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Matt Clarkson

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Matt Clarkson

List of Publications 

An up to date list of publications is maintained here, and citation analysis here.

Track Record and Research Interests

A short biography can be found here.

My research in medical imaging is focused on developing novel computational algorithms, applying rigorous software engineering practices and delivering clinical applications.

NifTK - A Translational Software Platform

My current role involves leading a software team to deliver a translational imaging platform. The aim is to produce a common imaging framework to maximise the translation of the computational imaging work of CMIC to the clinical research of the Institute of Neurology, to UCL and beyond. We have developed segmentation tools for clinical drugs trials at the Dementia Research Centre, and tools for the image guided surgery research at CMIC and the National Hospital for Neurology and Neurosurgery.

Imaging Bio-Markers for Alzheimer's Disease

Funded by the Technology Strategy Board, with Principal Investigators Sebastien Ourselin and Nick Fox, alongside Kelvin Leung, and in partnership with IXICO Ltd. we developed more accurate and robust bio-markers for Alzheimer's Disease. The aim was to use imaging to measure brain shape change over time, as the brain atrophies due to neurodegenerative diseases. Accurate measurement is of vital importance for clinical drug trials and basic neuroscience. In particular we have focussed on areas such as assessing scanner related changes, improving the robustness of whole brain atrophy measurement, and developing new methods for automatically measuring hippocampal volume change

A key interest of mine, in collaboration with Jorge Cardoso, Sebastien Ourselin and Nick Fox, is cortical thickness measurement. We have been studying voxel based techniques, comparing them to the more typical surface based methods such as provided by the software package FreeSurfer. We have developed an expectation maximisation (EM) based segmentation method, specifically tuned to the task of cortical segmentation, enabling accurate and robust cortical thickness estimation in a fraction of the time of surface based methods.

(a) We analyse different computational methods, to understand algorithm performance. This picture shows the standard deviation of the regional difference in thickness for 50 subjects that had two same-day scans for the popular FreeSurfer package. The values are colour coded, where values of 0 (blue) to 0.3 (red) are all good, given the accuracy of the scanner.


(b) Once algorithm performance is understood, we can measure the annual percentage change in thickness for healthy volunteers. In this case, averaged over 17 samples, we see small changes in thickness, generally < 2%. Again, the values are colour coded, where blue means thinning, and red means thickening.

(c) However, the annual percent change in Alzheimer's patients, averaged over 33 subjects can be seen to be much more negative. The stronger blue colours above indicate a greater reduction in thickness due to the atrophying processes.


(d) With both voxel and surface based methods, we can study the statistical difference between groups of healthy volunteers and different patient groups to understand and characterise the disease. In this case we have a statistical map showing areas of statistically significant (yellow and red) thinning between healthy volunteers and patients with Semantic Dementia.  

In addition, at the Dementia Research Centre, we have studied the patterns of thickness change in the cortex during ADAD and frontotemporal lobar degeneration (FTLD) and semantic dementia, progressive non-fluent aphasia and logophenic/phonological aphasia

Links & Other Responsibilities

Lecturer: M.Sc. Medical Image Computing, Image Processing module, "Cluster Computing"

Lecturer: M.Sc. Medical Image Computing, Information Processing in Medical Imaging module, Statistical Shape Modelling, C++ and ITK workshops.

Reviewer: SPIE-2011


Reviewer: TMI



ReviewerSignal, Video and Image Processing

ReviewerPLoS One

OrganiserDRC NeuroImaging Journal Club, 2009-2011

OrganiserPost MICCAI 2009 journal club presentations

Administrator: CMIC Trac

Contact Details

Centre for Medical Image Computing (CMIC)
Engineering Front Building
3rd Floor
University College London
Malet Place
Office: 3.09
Tel: 0207 679 0257 (shared)

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