Towards Patient-Specific Brain Networks Using Functional Magnetic Resonance Imaging

fMRI applications are rare in translational medicine and clinical practice. What can be inferred from a single fMRI scan is often unreliable due to the relative low signal-to-noise ratio compared to other neuroimaging modalities. However, the potential of fMRI is promising. It is one of the few neuroimaging modalities to obtain functional brain organisation of an individual during task engagement and rest. This work extends on current fMRI image processing approaches to obtain robust estimates of functional brain organisation in two resting-state fMRI cohorts. The first cohort comprises of young adults who were born at extremely low gestations and age-matched healthy controls. Group analysis between term- and preterm-born adults revealed differences in functional organisation, which were discovered to be predominantly caused by underlying structural and physiological differences. The second cohort comprises of elderly adults with young onset Alzheimer’s disease and age-matched controls. Their corresponding resting-state fMRI scans are short in scanning time resulting in unreliable spatial estimates with conventional dual regression analysis. This problem was addressed by the development of an ensemble averaging of matrix factorisations approach to compute single subject spatial maps characterised by improved spatial reproducibility compared to maps obtained by dual regression. The approach was extended with a haemodynamic forward model to obtain surrogate neural activations to examine the subject’s task behaviour. This approach applied to two task-fMRI cohorts showed that these surrogate neural activations matched with original task timings in most of the examined fMRI scans but also revealed subjects with task behaviour different than intended by the researcher. It is hoped that both the findings in this work and the novel matrix factorisation approach itself will benefit the fMRI community. To this end, the derived tools are made available online to aid development and validation of methods for resting-state and task fMRI experiments

Computer Vision without Vision : Methods and Applications of Radio and Audio Based SLAM

The central problem of this thesis is estimating receiver-sender node positions from measured receiver-sender distances or equivalent measurements. This problem arises in many applications such as microphone array calibration, radio antenna array calibration, mapping and positioning using ultra-wideband and mapping and positioning using round-trip-time measurements between mobile phones and Wi-Fi-units. Previous research has explored some of these problems, creating minimal solvers for instance, but these solutions lack real world implementation. Due to the nature of using different media, finding reliable receiver-sender distances is tough, with many of the measurements being erroneous or to a worse extent missing. Therefore in this thesis, we explore using minimal solvers to create robust solutions, that encompass small erroneous measurements and work around missing and grossly erroneous measurements.This thesis focuses mainly on Time-of-Arrival measurements using radio technologies such as Two-way-Ranging in Ultra-Wideband and a new IEEE standard 802.11mc found on many WiFi modules. The methods investigated, also related to Computer Vision problems such as Stucture-from-Motion. As part of this thesis, a range of new commercial radio technologies are characterised in terms of ranging in real world enviroments. In doing so, we have shown how these technologies can be used as a more accurate alternative to the Global Positioning System in indoor enviroments. Further to these solutions, more methods are proposed for large scale problems when multiple users will collect the data, commonly known as Big Data. For these cases, more data is not always better, so a method is proposed to try find the relevant data to calibrate large systems

Disruption in structural–functional network repertoire and time-resolved subcortical fronto-temporoparietal connectivity in disorders of consciousness

Understanding recovery of consciousness and elucidating its underlying mechanism is believed to be crucial in the field of basic neuroscience and medicine. Ideas such as the global neuronal workspace (GNW) and the mesocircuit theory hypothesize that failure of recovery in conscious states coincide with loss of connectivity between subcortical and frontoparietal areas, a loss of the repertoire of functional networks states and metastable brain activation. We adopted a time-resolved functional connectivity framework to explore these ideas and assessed the repertoire of functional network states as a potential marker of consciousness and its potential ability to tell apart patients in the unresponsive wakefulness syndrome (UWS) and minimally conscious state (MCS). In addition, the prediction of these functional network states by underlying hidden spatial patterns in the anatomical network, that is so-called eigenmodes, was supplemented as potential markers. By analysing time-resolved functional connectivity from functional MRI data, we demonstrated a reduction of metastability and functional network repertoire in UWS compared to MCS patients. This was expressed in terms of diminished dwell times and loss of nonstationarity in the default mode network and subcortical fronto-temporoparietal network in UWS compared to MCS patients. We further demonstrated that these findings co-occurred with a loss of dynamic interplay between structural eigenmodes and emerging time-resolved functional connectivity in UWS. These results are, amongst others, in support of the GNW theory and the mesocircuit hypothesis, underpinning the role of time-resolved thalamo-cortical connections and metastability in the recovery of consciousness

Incremental volume rendering using hierarchical compression

Includes bibliographical references.The research has been based on the thesis that efficient volume rendering of datasets, contained on the Internet, can be achieved on average personal workstations. We present a new algorithm here for efficient incremental rendering of volumetric datasets. The primary goal of this algorithm is to give average workstations the ability to efficiently render volume data received over relatively low bandwidth network links in such a way that rapid user feedback is maintained. Common limitations of workstation rendering of volume data include: large memory overheads, the requirement of expensive rendering hardware, and high speed processing ability. The rendering algorithm presented here overcomes these problems by making use of the efficient Shear-Warp Factorisation method which does not require specialised graphics hardware. However the original Shear-Warp algorithm suffers from a high memory overhead and does not provide for incremental rendering which is required should rapid user feedback be maintained. Our algorithm represents the volumetric data using a hierarchical data structure which provides for the incremental classification and rendering of volume data. This exploits the multiscale nature of the octree data structure. The algorithm reduces the memory footprint of the original Shear-Warp Factorisation algorithm by a factor of more than two, while maintaining good rendering performance. These factors make our octree algorithm more suitable for implementation on average desktop workstations for the purposes of interactive exploration of volume models over a network. This dissertation covers the theory and practice of developing the octree based Shear-Warp algorithms, and then presents the results of extensive empirical testing. The results, using typical volume datasets, demonstrate the ability of the algorithm to achieve high rendering rates for both incremental rendering and standard rendering while reducing the runtime memory requirements

Les Houches 2013: Physics at TeV Colliders: Standard Model Working Group Report

This Report summarizes the proceedings of the 2013 Les Houches workshop on Physics at TeV Colliders. Session 1 dealt primarily with (1) the techniques for calculating standard model multi-leg NLO and NNLO QCD and NLO EW cross sections and (2) the comparison of those cross sections with LHC data from Run 1, and projections for future measurements in Run 2.Comment: Proceedings of the Standard Model Working Group of the 2013 Les Houches Workshop, Physics at TeV Colliders, Les houches 3-21 June 2013. 200 page