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Rotationally-invariant mapping of scalar and orientational metrics of neuronal microstructure with diffusion MRI

Dmitry S. Novikov, Jelle Veraart, Ileana O. Jelescu, Els Fieremans
2018 NeuroImage  
Our framework reveals hidden degeneracies in MRI parameter estimation for neuronal tissue, provides microstructural and orientational maps in the whole brain without constraints or priors, and connects  ...  By employing a set of rotational invariants and their expansion in the powers of diffusion weighting, we analytically uncover the nontrivial topology of the parameter estimation landscape, showing that  ...  Research was supported by the National Institute of Neurological Disorders and Stroke of the NIH under award number R01NS088040.  ... 
doi:10.1016/j.neuroimage.2018.03.006 pmid:29544816 pmcid:PMC5949281 fatcat:6ewf4uqjybb7novur3roj34ale

q-Space Deep Learning for Twelve-Fold Shorter and Model-Free Diffusion MRI Scans [chapter]

Vladimir Golkov, Alexey Dosovitskiy, Philipp Sämann, Jonathan I. Sperl, Tim Sprenger, Michael Czisch, Marion I. Menzel, Pedro A. Gómez, Axel Haase, Thomas Brox, Daniel Cremers
2015 Lecture Notes in Computer Science  
This leads to high scan costs and makes advanced diffusion models such as diffusion kurtosis imaging (DKI) and neurite orientation dispersion and density imaging (NODDI) inapplicable for children and adults  ...  We demonstrate how deep learning, a group of algorithms in the field of artificial neural networks, can be applied to reduce diffusion MRI data processing to a single optimized step.  ...  Pölsterl and B. Menze (TU München) for discussions. V. Golkov is supported by the Deutsche Telekom Foundation.  ... 
doi:10.1007/978-3-319-24553-9_5 fatcat:q6k5nzqnkrgptge3dykmg72mfe

An Introduction to Visualization of Diffusion Tensor Imaging and Its Applications [chapter]

A. Vilanova, S. Zhang, G. Kindlmann, D. Laidlaw
2006 Mathematics and Visualization  
We conclude with an overview of open problems and research directions.  ...  Diffusion tensor imaging (DTI), a non-invasive MR technique, measures water self-diffusion rates and thus gives an indication of the underlying tissue microstructure.  ...  Acknowledgments We thank the BioMedical NMR group at the Eindhoven University of Tech-  ... 
doi:10.1007/3-540-31272-2_7 fatcat:7qpa7vswzreupbver3d23fxw2q

Elucidating the complex organization of neural micro-domains in the locust Schistocerca gregaria using dMRI [article]

Syed Salman Shahid, Christian M. Kerskens, Malcolm Burrows, Alice G Witney
2020 bioRxiv   pre-print
As dMRI can be applied non-invasively in live animals, future work offers the possibility of monitoring neuronal connectivity longitudinally, as well as providing metrics to quantify the effect of environmental  ...  The diffusion-weighted imaging (DWI) data were acquired on a horizontal bore 7T Biospec micro-MRI system (Bruker, Etlingen Germany) using a customised multi-shell diffusion MRI scheme.  ...  Hence, use of dMRI at micro-scale with multi-contrast 302 maps can be used to identify synapse-rich neuropil sub-structures, cell bodies and axonal tracts. 303 Rotationally invariant measures (FA, MD,  ... 
doi:10.1101/2020.01.17.910851 fatcat:xwbfzvqhw5arvi2wb4mw6upslq

Crystallinity characterization of white matter in the human brain [article]

Erin G. Teich, Matthew Cieslak, Barry Giesbrecht, Jean M. Vettel, Scott T. Grafton, Theodore D. Satterthwaite, Danielle S. Bassett
2020 arXiv   pre-print
White matter microstructure underpins cognition and function in the human brain through the facilitation of neuronal communication, and the non-invasive characterization of this structure remains a research  ...  Finally, we characterize the shapes of local white matter signatures through another tool from materials science - bond-orientational order parameters - and locate fiber crossings and fascicles with this  ...  Fotiadis, and S. Patankar for helpful discussions.  ... 
arXiv:2010.06644v1 fatcat:v54ljbr2rvd27imjpd3q4wrhrq

Comparison of Neurite Orientation Dispersion and Density Imaging and Two-Compartment Spherical Mean Technique Parameter Maps in Multiple Sclerosis

Daniel Johnson, Antonio Ricciardi, Wallace Brownlee, Baris Kanber, Ferran Prados, Sara Collorone, Enrico Kaden, Ahmed Toosy, Daniel C. Alexander, Claudia A. M. Gandini Wheeler-Kingshott, Olga Ciccarelli, Francesco Grussu
2021 Frontiers in Neurology  
Neurite orientation dispersion and density imaging (NODDI) and the spherical mean technique (SMT) are diffusion MRI methods providing metrics with sensitivity to similar characteristics of white matter  ...  from diffusion MRI data, alongside DTI metrics (fractional anisotropy, FA; axial/mean/radial diffusivity, AD/MD/RD).  ...  DTI relies on the hypothesis of Gaussian diffusion to evaluate an effective diffusion tensor for each voxel in an image, from which a number of rotationally-invariant scalar descriptors are obtained, such  ... 
doi:10.3389/fneur.2021.662855 pmid:34194382 pmcid:PMC8236830 fatcat:zigjlucdxvaanpph5k245hhjg4

Design and Validation of Diffusion MRI Models of White Matter

Ileana O. Jelescu, Matthew D. Budde
2017 Frontiers in Physics  
AUTHOR CONTRIBUTIONS All authors listed have made a substantial, direct, and intellectual contribution to the work, and approved it for publication.  ...  Rotationally Invariant Features: LEMONADE & co.  ...  [31] , a method dubbed mean apparent propagator (MAP-MRI).  ... 
doi:10.3389/fphy.2017.00061 pmid:29755979 pmcid:PMC5947881 fatcat:ai6ejv6rzfe55i4tl64l5dihem

Diffusion MRI and its Role in Neuropsychology

Bryon A. Mueller, Kelvin O. Lim, Laura Hemmy, Jazmin Camchong
2015 Neuropsychology Review  
In this review, we begin with a definition of diffusion and how diffusion is measured with MRI. Next we introduce the diffusion tensor model, the predominant model used in dMRI.  ...  We then touch on reliability and validity issues of diffusion measurements.  ...  From the kurtosis computation many rotationally invariant scalar metrics can be computed.  ... 
doi:10.1007/s11065-015-9291-z pmid:26255305 pmcid:PMC4807614 fatcat:xezun6rr3reddg5x4oxyd2vvri

The physical and biological basis of quantitative parameters derived from diffusion MRI

Gavin P Winston
2012 Quantitative Imaging in Medicine and Surgery  
models such as CHARMED, AxCaliber or NODDI being developed to estimate microstructural parameters including axonal diameter, axonal density and fiber orientations.  ...  However these are not yet in routine clinical use due to lengthy acquisition times.In this review, I discuss how molecular diffusion may be measured using diffusion MRI, the biological and physical bases  ...  The Big Lottery Fund, Wolfson Trust and the Epilepsy Society support the Epilepsy Society MRI scanner on which the example scans were acquired.  ... 
doi:10.3978/j.issn.2223-4292.2012.12.05 pmid:23289085 pmcid:PMC3533595 fatcat:bn4yg7sh3nhkxpvxvul7afzxda

Mean apparent propagator (MAP) MRI: A novel diffusion imaging method for mapping tissue microstructure

Evren Özarslan, Cheng Guan Koay, Timothy M. Shepherd, Michal E. Komlosh, M. Okan İrfanoğlu, Carlo Pierpaoli, Peter J. Basser
2013 NeuroImage  
We also define and map novel quantitative descriptors of diffusion that can be computed robustly using this MAP-MRI framework.  ...  contains only the orientational dependence of the diffusion process.  ...  Newman and Afonso C. Silva for the marmoset brain specimen and Liz Salak for editing the manuscript. Special thanks to Jian Cheng for pointing out an error in (Özarslan et al., 2009c).  ... 
doi:10.1016/j.neuroimage.2013.04.016 pmid:23587694 pmcid:PMC4059870 fatcat:ihzvrgdp7nf5lillgo4occbrra

The variability of MR axon radii estimates in the human white matter

Jelle Veraart, Erika P Raven, Luke J Edwards, Nikolaus Weiskopf, Derek K Jones
2021 Human Brain Mapping  
Accurate non-invasive mapping of micron-sized axon radii using commonly applied neuroimaging techniques, that is, diffusion-weighted MRI, has been bolstered by recent hardware developments, specifically  ...  The noninvasive quantification of axonal morphology is an exciting avenue for gaining understanding of the function and structure of the central nervous system.  ...  Critically, and as discussed below, diffusion-weighted MRI methods for mapping axon diameter are more sensitive to larger axons than smaller axons, and so this preferential loss of axons with large radii  ... 
doi:10.1002/hbm.25359 pmid:33576105 pmcid:PMC8046139 fatcat:2xfwl76ny5bprmkgwgxdjvb63i

Clinical applications of diffusion tensor imaging

Qian Dong, Robert C. Welsh, Thomas L. Chenevert, Ruth C. Carlos, Pia Maly-Sundgren, Diana M. Gomez-Hassan, Suresh K. Mukherji
2003 Journal of Magnetic Resonance Imaging  
This review describes the clinical utility of diffusion tensor imaging, including the basic principles of the technique, acquisition, data analysis, and the major clinical applications.  ...  Diffusion tensor imaging characterizes this directional nature of water motion and thereby provides structural information that cannot be obtained by standard anatomic imaging.  ...  ACKNOWLEDGMENTS We thank Suzanne Murphy for assistance with preparation of the manuscript.  ... 
doi:10.1002/jmri.10424 pmid:14696215 fatcat:ku3ltpqncrdppotxnmqn5kdcza

Double diffusion encoding and applications for biomedical imaging

Rafael N. Henriques, Marco Palombo, Sune N. Jespersen, Noam Shemesh, Henrik Lundell, Andrada Ianuş
2020 Journal of Neuroscience Methods  
Various DDE methodologies have been employed to probe compartment sizes (Section 3), decouple the effects of microscopic diffusion anisotropy from orientation dispersion (Section 4), probe displacement  ...  DDE measurements can also be used to improve the robustness of biophysical models (Section 5) and study intra-cellular diffusion via magnetic resonance spectroscopy of metabolites (Section 7).  ...  Acknowledgements The authors would like to acknowledge the following sources of financial support.  ... 
doi:10.1016/j.jneumeth.2020.108989 pmid:33144100 fatcat:qqjbwghlmngbzctpi2cs37gz4m

Diffusion Tensor Imaging in Preclinical Huntington's Disease

Vincent A. Magnotta, Jinsuh Kim, Tim Koscik, Leigh J. Beglinger, Daisy Espinso, Doug Langbehn, Peg Nopoulos, Jane S. Paulsen
2008 Brain Imaging and Behavior  
Fractional anisotropy scalar maps showed a positive correlation with five year probability of diagnosis (based upon gene repeat length and current age) in the putamen and a negative correlation in the  ...  This study shows that scalar maps generated from diffusion tensor imaging may be directly related to the earliest stages of disease progression within HD, even before a diagnosis is given.  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided  ... 
doi:10.1007/s11682-008-9051-2 pmid:21415933 pmcid:PMC3057188 fatcat:crfoz3cstzexrffm2tgfdotuqe

Single Encoding Diffusion MRI: A Probe to Brain Anisotropy [chapter]

Maëliss Jallais, Demian Wassermann
2021 Mathematics and Visualization  
AbstractThis chapter covers anisotropy in the context of probing microstructure of the human brain using single encoded diffusion MRI.  ...  The non-invasive imaging technique based on water motions known as diffusion MRI will be further presented, along with the difficulties that come with it.  ...  Acknowledgments This work was supported by the ERC-StG NeuroLang and the ANR/NSF NeuroRef grants.  ... 
doi:10.1007/978-3-030-56215-1_8 fatcat:ii25gxmmrbcsll3k5sbowhbumu
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