et al.

Science Advances, Journal Year: 2025, Volume and Issue: 11(18)

Published: May 1, 2025

Atlases of the brain are critical resources that make it possible to share data in a common reference frame. Unexpectedly, there is no three-dimensional (3D) stereotaxic atlas mouse provides whole coverage at macro single-cell levels. Diffusion tensor images from five perfusion-fixed (in skull) specimens were acquired 15 micrometers, highest resolution ever reported. imaging yields multiple 3D volumes, each which highlights unique cytoarchitecture. The averages mapped into micro-computed tomography skull create external landmarks (bregma and lambda). Light sheet same brains coregistered, providing cell maps space. Allen Reference Atlas was registered volume correct geometric distortion bring resulting multiscalar (13 terabytes) spatial framework anneal across molecular, structural, functional studies mice.

Language: Английский

Citations

0