Mark Jenkinson

Personal Details

Full Name : Mark Jenkinson    Nationality : Australian and British (dual)
Date of Birth : 8 February 1971 Place of Birth : Jamestown, SA

Academic Qualifications

1999 D.Phil., Robotics Research Group (University of Oxford)
Thesis title: Saliency in Image Analysis
Supervisor: Prof. Sir Michael Brady
1994 B.Sc. (Hons), First Class Honours in Mathematical Physics (University of Adelaide)
Graduated at top of the honours list.
Double major in Computer Science and Mathematical Physics.
1993 B.E. (Hons), First Class Honours in Engineering (Electrical and Electronic)
(University of Adelaide)
Graduated at top of the honours list with highest results in each year.

Research and Employment Details

2019-          Professor of NeuroImaging, Australian Institute for Machine Learning (AIML), School of Computer Science, University of Adelaide, Australia
2019-    Professor of NeuroImaging, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia
2014-    Professor of NeuroImaging, Nuffield Department of Clinical Neurosciences, University of Oxford
2003-2020Head of Structural Image Analysis, FMRIB Centre, University of Oxford
Research interests: statistical shaped-based anatomical segmentation of multiple brain structures leading to non-linear registration; simulation of the MRI processes for studying artefacts; joint estimation and correction of motion-based fMRI artefacts; EEG/MEG/fMRI integration modelling. Responsibilities: supervising students and post-doctoral scientists in collaborative research projects; software development and maintenance for FSL package utilities and libraries.
2002Post-Doctoral Scientist, NeuroImaging Group, Howard Florey Insitute, University of Melbourne
Research interests: non-linear registration of MRI; EEG/fMRI integration; database contruction and analysis of structural MRI sets; modelling of MRI processes and artefacts; modelling and inference in group studies.
1998-2001 Post-Doctoral Scientist, Image Analysis Group, FMRIB Centre, University of Oxford
Research interests: registration of MRI-MRI and fMRI-MRI; motion correction for fMRI; phase unwrapping; interpolation; spatial clustering and statistical analysis; correcting distortion of EPI images and the impact on statistical inference. Have written software for linear registration, motion correction, phase unwrapping and correction of EPI distortions. Extensive involvement in building up a local software development environment including a 4D image manipulation library. All software has been extensively tested and made freely available via the internet.
1995-1998Robotics Research Group, University of Oxford
Thesis entitled Saliency in Image Analysis under the supervision of Prof. Sir Michael Brady. The research looks at shape representations based on local symmetries. It deals with methods for extraction and decomposition for 2D shapes, with occlusion reasoning. Previous research experience in computer vision includes real-time tracking, object localisation and recognition, plus noise analysis of low-level image invariants.
2020-Developer, lecturer and co-ordinator for the course Using Machine Learning Tools (University of Adelaide / Pearson)
2002-Co-ordinator, lecturer and demonstrator for the FSL and FreeSurfer course (a 4-5 day course attracting international researchers and students covering the theory and practice of image analysis using FSL).
2003-2018Co-ordinator, lecturer and tutor for Image Analysis teaching in the FMRIB Graduate Training Program.
2006-2008Tutor for first-year undergraduate psychology students at St Anne's College in Introduction to Probability Theory and Statistics.
Additional experience in lecturing and tutoring students in image analysis and statistics at University level.


2020 Medical Research Future Fund (MRFF) -Chief Investigator B - Traumatic Brain Injury Mission: Forecasting Impairment and Neurodegenerative Disease risk following Traumatic Brain Injury (FIND-TBI): A computational neurology-driven method to predict long-term prognosis (total funds AU$2m)
2017 Wellcome Trust Centre for Integrative Neuroimaging (co-investigator) - Wellcome Trust Centre Grant (total funds £11m)
2013 Cancer Research UK - Oxford Cancer Imaging Centre (applicants in the Image Analysis Programme: Mike Brady, Michael Chappell, Vicente Grau, Mark Jenkinson, Peter Jezzard, and Julia Schnabel) (total funds of £16m across 6 Programmes)
2012 Wellcome Trust Strategic Award (co-investigator) - Integrated multimodal brain imaging for neuroscience research and clinical practice (total funds £2m)
2011 NERC Grant (co-investigator) - Constraining the response of the hydrological cycle, land surface and regional weather to global change (HYDRA) (total funds £121K)
2010 NIH Grant (co-investigator) - Mapping the Human Connectome: Structure, Function and Heritability (total funds US$30m)
2009 EPSRC Grant (co-applicant) - New Tools for Understanding White Matter Disease using Diffusion MRI (total funds £555K)
2006 GlaxoSmithKline Grant (co-applicant) - Integrated structural and diffusion imaging for Alzheimer's (total funds £121K)
2005 David Phillips Fellowship (principal investigator) from the UK BBSRC (total funds £395K)
2005 DTI Grant (co-applicant) - Functional brain imaging: Relating patient data to the population (total funds £150K)
2004 EPSRC Grant (co-applicant) - Integrated Brain Image Modelling (total funds £750K)
2003 EPSRC Grant (co-author) - Information eXtraction from Images (total funds £555K)
2002 GlaxoSmithKline Grant (co-author) - FMRI Group Statistics (total funds £190K)

Scholarships and Prizes

2021 In Clarivate Analytics' list of Highly Cited Researchers 2021
2020 In Clarivate Analytics' list of Highly Cited Researchers 2020
2019 In Clarivate Analytics' list of Highly Cited Researchers 2019
2018 In Clarivate Analytics' list of Highly Cited Researchers 2018
2016 In Thomson Reuters' list of Highly Cited Researchers 2016
2015 In Thomson Reuters' list of Highly Cited Researchers 2015
2015 Shortlisted (top 3) for Outstanding Tutor in the OUSU (Oxford University Student Union) Teaching Awards, Medical Sciences Division
2014 In Thomson Reuters' list of Highly Cited Researchers 2014 (The World's Most Influential Scientific Minds)
2014 ISMRM Outstanding Teacher Award (Thinking Outside the Black Box: fMRI)
2012 Teaching Excellence Award, University of Oxford
2009 ISMRM Outstanding Teacher Award (Quantitative Imaging and Data Analysis)
2004 Departmental Merit Award (Clinical Neurology)
1995 The Sir Robert Menzies Scholarship in Engineering
George Murray Scholarship
1993 The Electricity Trust Prize in Electrical Power Engineering
The Philips Industries Holdings Ltd. Prize in Electronics
1991 The Gerard Industries ``Clipsal'' Prize
The Chamber of Commerce and Industry Prize in Electrical Engineering
The Chamber of Commerce and Industry Prize in Electronic Engineering
The Sir William Goodman Scholarship
1990 The E.V. Clark Prize for Electrical Engineering
The Lincolne Scott Prize for Academic Excellence
1989 The Sir Robert Chapman Prize
The IEE (UK) Prize (for outstanding academic achievement)
1988 Electricity Trust of South Australia (ETSA) Studentship

Professional Activities and Memberships

Member of INCF Human Atlas Working Group 2015-
Member of ISMRM Scientific Annual Meeting Program Committee 2005-2008
Co-Organiser of Educational Courses on Advanced Data Analysis and Image Processing (ISMRM 2008)
Co-Organiser of Workshop on Pairwise and Groupwise Registration (MICCAI 2007)
Co-Organiser of Two Day Educational Course on Quantitative Data and Image Analysis (ISMRM 2006, 2007)
Member of NIH Data Format Working Group (NIfTI) 2004-2007
Member of WBIR 2006 Program Committee
Member of IEEE (Institute of Electrical and Electronic Engineers) 2003-
Member of ISMRM (International Society of Magnetic Resonance in Medicine) 2001-
Good Clinical Practice training: 29 July 2021
Reviewing for journals: NeuroImage, Human Brain Mapping, IEEE Transactions on Medical Imaging, Imaging and Computer Vision, Magnetic Resonance in Medicine, the Journal of Magnetic Resonance Imaging, Medical Image Analysis, Frontiers in Neuroscience, the International Journal of Computer Vision and the International Journal of Computer Assisted Radiology and Surgery.
Grant reviewing: EPSRC, BBSRC, Wellcome Trust, UK MS Society, Research Council of Norway, Australia Research Council, Netherlands Organisation for Scientific Research, Canadian Natural Sciences and Engineering Research Council, and the Ecole polytechnique federale de Lausanne (EPFL).
Conference reviewing: ISMRM, MICCAI, ISBI, IPMI, WBIR and OHBM.

Doctoral Students

2003 Dr Peter Bannister Motion Correction for Functional Magnetic Resonance Images
2007 Dr Ivana Drobnjak FMRI Simulator: Development and Applications
2007 Dr Caitlinn Loftus Integration of Functional Magnetic Resonance Imaging and Electroencephalography Data using Independent Component Analysis
2008 Dr Brian Patenaude Bayesian Statistical Models of Shape and Appearance for Subcortical Brain Segmentation
2011 Dr Aleksandar Petrovic Registration using Diffusion and Structural Imaging
2012 Dr Courtney Bishop (nee Birch) Image Analysis for Clinical Brain Imaging with MR and PET
2013 Dr Andri Tziortzi Quantitative Analysis of the Dopamine D3 receptor in-vivo in humans
2013 Dr Mattias Heinrich Deformable Lung Registration for Pulmonary Image Analysis of MRI and CT Scans
2013 Dr Manav Bhushan Motion Correction and Parameter Estimation in DCE-MRI Sequences: Application to Colorectal Cancer
2015 Dr Rebecca McKavanagh The Neuropathology of the Social Cognitive Network in Autism
2015 Dr Adam Levy Correcting Errors in Distribution of GCMs' Mean Climate to Create Greater Inter-Model Agreement on Trends
2018 Dr Antoine Saillant Estimation of physiological parameters in dynamic PET imaging
2019 Dr Patrick Pflanz Diffusion MRI in Premanifest Huntington's Disease and Early Parkinson's Disease: Tensor and Tractography Analyses
2019 Dr Zobair Arya Development of Neuroimaging Biomarkers for Neurodegeneration Using Multimodal Dynamic Atlases
2019 Dr Jolanta Mirecka Quantifying Spatial Heterogeneity in Tumours from Dynamic Contrast-Enhanced MRI Imaging
2020 Dr Vaanathi Sundaresan Detection of cerebral small vessel disease signs on brain MR images
2021 Dr Fidel Alfaro Almagro Brain Imaging in UK Biobank
2021 Dr Istvan Huszar Combining Digital Histology with Magnetic Resonance Imaging in Amyotrophic Lateral Sclerosis
2021 Dr Silvia Messina Structural, quantitative and functional brain MRI findings in MOGAD: a comparison with NMOSD-AQP4 and MS
2021 Dr Hanna Nowicka Neuroimaging methods for analysing connectivity in the presence of white matter lesions
2022 Dr Nicola Dinsdale Optimising Convolutional Neural Networks for Large-Scale Neuroimaging Studies
 Ms Lovena Chedumbarum Pillay Disease staging from amnestic mild cognitive Impairment to probable Alzheimer’s disease via region-specific quantification of [18F]flutemetamol PET brain images and the correlation with rate of conversion
 Ms Madeleine Wyburd Quantifying Cortical Folding from Fetal Ultrasound Volumes
 Mr Benjamin Ellul The Role of the Neuroimaging in the prediction of cognitive and mood changes following Traumatic Brain Injury and in Parkinson’s Disease
 Mr Fengbei Liu Adapting deep learning for real-world image datasets
 Ms Minyan Zeng Prognostic prediction of large-vessel stroke using machine learning methods
 Ms Georgia Kenyon Anatomically-based Deep Learning Models for Improved Neuroimaging Analysis

Programming Expertise

Experience in : Keras/TF, Python, MATLAB, shell scripting, C and C++


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