~ Jonathan D. Clayden

Photo

I am a Lecturer (Assistant Professor) in neuroimaging and biophysics at the Institute of Child Health (ICH) within University College London (UCL). My interests centre on furthering understanding of connectivity and information processing in the brain, and the mechanisms by which these change due to normal development and disease. I take a high level imaging-based approach to studying these questions, and work on new computational and modelling methods for image analysis, as well as clinical applications.

I presently collaborate with colleagues from within ICH, as well as at UCL's Wellcome Trust Centre for Neuroimaging, Institute of Neurology and Centre for Medical Image Computing, as well as externally. I also act as webmaster for the UK diffusion MRI interest group.

One important tool that is available to explore connectivity is diffusion magnetic resonance imaging based fibre tracking, which can elucidate the patterns of “wiring” in the living brain. It is assumed that if these pathways are interrupted, the brain will become internally disconnected, with negative consequences for cognition. Additionally, functional magnetic resonance imaging can provide complementary information about interrelated patterns of brain activity. The combination of these imaging methods with sophisticated modelling and analytical techniques represents a versatile toolbox for investigating connectivity.

In addition to these pages, I have profiles on Google Scholar and LinkedIn. I tweet as @jonclayden.

Research

Contact

Developmental Imaging & Biophysics Section
UCL Institute of Child Health
30 Guilford Street
London WC1N 1EH
United Kingdom

phone: +44 (0)20 7905 2708
e-mail: j.clayden at ucl.ac.uk

Curriculum Vitae/Résumé

Some of the long-terms aims of my research are

A more discursive general overview of major themes in my research is also available, and may be a useful place to start if you are trying to work out whether my work is of interest to you!

PhD students and postdocs currently working with me include Fani Deligianni, Chris Parker, Clare Gibbard, Matthew Grech-Sollars and Rosie Coleman. If you are interested in doing a PhD, please feel free to get in touch by e-mail. Relevant sources of studentship funding include the UCL EPSRC Centre for Doctoral Training in Medical Imaging, UCL SLMS Grand Challenge Studentships and ICH Child Health Research PhD Programme.

Teaching

I currently teach on the UCL Masters courses in Neuroscience and Advanced Neuroimaging. Further information on these courses is available through the preceding links.

I also give internal teaching lectures at ICH on imaging-related topics. Slides for a recent (2015) version of these lectures are available on the following topics. The material is pitched at a fairly introductory level.

Software

I am the main author and maintainer of the TractoR MRI analysis project, which consists of a set of tools for performing image processing, tractography and white matter segmentation using methods described in some of the publications listed below. TractoR is free software, available under the GPL licence.

I also maintain

Further information about these projects can be found through the software page on this site.

Publications

The following list is subdivided into reviews, other journal papers, conference papers and conference abstracts. My PhD thesis has a page of its own. Please get in touch if you want a copy of a paper or abstract of mine that isn't provided here.

Reviews

J.D. Clayden (2013). Imaging connectivity: MRI and the structural networks of the brain. Functional Neurology 28(3):197-203. [Invited review; pdf (9880 KiB); PubMed; Functional Neurology (open access)]

Other journal papers

F.J. Liégeois, J. Butler, A.T. Morgan, J.D. Clayden & C.A. Clark (in press). Anatomy and lateralization of the human corticobulbar tracts: An fMRI-guided tractography study. To appear in Brain Structure and Function. [PubMed; SpringerLink]

J.D. Clayden, Z. Nagy, N. Weiskopf, D.C. Alexander & C.A. Clark (in press). Microstructural parameter estimation in vivo using diffusion MRI and structured prior information. To appear in Magnetic Resonance in Medicine. [pdf (2034 KiB); PubMed; Wiley (open access)]

J.M. Kawadler, F.J. Kirkham, J.D. Clayden, M. Hollocks, E. Seymour, R. Edey, P. Telfer, A. Robins, O. Wilkey, S. Barker, T. Cox & C.A. Clark (2015). White matter damage relates to oxygen saturation in children with sickle cell anemia without silent cerebral infarcts. Stroke 46(7):1793–1799. [PubMed; American Heart Association]

D. Anblagan, M.E. Bastin, S. Sparrow, C. Piyasena, R. Patakya, E.J. Moore, A. Serag, A.G. Wilkinson, J.D. Clayden, S.I. Semple & J.P. Boardman (2015). Tract shape modeling detects changes associated with preterm birth and neuroprotective treatment effects. NeuroImage: Clinical 8:51–58. [ScienceDirect]

M. Grech-Sollars, P.W. Hales, K. Miyazaki, F. Raschke, D. Rodriguez, M. Wilson, S.K. Gill, T. Banks, D.E. Saunders, J.D. Clayden, M.N. Gwilliam, T.R. Barrick, P.S. Morgan, N.P. Davies, J. Rossiter, D.P. Auer, R. Grundy, M.O. Leach, F.A. Howe, A.C. Peet & C.A. Clark (2015). Multi-centre reproducibility of diffusion MRI parameters for clinical sequences in the brain. NMR in Biomedicine 28(4):468–485. [PubMed; Wiley (open access)]

S. Muñoz Maniega, M. Valdés Hernández, J.D. Clayden, N.A. Royle, C. Murray, Z. Morris, B.S. Aribisala, A.J. Gow, J.M. Starr, M.E. Bastin, I.J. Deary & J.M. Wardlaw (2015). White matter hyperintensities and normal-appearing white matter integrity in the ageing brain. Neurobiology of Aging 36(2):909–918. [PubMed; ScienceDirect (open access)]

C.S. Parker, F. Deligianni, M.J. Cardoso, P. Daga, M. Modat, M. Dayan, C.A. Clark, S. Ourselin & J.D. Clayden (2014). Consensus between pipelines in structural brain networks. PLoS ONE 9(10):e111262. [PubMed; Public Library of Science (open access)]

F. Deligianni, M. Centeno, D.W. Carmichael & J.D. Clayden (2014). Relating resting-state fMRI and EEG whole-brain connectomes across frequency bands. Frontiers in Neuroscience 8:258. [Frontiers (open access)]

M. Grech-Sollars, D.E. Saunders, K.P. Phipps, R. Kaur, S.M.L. Paine, T.S. Jacques, J.D. Clayden & C.A. Clark (2014). Challenges for the functional diffusion map in paediatric brain tumours. Neuro-Oncology 16(3):449-456. [PubMed; Oxford University Press (open access)]

C.R. Gibbard, J. Ren, K.K. Seunarine, J.D. Clayden, D.H. Skuse & C.A. Clark (2013). White matter microstructure correlates with autism trait severity in a combined clinical-control sample of high-functioning adults. NeuroImage: Clinical 3:106-114. [PubMed; ScienceDirect (open access)]

A. Ranpura, E. Isaacs, C. Edmonds, M. Rogers, J. Lanigan, A. Singhal, J.D. Clayden, C.A. Clark & B. Butterworth (2013). Developmental trajectories of grey and white matter in dyscalculia. Trends in Neuroscience and Education 2(2):56-64. [ScienceDirect]

J.M. Kawadler, J.D. Clayden, F.J. Kirkham, T.C. Cox, D.E. Saunders & C.A. Clark (2013). Subcortical and cerebellar volumetric deficits in paediatric sickle cell anaemia. British Journal of Haematology 163(3):373-376. [PubMed; Wiley]

J. Bathelt, H. O'Reilly, J.D. Clayden, J.H. Cross & M. de Haan (2013). Functional brain network organisation of children between 2 and 5 years derived from reconstructed activity of cortical sources of high-density EEG recordings. NeuroImage 82:595-604. [PubMed; ScienceDirect]

J.D. Clayden, M. Dayan & C.A. Clark (2013). Principal networks. PLoS ONE 8(4):e60997. [pdf (1520 KiB); PubMed; Public Library of Science (open access)]

E.A. Webb, M.A. O'Reilly, J.D. Clayden, K.K. Seunarine, N. Dale, A. Salt, C.A. Clark & M.T. Dattani (2013). Reduced ventral cingulum integrity and increased behavioral problems in children with isolated optic nerve hypoplasia and mild to moderate or no visual impairment. PLoS ONE 8(3):e59048. [PubMed; Public Library of Science (open access)]

M. Grech-Sollars, D.E. Saunders, K. Phipps, J.D. Clayden & C.A. Clark (2012). Survival analysis for apparent diffusion coefficient measures in children with embryonal brain tumours. Neuro-Oncology 14(10):1285-1293. [PubMed; Oxford University Press]

J.D. Clayden, S. Jentschke, M. Muñoz, J.M. Cooper, M.J. Chadwick, T. Banks, C.A. Clark & F. Vargha-Khadem (2012). Normative development of white matter tracts: Similarities and differences in relation to age, gender and intelligence. Cerebral Cortex 22(8):1738-1747. [pdf (1632 KiB); PubMed; Oxford University Press]

E.A. Webb, M.A. O'Reilly, J.D. Clayden, K.K. Seunarine, W.K. Chong, N. Dale, A. Salt, C.A. Clark & M.T. Dattani (2012). Effect of growth hormone deficiency on brain structure, motor function and cognition. Brain 135(1):216-227. [PubMed; Oxford University Press]

J.M. Wardlaw, M.E. Bastin, M.C. Valdés Hernández, S. Muñoz Maniega, N.A. Royle, Z. Morris, J.D. Clayden, E.M. Sandeman, E. Eadie, C. Murray, J.M. Starr & I.J. Deary (2011). Brain ageing, cognition in youth and old age, and vascular disease in the Lothian Birth Cohort 1936: Rationale, design and methodology of the imaging protocol. International Journal of Stroke 6(6):547-559. [PubMed; Wiley]

M. Cutajar, J.D. Clayden, C.A. Clark & I. Gordon (2011). Test-retest reliability and repeatability of renal diffusion tensor MRI in healthy subjects. European Journal of Radiology 80(3):e263-e268. [PubMed; ScienceDirect]

J.D. Clayden, S. Muñoz Maniega, A.J. Storkey, M.D. King, M.E. Bastin & C.A. Clark (2011). TractoR: Magnetic resonance imaging and tractography with R. Journal of Statistical Software 44(8):1-18. [pdf (1876 KiB); Journal of Statistical Software (open access)]

K. Tabelow, J.D. Clayden, P. Lafaye de Micheaux, J. Polzehl, V.J. Schmid & B.J. Whitcher (2011). Image analysis and statistical inference in neuroimaging with R. NeuroImage 55(4):1686-1693. [PubMed; ScienceDirect]

L. Penke, S. Muñoz Maniega, C. Murray, A.J. Gow, M.C. Valdés Hernández, J.D. Clayden, J.M. Starr, J.M. Wardlaw, M.E. Bastin & I.J. Deary (2010). A general factor of brain white matter integrity predicts information processing speed in healthy older people. The Journal of Neuroscience 30(22):7569-7574. [PubMed; The Journal of Neuroscience]

M.E. Bastin, S. Muñoz Maniega, K.J. Ferguson, L.J. Brown, J.M. Wardlaw, A.M. MacLullich & J.D. Clayden (2010). Quantifying the effects of normal ageing on white matter structure using unsupervised tract shape modelling. NeuroImage 51(1):1-10. [PubMed; ScienceDirect]

L. Penke, S. Muñoz Maniega, L.M. Houlihan, C. Murray, A.J. Gow, J.D. Clayden, M.E. Bastin, J.M. Wardlaw & I.J. Deary (2010). White matter integrity in the splenium of the corpus callosum is related to successful cognitive aging and partly mediates the protective effect of an ancestral polymorphism in ADRB2. Behavior Genetics 40(2):146-156. [PubMed; SpringerLink]

J.D. Clayden, A.J. Storkey, S. Muñoz Maniega & M.E. Bastin (2009). Reproducibility of tract segmentation between sessions using an unsupervised modelling-based approach. NeuroImage 45(2):377-385. [pdf (1724 KiB); PubMed; ScienceDirect]

E. Sprooten, G.K.S. Lymer, S. Muñoz Maniega, J. McKirdy, J.D. Clayden, M.E. Bastin, D.J. Porteous, E.C. Johnstone, S.M. Lawrie, J. Hall & A.M. McIntosh (2009). The relationship of anterior thalamic radiation integrity to psychosis risk associated neuregulin-1 variants. Molecular Psychiatry 14(3):237-238. [PubMed; Nature Publishing Group]

M.E. Bastin, J.D. Clayden, A. Pattie, I.F. Gerrish, J.M. Wardlaw & I.J. Deary (2009). Diffusion tensor and magnetization transfer MRI measurements of periventricular white matter hyperintensities in old age. Neurobiology of Aging 30(1):125-136. [PubMed; ScienceDirect]

A.M. McIntosh, S. Muñoz Maniega, G.K.S. Lymer, J. McKirdy, J. Hall, J.E.D. Sussmann, M.E. Bastin, J.D. Clayden, E.C. Johnstone & S.M. Lawrie (2008). White matter tractography in bipolar disorder and schizophrenia. Biological Psychiatry 64(12):1088-1092. [PubMed; ScienceDirect]

M.E. Bastin, J.P. Piątkowski, A.J. Storkey, L.J. Brown, A.M. MacLullich & J.D. Clayden (2008). Tract shape modelling provides evidence of topological change in corpus callosum genu during normal ageing. NeuroImage 43(1):20-28. [PubMed; ScienceDirect]

J.D. Clayden, A.J. Storkey & M.E. Bastin (2007). A probabilistic model-based approach to consistent white matter tract segmentation. IEEE Transactions on Medical Imaging 26(11):1555-1561. [pdf (1040 KiB); PubMed; IEEE Xplore]

J.D. Clayden, M.E. Bastin & A.J. Storkey (2006). Improved segmentation reproducibility in group tractography using a quantitative tract similarity measure. NeuroImage 33(2):482-492. [pdf (1061 KiB); PubMed; ScienceDirect]

I.J. Deary, M.E. Bastin, A. Pattie, J.D. Clayden, L.J. Whalley, J.M. Starr & J.M. Wardlaw (2006). White matter integrity and cognition in childhood and old age. Neurology 66(4):505-512. [PubMed]

Full length conference papers

F. Deligianni, C.A. Clark & J.D. Clayden (2013). A framework to compare tractography algorithms based on their performance in predicting functional networks. In L. Shen, T. Liu, P.-T. Yap, H. Huang, D. Shen & C.-F. Westin (eds), Proceedings of the 3rd International Workshop on Multimodal Brain Image Analysis (MBIA). Lecture Notes in Computer Science, vol. 8159, pp. 211-221. Springer-Verlag. [SpringerLink]

J.D. Clayden, M.D. King & C.A. Clark (2009). Shape modelling for tract selection. In G.-Z. Yang, D.J. Hawkes, D. Rueckert, A. Noble & C. Taylor (eds), Proceedings of the 12th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI). Lecture Notes in Computer Science, vol. 5762, pp. 150-157. Springer-Verlag. [pdf (1056 KiB); SpringerLink]

J.D. Clayden, Z. Nagy, M.G. Hall, C.A. Clark & D.C. Alexander (2009). Active imaging with dual spin-echo diffusion MRI. In J.L. Prince, D.L. Pham & K.J. Myers (eds), Proceedings of the 21st International Conference on Information Processing in Medical Imaging (IPMI). Lecture Notes in Computer Science, vol. 5636, pp. 264-275. Springer-Verlag. [pdf (800 KiB); SpringerLink]

Selected peer-reviewed conference abstracts

J.D. Clayden, Z. Nagy, N. Weiskopf, D.C. Alexander & C.A. Clark (2013). Mapping axon radius in the human corpus callosum using dual spin-echo diffusion MRI. In Proceedings of the ISMRM 21st Scientific Meeting & Exhibition, Salt Lake City, USA; p. 2065. [pdf (172 KiB)]

J.D. Clayden, S. Muñoz Maniega, M.E. Bastin & C.A. Clark (2013). A comparison of two automated and probabilistic tract segmentation methods. In Proceedings of the ISMRM 21st Scientific Meeting & Exhibition, Salt Lake City, USA; p. 2140. [pdf (148 KiB)]

J.D. Clayden, S. Muñoz Maniega, A.J. Storkey, M.D. King, M.E. Bastin & C.A. Clark (2013). Tractography and connectivity analysis with the TractoR software package. In Proceedings of the ISMRM 21st Scientific Meeting & Exhibition, Salt Lake City, USA; p. 2139. [pdf (196 KiB)]

J.D. Clayden (2012). Principal networks: A new approach to graph-based neural connectivity analysis. In Proceedings of the 18th Annual Meeting of the Organization for Human Brain Mapping, Beijing, China. [pdf (2640 KiB)]

J.D. Clayden, P.W. Hales & C.A. Clark (2011). A Bayesian Markov chain Monte Carlo approach to estimating the IVIM diffusion–perfusion model. In Proceedings of the Annual Meeting of the ISMRM British Chapter, Manchester, UK; p. P11.

J.D. Clayden (2011). Robust and efficient white matter analysis using tract shape modelling and principal components analysis. In Proceedings of the ISMRM 19th Scientific Meeting & Exhibition, Montréal, Canada; p. 1934. [pdf (252 KiB)]

J.D. Clayden, S. Jentschke, M. Muñoz, J. Cooper, T. Banks, F. Vargha-Khadem & C.A. Clark (2010). Gender differences in the rate of white matter microstructural development during late childhood and adolescence. In Proceedings of the ISMRM-ESMRMB Joint Annual Meeting, Stockholm, Sweden; p. 2035. [pdf (493 KiB)]

J.D. Clayden & C.A. Clark (2010). On the importance of appropriate fibre population selection in diffusion tractography. In Proceedings of the ISMRM-ESMRMB Joint Annual Meeting, Stockholm, Sweden; p. 1679. [pdf (258 KiB)]

J.D. Clayden, C.J. Riney, J. Cooper, M. Muñoz & C.A. Clark (2009). Segmentation goodness-of-fit can modulate age effects on anisotropy. In Proceedings of the Annual Meeting of the ISMRM British Chapter, Cardiff, UK; p. P33.

J.D. Clayden, C.J. Riney, J. Cooper, M. Muñoz & C.A. Clark (2009). Segmentation and characterisation of white matter tracts in late childhood and adolescence. In Proceedings of the ISMRM 17th Scientific Meeting & Exhibition, Honolulu, USA; p. 1454. [pdf (140 KiB)]

J.D. Clayden, Z. Nagy, D.C. Alexander & C.A. Clark (2009). Axon radius estimation using optimised Stejskal–Tanner and dual spin-echo sequences at modest SNR. In Proceedings of the ISMRM 17th Scientific Meeting & Exhibition, Honolulu, USA; p. 1397. [pdf (80 KiB)]

J.D. Clayden & C.A. Clark (2009). Model-based streamline rejection for probabilistic tractography. In Proceedings of the ISMRM 17th Scientific Meeting & Exhibition, Honolulu, USA; p. 1440. [pdf (496 KiB)]

J.D. Clayden, A.J. Storkey & M.E. Bastin (2008). A comparison of seeding strategies for group tractography. In Proceedings of the ISMRM 16th Scientific Meeting & Exhibition, Toronto, Canada; p. 1839. [pdf (237 KiB)]

J.D. Clayden, A.J. Storkey & M.E. Bastin (2008). Probabilistic combination of tractography data from multiple seed points for white matter segmentation. In Proceedings of the ISMRM 16th Scientific Meeting & Exhibition, Toronto, Canada; p. 1840. [pdf (164 KiB)]

J.D. Clayden, A.J. Storkey & M.E. Bastin (2007). A probabilistic model-based approach to consistent white matter tract segmentation. In Proceedings of the ISMRM-ESMRMB Joint Annual Meeting, Berlin, Germany; p. 78. [pdf (127 KiB)]

J.D. Clayden, S. Zhang, S. Correia & D.H. Laidlaw (2007). Fine-grained comparison of anisotropy differences between groups of white matter tracts. In Proceedings of the ISMRM-ESMRMB Joint Annual Meeting, Berlin, Germany; p. 82. [pdf (138 KiB)]

J.D. Clayden, M.E. Bastin & A.J. Storkey (2006). Neighbourhood tractography: a new approach to seed point placement for group fibre tracking. In Proceedings of the Annual Meeting of the ISMRM British Chapter, Guildford, UK; p. P34. [pdf (422 KiB)]

J.D. Clayden, M.E. Bastin & A.J. Storkey (2006). Automated assessment of tract similarity in group diffusion MRI data. In Proceedings of the ISMRM 14th Scientific Meeting & Exhibition, Seattle, USA; p. 2742. [pdf (118 KiB)]

J.D. Clayden, D.K.S. Marjoram, M.E. Bastin, E.C. Johnstone & S.M. Lawrie (2005). Towards an automated method for white matter integrity comparison between populations. In Proceedings of the ESMRMB 22nd Annual Meeting, Basel, Switzerland; p. 508.


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