Stuart Clare, PhD

Details

Education and Positions

Awards

• 1994. University of Nottingham, George Green Prize for Physics.
• 2007. University of Oxford, Award for Teaching Excellence.

Professional Experience

• Extensive experience in MRI and fMRI, including pulse sequence programming, image reconstruction, data analysis and stimulus presentation.
• Technical experience in maintenance of all scanner hardware including console electronics and power amplifiers, and their interface to other external hardware.
• Specified and project managed the installation of a state-of-the-art gradient coil (£200k project)
• Line management of technical support staff, including recruitment, induction and appraisal.
• Supervision of MSc projects and MPhil/PhD students.
• Course organiser and lecturer on the Graduate Training Program in fMRI within the Department, which has trained over 20 students over the past three years.
• Extensive programming experience in C, C++ (Unix and Windows), Perl, TCL, Matlab and proprietary scanner software (Varian). Some experience in IDL and QT.
• Development of web pages and web applications in html, cgi, perl, mysql, including a scanner database and billing application.
• Development of Windows and Linux applications involve external interfacing.

Publications

Refereed Papers in Journals

Devlin, J.T., Sillery, E.L., Hall, D.A., Hobden, P., Behrens, T.E.J., Nunes, R.G., Clare, S., Matthews, P.M., Moore, D.R., Johansen-Berg, H. (2006) 'Reliable identification of the auditory thalamus using multi-modal structural analyses'. Neuroimage. 30, 1112-1120.

Clare, S., Evans, J., Jezzard, P. (2006) 'Requirements for Room Temperature Shimming of the Human Brain'. Magnetic Resonance in Medicine. 55, 210-214.

Bridge, H., Clare, S. (2006) 'High Resolution MRI. In vivo Histology?' Philosophical Transactions of the Royal Society B. 361, 137-146.

Nunes, R., Jezzard, P., Clare, S. (2005) 'Investigations on the efficiency of cardiac-gated methods for the acquisition of diffusion-weighted images'. Journal of Magnetic Resonance. 117, 102-110.

Clare, S., Bridge, H. (2005) 'Methodological Issues Relating to in vivo Cortical Myelography using MRI'. Human Brain Mapping. 26(4), 240-250.

Figueiredo, P., Clare, S., Jezzard, P. (2005) 'Quantitative Perfusion Measurements using Pulsed Arterial Spin Labelling: Effects of Large ROI Analysis'. Journal of Magnetic Resonance Imaging. 21, 676-682.

Nunes, R., Jezzard, P., Behrens, T., Clare, S. (2005) 'A Self-Navigated Multi-Shot Echo-Planar Pulse Sequence for High Resolution Diffusion-Weighted Imaging'. Magnetic Resonance in Medicine, 53, 1474-1478.

Bridge, H., Clare, S., Jenkinson, M., Jezzard, P., Parker, A.J., Matthews, P.M., (2004) 'Independent anatomical and functional measures of the V1/V2 boundary in human visual cortex'. Journal of Vision, 5, 93-102.

Behrens, T.E.J., Woolrich, M.W., Jenkinson, M., Johansen-Berg, S., Nunes, R.G., Clare, S., Matthews, P.M., Brady, J.M. and Smith, S.M. (2003) 'Characterization and Propagation of Uncertainty in Diffusion-Weighted MR Imaging'. Magnetic Resonance in Medicine. 50, 1077-1088.

Parry, A., Clare, S., Jenkinson, M., Smith, S., Palace, J., Matthews, P.M. (2003) 'MRI brain T1 relaxation time changes in MS patients increase over time in both white matter and the cortex'. Journal of Neuroimaging. 13, 234-239.

Parry, A., Clare, S., Jenkinson, M., Smith, S., Palace, J., Matthews, P.M. (2002) 'White matter and lesion T1 relaxation times increase in parallel and correlate with disability in multiple sclerosis'. Journal of Neurology, 249, 1279-1286.

Tracey, I., Ploghaus, A., Gati, J.S., Clare, S. Smith, S., Menon, R.S., and Matthews, P.M. (2002) 'Imaging Attentional Modulation of Pain in the Periaqueductal Gray in Humans' Journal of Neuroscience, 22, 2748

Bantick S., Wise R., Ploghaus A., Clare S., Smith, S., Tracey I. (2002) 'Imaging how attention modulates pain in humans using functional MRI. Brain 125, 310-319.

Clare, S., Alecci, M., Jezzard, P. (2001) 'Compensating for B1 Inhomogeneity using Active Transmit Power Modulation'. Magnetic Resonance Imaging. 19, 1349-1352.

Clare, S., Jezzard, P. (2001) 'Rapid T1 Mapping using Multislice Echo Planar Imaging'. Magnetic Resonance in Medicine. 45, 630-634.

Clare, S., Francis, S., Morris, P.G. and Bowtell, R. (2001) 'Single Shot T2* Measurement to Establish Optimum Echo Time for fMRI: Studies of the Visual, Motor and Auditory Cortices at 3.0T'. Magnetic Resonance in Medicine. 45, 930-933.

Ploghaus A., Narain C., Beckmann C.F., Clare S., Bantick S., Wise R., Matthews P.M., Rawlins J.N., Tracey I. (2001) 'Exacerbation of Pain by Anxiety Is Associated with Activity in a Hippocampal Network' Journal of Neuroscience 21, 9896-9903.

Ploghaus, A., Tracey, I., Clare, S., Gati, J.S., Rawlins, J.N.P., and Matthews, P.M. (2000) 'Learning about pain: The neural substrate of the prediction error for aversive events' Proc. Natl. Acad. Sci. USA, 97, 9281-9286.

Jezzard, P., Clare, S. (1999) 'Sources of Distortion in Functional MRI Data' Human Brain Mapping 8, 80-85.

Ploghaus, A., Tracey, I., Gati, J.S., Clare, S., Menon, R.S., Matthews, P.M., Rawlins, J.N.P. (1999) 'Dissociating Pain from Its Anticipation in the Human Brain' Science 284, 1979-1981.

Matthews, P., Clare, S., Adcock, J. (1999) 'Functional Magnetic Resonance Imaging: Clinical Applications and Potential'. Journal of Inherited Metabolic Disease 22, 337-352.

Clare, S., Humberstone, M., Hykin, J., Blumhardt, L., Bowtell, R. and Morris, P. (1999) 'Detecting Activations in Event-Related fMRI Using Analysis of Variance'. Magnetic Resonance in Medicine. 42, 1117-1122.

Atkinson, D., Hill, D.L.G., Stoyle, P.N.R.,Summers, P.E., Clare, S., Bowtell, R. and Keevil, S.F. (1999) 'Automatic Compensation of Motion Artefacts in MRI'. Magnetic Resonance in Medicine. 41,163-170.

Francis, S., Rolls, E.T., Bowtell, R., McGlone F., ODoherty, J., Browning, A., Clare, S. and Smith, E. (1999) 'The representation of pleasant touch in the brain and its relationship with taste and olfactory areas'. Neuroreport 10, 453-459.

Hykin, J., Moore, R., Duncan, K., Clare, S., Baker, P., Johnson, I., Bowtell, R., Mansfield, P. and Gowland, P. (1999) 'Fetal brain activity demonstrated by functional magnetic resonance imaging'. Lancet 354, 645-646.

Humberstone, M., Sawle, G., Clare, S., Hykin, J., Coxon, R., Bowtell, R., Macdonald, I. and Morris P. (1997) 'Functional Magnetic Resonance Imaging Reveals Human Presupplementary Motor Area'. Annals of Neurology. 42, 632-637.

Book Chapters

Clare, S. (2004) 'Magnetic Resonance Imaging of Brain Function', Methods in Enzymology, Volume 385 'Imaging in Biomedical Research Part A'. Edited by Conn, Elsivier Academic Press. pp 143-148.

Parry, A., Clare, S., Matthews, P.M. (2004) 'Rapid, whole brain T1 relaxation time measurements for the quantitative definition of pathological change in multiple sclerosis. Normal appearing white and grey matter damage in multiple sclerosis. Topics in Neuroscience Edited by Filippi, Comi, Rovaris. Chapter 6. Springer-Verlag Italia.

Jezzard, P. and Clare, S. (2001) 'Principles of Nuclear Magnetic Resonance and MRI', in 'Functional Magnetic Resonance Imaging: An Introduction to Methods', Edited by Jezzard, Matthews and Smith, Oxford University Press, Oxford, pp.67-92

Clare, S. (1997) Functional Magnetic Resonance Imaging: Methods and Applications. PhD Thesis, University of Nottingham.

Refereed Abstracts

Clare, S., Evans, J. Benefits and Requirements for Dynamic Shimming of the Human Brain. (2006) European Society for Magnetic Resonance in Medicine and Biology, 143.

Starewicz, P., Diduch, P., Clare, S., Jastrzebski, P., Jezzard, P. (2006) “Real-time” shim adjustment in a multi-slice EPI (2006) European Society for Magnetic Resonance in Medicine and Biology, 143.

Clare, S., Evans, J., Wilson, J., Jezzard, P. (2005) Requirements for RT Shimming of the Brain at 3 Tesla. Proc. 13^th Meeting International Society for Magnetic Resonance in Medicine, 412.

Nunes, R., Drobnjak, I., Clare, S., Jezzard, P., Jenkinson, M. (2005) Quantitative Simulation of Affine Registration for Correction of Eddy Current Distortions in Diffusion-Weighted Images. Proc. 13^th Meeting International Society for Magnetic Resonance in Medicine, 2279.

Clare, S., Bridge, H. (2005) Defining Informative Voxels for Detection of Cortical Structure in High-Resolution MRI. Proc. 13^th Meeting International Society for Magnetic Resonance in Medicine, 1273.

Nunes, R., Jezzard, P., Clare, S. (2005) An Efficient Method for Acquiring Cardiac-Gated Diffusion-Weighted Images. Proc. 13^th Meeting International Society for Magnetic Resonance in Medicine, 4.

Nunes, R., Jezzard, P., Clare, S. (2004) Nonlinear Motion Correction for Diffusion Imaging Using a Self-Navigated Cartesian Based Sequence. Proc. 12^th Meeting International Society for Magnetic Resonance in Medicine,2156.

Nunes, R., Jezzard, P., Johansen-Berg, H., Behrens, T., Clare, S. (2004) An EPIK Navigation towards High-Resolution Diffusion Weighted Imaging. Proc. 12^th Meeting International Society for Magnetic Resonance in Medicine,2467.

Clare, S., Bridge, H., Jezzard, P., Parker, A., Matthews, PM. (2003) Correspondence of Structurally and Functionally Determined Human Visual Cortex. Proc. 11^th Meeting International Society for Magnetic Resonance in Medicine, 658.

Clare, S. (2003) Iterative Nyquist Ghost Correction for Single and Multi-shot EPI using an Entropy Measure. Proc. 11^th Meeting International Society for Magnetic Resonance in Medicine, 1041.

Nunes, R., Jezzard, P., Clare, S. (2003) Assessment of the quality of Diffusion Tensor Data for Fibre Tracking: a Comparison between 1.5 and 3.0 T. Proc. 11^th Meeting International Society for Magnetic Resonance in Medicine, 2130.

Bridge, H., Clare, S., Jezzard, P., Parker, A.J., Matthews, P.M. (2003) A comparison of structurally and functionally defined human primary visual cortex. Journal of Vision, 3(9).

Clare, S., Jezzard, P., Matthews, P.M. (2002) Identification of the myelinated layers in striate cortex on high resolution MRI at 3 Tesla. Proc. 10th Meeting International Society for Magnetic Resonance in Medicine, 1465.

De Luca, M., Beckmann, C., Behrens, T., Clare, S., De Stefano, N., Matthews, P., Woolrich, M., Smith, S. (2002) Low Frequency Signals in FMRI - Resting State Networks and the Intensity Normalisation Problem. Proc. 10th Meeting International Society for Magnetic Resonance in Medicine, 1459.

Clare, S., Parry, A., Jezzard, P. (2001) Whole brain T₁ Relaxometry in Multiple Sclerosis. Proc. Joint Annual Meeting International Society for Magnetic Resonance and European Society for Magnetic Resonance in Medicine and Biology, 155.

Clare, S., Jezzard, P. (2000) Rapid Relaxation Time Mapping using Multislice EPI. Proc 17th Meeting European Society for Magnetic Resonance in Medicine and Biology, 329.

Clare, S., Jezzard, P. (2000) Fast T₁ Mapping using Multislice EPI. Proc. 8th Meeting International Society for Magnetic Resonance in Medicine, 430.

Clare, S., Alecci, M., Jezzard, P. (1999) B₁ Inhomogeneity Compensation by Active Transmit Power Modulation. Proc. 7th Meeting International Society for Magnetic Resonance in Medicine, 1976.

Hykin, J., Moore, R., Duncan, K., Baker, P., Johnson, I., Clare, S., Bowtell, R., Mansfield, P. and Gowland, P. (1999) The Demonstration of Human Fetal Brain Activity in utero Using Function Magnetic Resonance Imaging. Proc. 7th Meeting International Society for Magnetic Resonance in Medicine, 446.

Clare, S., Humberstone, M., Bowtell, R.W. and Morris, P.G. (1998) Single Shot T2* Measurement to establish optimum echo time for fMRI at 3.0T. Proc. 6th Meeting International Society for Magnetic Resonance in Medicine, 1461.

Clare, S., Bowtell, R.W. and Morris, P.G. (1998) Ghost artefact in fMRI: Comparison of the techniques for reducing the N/2 ghost. Proc. 6th Meeting International Society for Magnetic Resonance in Medicine, 2137.

Tracey, I., Clare, S., Miall, R.C., Smith, S.M., Morris, P.G. and P.M. Matthews (1998) Implicit and Explicit Memory: fMRI of a pre-learned motor sequence. 4th International Conference on Functional Mapping of the Human Brain, 834.

Atkinson, D., Hill, D.L.G., Stoyle, P.N.R., Summers, P.E., Clare, S., Bowtell, R. and Keevil, S.F. (1998) Motion Artefact Reduction in a Variety of MR Sequences. Proc. 6th Meeting International Society for Magnetic Resonance in Medicine, 2114.

Clare, S., Bowtell, R.W. and Morris, P.G. (1997) Single Shot T2* Measurement During Visual and Motor Activation. Proc. 14th Meeting European Society for Magnetic Resonance in Medicine and Biology, 229.

Clare, S., Humberstone, M., Bowtell, R.W. and Morris, P.G. (1997) A Non-Directed Method for the Analysis of fMRI data. Proc. 14th Meeting European Society for Magnetic Resonance in Medicine and Biology, 330.

Humberstone, M., Clare, S., Hykin, J., Sawle, G.V. and Morris, P.G. (1997) Paradigms for Studying Single Cognitive / Motor Events with Functional MRI. Proc. 5th Meeting International Society for Magnetic Resonance in Medicine, 1646.

Humberstone, M., Clare, S., Hykin, J., Morris, P.G. and Sawle, G.V. (1997) The Roles of pre-SMA and SMA-proper in Motor Initiation and Decision Making; Studies using 'Event Related' fMRI. 3rd International Conference on Functional Mapping of the Human Brain, 267.

Rolls, E.T., Francis, S., Bowtell, R.W., Browning, A.S., Clare, S., Smith, E. and McGlone, F. (1997) Pleasant Touch Activates the Orbitofrontal Cortex. 3rd International Conference on Functional Mapping of the Human Brain, 17.

Rolls, E.T., Francis, S., Bowtell, R.W., Browning, A.S., Clare, S., Smith, E. and McGlone, F. (1997) Taste and Olfactory Activation of the Orbitofrontal Cortex. 3rd International Conference on Functional Mapping of the Human Brain, 199.

Ludman, C.N., Hykin, J., Summerfield, A.Q., Clare, S., Elliott, M., Foster, J., Bowtell, R.W., Morris, P.G. and Worthington, B. (1997) Functional Magnetic Resonance Imaging During the Silent Lip-reading of Sentences. Radiological Society of North America.

Clare, S., Hykin, J., Bowtell, R.W., Coxon, R. and Morris, P.G. (1996) Sub-Millimeter Resolution Functional Brain Imaging with Multislice Interleaved EPI at 3.0 T. Proc. 4th Meeting International Society for Magnetic Resonance in Medicine, 1821.

Humberstone, M., Clare, S., Hykin, J., Morris, P.G. and Sawle, G.V. (1996) Identifying Spatial Patterns of Activation for a Single Motor Event Using Whole Brain fMRI. 4th International Congress of Movement Disorders.

Humberstone, M., Clare, S., Hykin, J., Morris, P.G. and Sawle, G.V. (1996) High Resolution Time Course Analysis of fMRI Signal Change in Single Motor Events. 4th International Congress of Movement Disorders.

Humberstone, M., Clare, S., Hykin, J., Morris, P.G. and Sawle, G.V. (1996) Whole Brain fMRI Comparison of Self vs Externally Initiated Movement. 4th International Congress of Movement Disorders.

Humberstone, M., Clare, S., Hykin, J., Morris, P.G. and Sawle, G.V. (1996) Non-Directed Technique for the Detection of Functional Activation in Whole Brain fMRI Series. 4th International Congress of Movement Disorders.

Hykin, J., Bowtell, R.W., Worthington, B., Coxon, R., Clare, S., Blumhardt, L.D., Mansfield, P. and Morris, P.G. (1996) Echo Planar and Echo Volume Functional MRI at 3.0 T and Temporal Connectivity in the Brain. Radiology UK.

Hykin, J., Clare, S., Bowtell, R.W., Humberstone, M., Coxon, R., Worthington, B., Blumhardt, L.D. and Morris, P.G. (1996) A Non-Directed Method in the Analysis of Functional Magnetic Resonance Imaging (fMRI) and its Application to Studies of Short Term Memory. Proc. 13th Meeting European Society for Magnetic Resonance in Medicine and Biology, 366.

Humberstone, M., Barlow, M., Clare, S., Coxon, R., Glover, P., Hykin, J. and Macdonald, I.A. (1995) Functional Magnetic Resonance Imaging of Single Motor Events with Echo Planar Imaging at 3T, using a Signal Averaging Technique. Proc. 3rd Meeting Society of Magnetic Resonance, 858.

Professional Activities

Memberships

• International Society for Magnetic Resonance in Medicine
• British Chapter of the International Society for Magnetic Resonance in Medicine
  • Local Organising Committee, Annual Meeting, Oxford (2005)

Reviewing Activities

Journal reviewing

• Experimental Brain Research
• International Journal of Biomedical Imaging
• Journal of Magnetic Resonance
• Journal of Magnetic Resonance Imaging
• Magnetic Resonance in Medicine
• Neuroimage
• Transactions in Medical Imaging

Grant reviewing

• Medical Research Council, UK
• Wellcome Trust, UK

Invited Talks and Session Moderation

• Invited Session Moderator, ESMRMB Annual Meeting, Warsaw, Poland, September 2006
• Invited Lecturer, ESMRMB Annual Meeting, Warsaw, Poland, September 2006.
• Invited Session Moderator, ISMRM Annual Meeting, Seattle, May 2006
• Invited Lecturer, ESMRMB Lectures on Magnetic Resonance, Nijmegen, Netherlands, September 2004
• Institute of Medicine, Forschungszentrum Juelich, Germany, December 2003
• Invited Speaker, Oxford Opthalmological Congress, July 2003
• Institute of Child Health, London, UK, February 2001

Department Responsibilities

• Member of the Departmental Graduate Studies Board
  
• Harassment Advisor
  

Additional Training

• Good Clinical Practice - 30^th May 2006
• Taking Informed Consent - 10^th August 2006
• Harassment Advisor Training - 15th May 2007