About
42
Publications
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Introduction
Current institution
Additional affiliations
December 2014 - March 2016
September 2010 - September 2014
Position
- DPhil student
Description
- Highly efficient quantum spin dynamics simulation algorithms; supervised by Dr Ilya Kuprov, co-supervised by Dr C.R. Timmel.
Education
September 2010 - September 2014
October 2006 - July 2010
Publications
Publications (42)
Despite the importance of short association fibres (SAF) for human brain function, their structures remain understudied. It is not known how SAF are organised across the brain, and how consistent their geometries and locations are across individuals. To address this gap, we mapped the precise structures of SAF in the primary (V1) and secondary (V2)...
The MRI-visible axon radius is a potential clinical biomarker for, e.g., neurological disorders. However, its clinical potential remains untapped, as in-vivo MRI-based estimation lacks validation in humans and currently requires specialized research scanners. Here, we assess state-of-the-art MRI methods for axon radius estimation against a new, ope...
Chimpanzee brain maturation provides an invaluable framework for understanding the evolution of the human brain. We performed ultra-high resolution quantitative magnetic resonance imaging (qMRI) with histological validation on post mortem brains from captive and wild chimpanzees with a broad age range. We mapped developmental myelination and age-re...
Short association fibres (SAF) are the most abundant fibre pathways in the human white matter. Until recently, SAF could not be mapped comprehensively in vivo because diffusion weighted magnetic resonance imaging with sufficiently high spatial resolution needed to map these thin and short pathways was not possible. Recent developments in acquisitio...
Purpose
To compare MR axon radius estimation in human white matter using a multiband spiral sequence combined with field monitoring to the current state‐of‐the‐art echo‐planar imaging (EPI)‐based approach.
Methods
A custom multiband spiral sequence was used for diffusion‐weighted imaging at ultra‐high b$$ b $$‐values. Field monitoring and higher o...
The extraordinary number of short association fibres (SAF) connecting neighbouring cortical areas is a prominent feature of the large gyrified human brain. The contribution of SAF to the human connectome is largely unknown because of methodological challenges in mapping them. We present a method to characterise cortico–cortical connectivity mediate...
To decipher the evolution of the hominoid brain and its functions, it is essential to conduct comparative studies in primates, including our closest living relatives. However, strong ethical concerns preclude in vivo neuroimaging of great apes. We propose a responsible and multidisciplinary alternative approach that links behavior to brain anatomy...
Background
Cortical grey matter (CGM) and superficial white matter (SWM) undergo pathological changes, but standard MRI spatial resolutions make interpreting disease‐related effects at their interface challenging. We present findings from a study investigating the grey/white interface in typical amnestic Alzheimer’s disease (tAD), posterior cortica...
Quantitative multi-parameter mapping (MPM) at 7T can provide detailed information about brain microstructure. However, it is limited by B1+ radio-frequency (RF) transmit field inhomogeneities leading to bias and dropouts. We implemented a kt-points RF pulse approach in 500 µm resolution multi-echo spoiled GRE acquisitions and AFI B1+ mapping used f...
The characterization of cortical myelination is essential for the study of structure-function relationships in the human brain. However, knowledge about cortical myelination is largely based on post-mortem histology, which generally renders direct comparison to function impossible. The repeating pattern of pale-thin-pale-thick stripes of cytochrome...
The selection pressures that drove dramatic encephalisation processes through the mammal lineage remain elusive, as does knowledge of brain structure reorganisation through this process. In particular, considerable structural brain changes are present across the primate lineage, culminating in the complex human brain that allows for unique behaviou...
Quantitative magnetic resonance imaging (qMRI) allows extraction of reproducible and robust parameter maps. However, the connection to underlying biological substrates remains murky, especially in the complex, densely packed cortex. We investigated associations in human neocortex between qMRI parameters and neocortical cell types by comparing the s...
Purpose
Magnetization transfer saturation (MTsat$$ \mathrm{MTsat} $$) is a useful marker to probe tissue macromolecular content and myelination in the brain. The increased B1+$$ {B}_1^{+} $$‐inhomogeneity at ≥7$$ \ge 7 $$ T and significantly larger saturation pulse flip angles which are often used for postmortem studies exceed the limits where prev...
Multi-Parameter Mapping (MPM) is a comprehensive quantitative neuroimaging protocol that enables estimation of four physical parameters (longitudinal and effective transverse relaxation rates R1 and R2*, proton density PD, and magnetization transfer saturation MTsat) that are sensitive to microstructural tissue properties such as iron and myelin co...
Purpose
Magnetization transfer saturation (MTsat) is a useful marker to probe tissue macromolecular content and myelination in the brain. The increased -inhomogeneity at ≥ 7T and significantly larger saturation pulse flip angles which are often used for postmortem studies exceed the limits where previous MTsat correction methods are applicable. Her...
The characterization of cortical myelination is essential for the study of structure-function relationships in the human brain. However, knowledge about cortical myelination is largely based on post mortem histology, which shows conflicting results depending on the staining method used, and generally renders direct comparison to function impossible...
Purpose
High‐resolution quantitative multi‐parameter mapping shows promise for non‐invasively characterizing human brain microstructure but is limited by physiological artifacts. We implemented corrections for rigid head movement and respiration‐related B0‐fluctuations and evaluated them in healthy volunteers and dementia patients.
Methods
Camera‐...
Quantitative MRI (qMRI) allows extraction of reproducible and robust parameter maps. However, the connection to underlying biological substrates remains murky, especially in the complex, densely packed cortex. We investigated associations in human neocortex between qMRI parameters and neocortical cell types by comparing the spatial distribution of...
Multi-Parameter Mapping (MPM) is a comprehensive quantitative neuroimaging protocol that enables estimation of four physical parameters (longitudinal and effective transverse relaxation rates R1 and R2*, proton density PD, and magnetization transfer saturation MTsat) that are sensitive to microstructural tissue properties such as iron and myelin co...
PURPOSE
High-resolution quantitative multi-parameter mapping shows promise for non-invasively characterizing human brain microstructure but is limited by physiological artifacts. We implemented corrections for rigid head movement and respiration-related B0-fluctuations and evaluated them in healthy volunteers and dementia patients.
METHODS
Camera-...
Ultra‐high field MRI across the depth of the cortex has the potential to provide anatomically precise biomarkers and mechanistic insights into neurodegenerative disease like Huntington's disease that show layer‐selective vulnerability. Here we compare multi‐parametric mapping (MPM) measures across cortical depths for a 7T 500 μm whole brain acquisi...
Quantitative magnetic resonance imaging (qMRI) goes beyond conventional MRI, which aims primarily at local image contrast. It provides specific physical parameters related to the nuclear spin of protons in water, such as relaxation times. These parameters carry information about the local microstructural environment of the protons (such as myelin i...
The noninvasive quantification of axonal morphology is an exciting avenue for gaining understanding of the function and structure of the central nervous system. 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,...
The noninvasive quantification of axonal morphology provides an exciting avenue to gain understanding of the function and structure of the central nervous system. Accurate non-invasive mapping of micron-sized axon radii using commonly applied neuroimaging techniques, i.e., diffusion-weighted MRI, has been bolstered by recent hardware developments....
Short association fibers (U-fibers) connect proximal cortical areas and constitute the majority of white matter connections in the human brain. U-fibers play an important role in brain development, function, and pathology but are underrepresented in current descriptions of the human brain connectome, primarily due to methodological challenges in di...
Cortical layer-specific ultra-high field MRI has the potential to provide anatomically precise biomarkers and mechanistic insights into neurodegenerative disease. Here we compare cortical layer-specificity for a 7T multi-parametric mapping (MPM) microns whole brain acquisition to the von Economo and Big Brain post-mortem histology atlases. We also...
Purpose
To propose and validate an efficient method, based on a biophysically motivated signal model, for removing the orientation‐dependent part of R2* using a single gradient‐recalled echo (GRE) measurement.
Methods
The proposed method utilized a temporal second‐order approximation of the hollow‐cylinder‐fiber model, in which the parameter descr...
The neocortex of the human brain is the seat of higher brain function. Modern imaging techniques, chief among them magnetic resonance imaging (MRI), allow non-invasive imaging of this important structure. Knowledge of the microstructure of the neocortex has classically come from post-mortem histological studies of human tissue, and extrapolations f...
The NODDI-DTI signal model is a modification of the NODDI signal model that formally allows interpretation of standard single-shell DTI data in terms of biophysical parameters in healthy human white matter (WM). The NODDI-DTI signal model contains no CSF compartment, restricting application to voxels without CSF partial-volume contamination. This m...
NODDI-DTI is a simplification of the NODDI model that, when its underlying assumptions are met, allows extraction of biophysical parameters from standard single-shell DTI data, permitting biophysical analysis of DTI datasets.
In contrast to the NODDI signal model, the NODDI-DTI signal model contains no CSF compartment, restricting its application t...
To understand the properties and/or reactivity of an organic molecule, an understanding of its three-dimensional structure is necessary. Simultaneous determination of configuration and conformation often poses a daunting challenge. Thus, the more information accessible for a given molecule, the better. Additionally to (3)J-couplings, two sources of...
Spin dynamics simulations are used to gain insight into important magnetic resonance experiments in the fields of chemistry, biochemistry, and physics. Presented in this thesis are investigations into how to accelerate these simulations by making them more efficient.
Chapter 1 gives a brief introduction to the methods of spin dynamics simulation...
Nuclear magnetic resonance spectroscopy is one of the few remaining areas of
physical chemistry for which polynomially scaling simulation methods have not
so far been available. Here, we report such a method and illustrate its
performance by simulating common 2D and 3D liquid state NMR experiments
(including accurate description of spin relaxation...
An algorithm for simulating coherence selection due to a pulse sequence element consisting of two pulsed field gradients separated by a short collection of pulses and delays is introduced. This algorithm involves computation of the matrix exponential of an auxiliary matrix twice the size of the system Liouvillian, a dimensional increase smaller tha...
We demonstrate that Fokker-Planck equations in which spatial coordinates are treated on the same conceptual level as spin coordinates yield a convenient formalism for treating magic angle spinning NMR experiments. In particular, time dependence disappears from the background Hamiltonian (sample spinning is treated as an interaction), spherical quad...
A strategy is described for simulations of solid effect dynamic nuclear polarisation that reduces substantially the dimension of the quantum mechanical problem. Averaging the Hamiltonian in the doubly rotating frame is used to confine the active space to the zero quantum coherence subspace. A further restriction of the Liouville space is made by tr...
Several methods for density matrix propagation in parallel computing environments are proposed and evaluated. It is demonstrated that the large communication overhead associated with each propagation step (two-sided multiplication of the density matrix by an exponential propagator and its conjugate) may be avoided and the simulation recast in a for...
We present an algebraic foundation for the state space restriction approximation in spin dynamics simulations and derive applicability criteria as well as minimal basis set requirements for practically encountered simulation tasks. The results are illustrated with nuclear magnetic resonance (NMR), electron spin resonance (ESR), dynamic nuclear pola...
We propose a novel avenue for state space reduction in time domain Liouville space spin dynamics simulations, using detectability as a selection criterion--only those states that evolve into or affect other detectable states are kept in the simulation. This basis reduction procedure (referred to as destination state screening) is formally exact and...
