Jonathan Clayden's home page

~ Jonathan D. Clayden

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; and at the University of Edinburgh.

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.

A general overview of major themes in my research is available, and may be a useful place to start if you are trying to work out whether my work is of interest to you! You can also find my profiles on Google Scholar and LinkedIn.

Contact

Imaging & Biophysics Unit
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

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.

Software

I am the main author and maintainer of the TractoR diffusion MRI analysis project, which consists of a set of tools for performing tractography and white matter segmentation using methods described in some of the publications listed below. TractoR is free software, available under the GPL licence (version 2).

I also maintain RNiftyReg, an R package built on top of the NiftyReg image registration tools developed at UCL; and an R implementation of the Self-Organising Migrating Algorithm, a general-purpose stochastic optimisation algorithm.

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

Publications

The following list is subdivided into 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.

Journal papers

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 (in press). Effect of growth hormone deficiency on brain structure, motor function and cognition. To appear in Brain. [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 (in press). Normative development of white matter tracts: Similarities and differences in relation to age, gender and intelligence. To appear in Cerebral Cortex. [pdf (1632 KiB); 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

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]

Peer-reviewed conference abstracts

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.

C.S. Parker, C.A. Clark & J.D. Clayden (2011). Reproducibility of whole-brain structural connectivity networks. In Proceedings of the Annual Meeting of the ISMRM British Chapter, Manchester, UK; p. P25.

M. Grech-Sollars, D. Saunders, K. Phipps, J.D. Clayden & C.A. Clark (2011). Survival analysis for apparent diffusion coefficient measures in children with embryonal brain tumours. In Proceedings of the Annual Meeting of the ISMRM British Chapter, Manchester, UK; p. P50.

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)]

E. A. Webb, M.A. O'Reilly, J.D. Clayden, K.K. Seunarine, T. Banks, W. Chong, N. Dale, A. Salt, M.T. Dattani & C. A. Clark (2011). Neuroanatomical associates of the cognitive and motor abnormalities found in children with Isolated Growth Hormone Deficiency. In Proceedings of the ISMRM 19th Scientific Meeting & Exhibition, Montréal, Canada; p. 2485.

K. K. Seunarine, J.D. Clayden, S. Jentschke, M. Muñoz, J. Cooper, M.J. Chadwick, T. Banks, F. Vargha-Khadem & C. A. Clark (2011). Sexual dimorphism in white matter development in pre-adolescence: a tract based spatial statistics study. In Proceedings of the ISMRM 19th Scientific Meeting & Exhibition, Montréal, Canada; p. 2001.

E.A. Webb, M.A. O'Reilly, J.D. Clayden, K.K. Seunarine, N. Dale, A. Salt, C.A Clark & M.T. Dattani (2010). Diffusion tensor imaging reveals specific white matter abnormalities in children with Isolated Growth Hormone Deficiency. In Proceedings of the 49th Annual Meeting of the European Society for Paediatric Endocrinology (ESPE), Prague, Czech Republic.

K. Tabelow, J.D. Clayden, P. Lafaye de Micheaux, J. Polzehl, V.J. Schmid & B.J. Whitcher (2010). Image analysis and statistical inference in neuroimaging with R. In Proceedings of the 16th Annual Meeting of the Organization for Human Brain Mapping, Barcelona, Spain. [pdf (1044 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)]

M. Cutajar, S.D. Marks, J.D. Clayden, C.A. Clark & I. Gordon (2010). Evaluation of the feasibility and reproducibility of renal DTI MRI in healthy volunteers. In Proceedings of the ISMRM-ESMRMB Joint Annual Meeting, Stockholm, Sweden; p. 4692.

S. Muñoz Maniega, L. Penke, M.C. Valdés Hernández, C. Murray, N.A. Royle, A.J. Gow, J.D. Clayden, J.M. Starr, M.E. Bastin, I.J. Deary & J.M. Wardlaw (2010). A multiparametric study of white matter integrity and cognition in old age. In Proceedings of the ISMRM-ESMRMB Joint Annual Meeting, Stockholm, Sweden; p. 1998.

C.S. Hill, J.D. Clayden, N. Kitchen, J. Bull, W. Harkness & C.A. Clark (2009). A feasibility study of neighbourhood tractography in the presence of paediatric brain tumours. In Proceedings of the Autumn Meeting of the Society of British Neurological Surgeons, Dublin, Republic of Ireland.

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.

E.A. Webb, M.A. O'Reilly, K.K. Seunarine, J.D. Clayden, N. Dale, A. Salt, C.A. Clark & M.T. Dattani (2009). Parahippocampal aberrations in children with growth hormone deficiency: A diffusion tensor imaging study. In Proceedings of the Annual Meeting of the ISMRM British Chapter, Cardiff, UK; p. O22.

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)]

M.E. Bastin, S. Muñoz Maniega, J.D. Clayden, A.J. Storkey, L.J. Brown & A.M. MacLullich (2009). Comparison of neighborhood tractography methods for segmenting white matter tracts in the aging brain. In Proceedings of the ISMRM 17th Scientific Meeting & Exhibition, Honolulu, USA; p. 1042. [pdf (72 KiB)]

S. Muñoz Maniega, L. Penke, J.D. Clayden, C. Murray, M.E. Bastin, A.J. Gow, J.M. Wardlaw & I.J. Deary (2009). Tract-specific white matter integrity and cognitive ability in youth and old age. In Proceedings of the ISMRM 17th Scientific Meeting & Exhibition, Honolulu, USA; p. 3236. [pdf (96 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)]

S. Muñoz Maniega, M.E. Bastin, A.M. McIntosh, S.M. Lawrie & J.D. Clayden (2008). Atlas-based reference tracts improve automatic white matter segmentation with neighbourhood tractography. In Proceedings of the ISMRM 16th Scientific Meeting & Exhibition, Toronto, Canada; p. 3318. [pdf (261 KiB)]

M.E. Bastin, J.D. Clayden, J.P. Piątkowski, A.J. Storkey, L.J. Brown & A.M. MacLullich (2008). Robust segmentation of white matter tracts in the aging brain. In Proceedings of the ISMRM 16th Scientific Meeting & Exhibition, Toronto, Canada; p. 2092. [pdf (76 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)]

M.E. Bastin, J.D. Clayden, A. Pattie, I.F. Gerrish, J.M. Wardlaw & I.J. Deary (2007). DTI and MTI parameters correlate in periventricular white matter hyperintensities in old age. In Proceedings of the ISMRM-ESMRMB Joint Annual Meeting, Berlin, Germany; p. 2160. [pdf (44 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.

I.J. Deary, M.E. Bastin, A. Pattie, J.D. Clayden & J.M. Wardlaw (2005). Cognitive ageing and white matter integrity: a diffusion tensor and magnetisation transfer MRI study. In Proceedings of the ISMRM 13th Scientific Meeting & Exhibition, Miami, USA. [pdf (25 KiB)]

I.J. Deary, M.E. Bastin, A. Pattie, J.D. Clayden, J.M. Starr & J.M. Wardlaw (2005). White matter integrity and cognition in childhood and old age: a diffusion tensor MRI study. Methods for Quantitative MRI of Human Brain. ISMRM Workshop, Lake Louise, Canada. [pdf (40 KiB)]

Everything not work related can be found on my other site. A slowly accumulating group of computing (LaTeX, UNIX, etc.) related tips may be of interest to some.