Jonathan D. Clayden

Photo

I am Associate Professor in neuroimaging and biophysics at the UCL Great Ormond Street Institute of Child Health (GOS 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.

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.

I collaborate with colleagues from across GOS ICH, as well as from other UCL departments—notably the Wellcome Trust Centre for Neuroimaging, Institute of Neurology and Centre for Medical Image Computing—and other universities. I also chair the GOS ICH equality, diversity and inclusion committee.

In addition to these pages, I have profiles on Google Scholar, ORCID, LinkedIn and GitHub. I tweet as @jonclayden and I’m also on Mastodon, which I favour since The Musking.

Contact details

Developmental Neurosciences Research and Teaching Department
UCL Great Ormond Street 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

Research

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!

UKCGE Recognised Research Supervisor

I supervise (advise) several PhD students, and have been recognised by the UK Council for Graduate Education, for my supervisory practice. If you are interested in doing a PhD with me, feel free to get in touch by e-mail to discuss your interests, but please be aware that most studentships are awarded through larger programmes such as the i4health Centre for Doctoral Training and GOS ICH Child Health Research PhD Programme. In these schemes, students apply to the programme as a whole in the first instance, go through an interview stage, and then meet potential supervisors and choose their projects once accepted. Do please make any queries specific, rather than generic.

Teaching

I currently teach on the UCL Masters-level courses in Neuroscience, Computer Graphics, Vision and Imaging, Physics and Engineering in Medicine, Advanced Neuroimaging and Advanced Biomedical Imaging. Further information on these courses is available through the preceding links.

I also give internal teaching lectures at GOS ICH on imaging-related topics. Slides for a reasonably recent (2016) 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; PubMed Central (open access)]

Other journal papers

S. Gurung, S. Karamched, D. Perocheau, K.K. Seunarine, T. Baldwin, H. Al Rashidi, L. Touramanidou, C. Duff, N. Elkhateeb, K.M. Stepien, R. Sharma, A. Morris, T. Hartley, L. Crowther, S. Grunewald, M. Cleary, H. Mundy, A. Chakrapani, S. Batzios, J. Davison, E. Footitt, K. Tuschl, R. Lachmann, E. Murphy, S. Santra, M.-L. Uudelepp, M. Yeo, P.F. Finn, A. Cavedon, S. Siddiqui, L. Rice, P.G.V. Martini, A. Frassetto, S. Heales, P.B. Mills, P. Gissen, J.D. Clayden, C.A. Clark, S. Eaton, T.L. Kalber & J. Baruteau (in press). The incidence of movement disorder increases with age and contrasts with subtle and limited neuroimaging abnormalities in argininosuccinic aciduria. To appear in Journal of Inherited Metabolic Disease. [PubMed; DOI direct link]

F. Young, K. Aquilina, K.K. Seunarine, L. Mancini, C.A. Clark & J.D. Clayden (2024). Fibre orientation atlas guided rapid segmentation of white matter tracts. Human Brain Mapping 45(2):e26578. [DOI direct link]

W. Lapidaire, J.D. Clayden, M.S. Fewtrell & C.A. Clark (2024). Increased white matter fibre dispersion and lower IQ scores in adults born preterm. Human Brain Mapping 45(1):e26545. [PubMed; DOI direct link]

J.D. Clayden, S. Hope, F. Argyri, S. Goksan, A. Stefani, L. Wei & F.J. Liegeois (2023). The impact of multiple language exposure on cognition during childhood: Evidence from the UK Millennium Cohort Study. Frontiers in Psychology 14:1158333. [PubMed; DOI direct link]

S. Hamdule, M. Kölbel, H. Stotesbury, R. Murdoch, J.D. Clayden, S. Sahota, A.M. Hood, C.A. Clark & F.J. Kirkham (2023). Effects of regional brain volumes on cognition in sickle cell anemia: A developmental perspective. Frontiers in Neurology 14:1101223. [PubMed; DOI direct link]

J.D. Clayden, H. Stotesbury, J.M. Kawadler, A. Slee, M. Koelbel, D.E. Saunders, A.M. Hood, O. Wilkey, M. Layton, B. Inusa, M. Pelidis, S. Chakravorty, D.C. Rees, J. Howard, M. Awogbade, C. Liossi, F.J. Kirkham & C.A. Clark (2023). Structural connectivity mediates the relationship between blood oxygenation and cognitive function in sickle cell anemia. Blood Advances 7(11):2297–2308. [PubMed; DOI direct link]

S.M. Toescu, P.W. Hales, J. Cooper, E.W. Dyson, K. Mankad, J.D. Clayden, K. Aquilina & C.A. Clark (2022). Arterial spin-labeling perfusion metrics in pediatric posterior fossa tumor surgery. American Journal of Neuroradiology 43(10):1508–1515. [PubMed; DOI direct link]

E. Powell, T. Schneider, M. Battiston, F. Grussu, A. Toosy, J.D. Clayden & C.A.M. Gandini Wheeler–Kingshott (2022). SENSE EPI reconstruction with 2D phase error correction and channel-wise noise removal. Magnetic Resonance in Medicine 88(5):2157–2166. [PubMed; DOI direct link]

H. Stotesbury, J.M. Kawadler, J.D. Clayden, D.E. Saunders, A.M. Hood, M. Koelbel, S. Sahota, D.C. Rees, O. Wilkey, M. Layton, M. Pelidis, B.P.D. Inusa, J. Howard, S. Chakravorty, C.A. Clark & F.J. Kirkham (2022). Quantification of silent cerebral infarction on high-resolution FLAIR and cognition in sickle cell anemia. Frontiers in Neurology 13:867329. [PubMed; DOI direct link]

W. Lapidaire, A. Lucas, J.D. Clayden, C.A. Clark & M.S. Fewtrell (2022). Human milk feeding and cognitive outcome in preterm infants: the role of infection and NEC reduction. Pediatric Research 91(5):1207–1214. [PubMed; DOI direct link]

S. Goksan, F. Argyri, J.D. Clayden, F. Liegeois & L. Wei (2020). Early childhood bilingualism: Effects on brain structure and function [version 2; peer review: 2 approved]. F1000Research 9:370. [PubMed; DOI direct link]

L.M. Lacerda, J.D. Clayden, S.E. Handley, G.P. Winston, E. Kaden, M. Tisdall, J.H. Cross, A. Liasis & C.A. Clark (2020). Microstructural investigations of the visual pathways in pediatric epilepsy neurosurgery: Insights from multi-shell diffusion magnetic resonance imaging. Frontiers in Neuroscience 14:269. [PubMed; DOI direct link]

T. Charalambous, J.D. Clayden, E. Powell, F. Prados, C. Tur, B. Kanber, D. Chard, S. Ourselin, C.A.M. Gandini Wheeler-Kingshott, A.J. Thompson & A.T. Toosy (2020). Disrupted principal network organisation in multiple sclerosis relates to disability. Scientific Reports 10(1):3620. [PubMed; DOI direct link]

J.D. Clayden, D.L. Thomas & A. Kraskov (2019). Tractography-based parcellation does not provide strong evidence of anatomical organisation within the thalamus. NeuroImage 199:418–426. [pdf (3420 KiB); preprint; PubMed; DOI direct link]

M. Córcoles-Parada, R. Giménez-Mateo, V. Serrano-Del-Pueblo, L. López, E. Pérez-Hernández, F. Mansilla, A. Martínez, I. Onsurbe, P. San Roman, M. Ubero-Martinez, J.D. Clayden, C.A. Clark & M. Muñoz-López (2019). Born too early and too small: Higher order cognitive function and brain at risk at ages 8-16. Frontiers in Psychology 10:1942. [PubMed; DOI direct link]

J. Muschelli, A. Gherman, J.-P. Fortin, B. Avants, B. Whitcher, J.D. Clayden, B.S. Caffo & C.M. Crainiceanu (2019). Neuroconductor: An R platform for medical imaging analysis. Biostatistics 20(2):218–239. [PubMed; DOI direct link]

C. Tur, F. Grussu, F. Prados, T. Charalambous, S. Collorone, B. Kanber, N. Cawley, D.R. Altmann, S. Ourselin, F. Barkhof, J.D. Clayden, A.T. Toosy, C.A.M. Gandini Wheeler-Kingshott & O. Ciccarelli (2019). A multi-shell multi-tissue diffusion study of brain connectivity in early multiple sclerosis. Multiple Sclerosis Journal 1352458519845105. [PubMed; DOI direct link]

T. Charalambous, C. Tur, F. Prados, B. Kanber, D.T. Chard, S. Ourselin, J.D. Clayden, C.A.M. Gandini Wheeler-Kingshott, A.J. Thompson & A.T. Toosy (2019). Structural network disruption markers explain disability in multiple sclerosis. Journal of Neurology, Neurosurgery & Psychiatry 90(2):219–226. [PubMed; DOI direct link]

C. Tur, A. Eshaghi, D.R. Altmann, T.M. Jenkins, F. Prados, F. Grussu, T. Charalambous, A. Schmidt, S. Ourselin, J.D. Clayden, C.A.M. Wheeler-Kingshott, A.J. Thompson, O. Ciccarelli & A.T. Toosy (2018). Structural cortical network reorganization associated with early conversion to multiple sclerosis. Scientific Reports 8(1):10715. [PubMed; DOI direct link]

H. Stotesbury, F.J. Kirkham, M. Kölbel, P. Balfour, J.D. Clayden, S. Sahota, S. Sakaria, D.E. Saunders, J. Howard, R. Kesse-Adu, B. Inusa, M. Pelidis, S. Chakravorty, D.C. Rees, M. Awogbade, O. Wilkey, M. Layton, C.A. Clark & J.M. Kawadler (2018). White matter integrity and processing speed in sickle cell anemia. Neurology 90(23):e2042–e2050. [PubMed; DOI direct link]

C.R. Gibbard, J. Ren, D.H. Skuse, J.D. Clayden & C.A. Clark (2018). Structural connectivity of the amygdala in young adults with autism spectrum disorder. Human Brain Mapping 39(3):1270–1282. [PubMed; DOI direct link]

E.A. Webb, L. Elliott, D. Carlin, M. Wilson, K. Hall, J. Netherton, J. Reed, T.G. Barrett, V. Salwani, J.D. Clayden, W. Arlt, N. Krone, A.C. Peet & A.G. Wood (2018). Quantitative MRI brain in congenital adrenal hyperplasia: In vivo assessment of the cognitive and structural impact of steroid hormones. The Journal of Clinical Endocrinology & Metabolism 103(4):1330–1341. [PubMed; DOI direct link]

S. Muñoz Maniega, M.E. Bastin, I.J. Deary, J.M. Wardlaw & J.D. Clayden (2018). Reference tracts and generative models for brain white matter tractography. Journal of Imaging 4(1):8. [DOI direct link]

C.S. Parker, J.D. Clayden, M.J. Cardoso, R. Rodionov, J.S. Duncan, C. Scott, B. Diehl & S. Ourselin (2018). Structural and effective connectivity in focal epilepsy. NeuroImage: Clinical 17:943–952. [PubMed; DOI direct link]

J.M. Kawadler, J.D. Clayden, C.A. Clark & F.J. Kirkham (2016). Intelligence quotient in paediatric sickle cell disease: A systematic review and meta-analysis. Developmental Medicine & Child Neurology 58(7):672–679. [PubMed; DOI direct link]

F.J. Liégeois, J. Butler, A.T. Morgan, J.D. Clayden & C.A. Clark (2016). Anatomy and lateralization of the human corticobulbar tracts: An fMRI-guided tractography study. Brain Structure and Function 221(6):3337–3345. [PubMed; DOI direct link]

F. Deligianni, D.W. Carmichael, G.H. Zhang, C.A. Clark & J.D. Clayden (2016). NODDI and tensor-based microstructural indices as predictors of functional connectivity. PLoS ONE 11(4):e0153404. [PubMed; DOI direct link]

K.K. Seunarine, J.D. Clayden, S. Jentschke, M. Muñoz, J.M. Cooper, M.J. Chadwick, T. Banks, F. Vargha-Khadem & C.A. Clark (2016). Sexual dimorphism in white matter developmental trajectories using tract-based spatial statistics. Brain Connectivity 6(1):37–47. [PubMed; DOI direct link]

J.D. Clayden, Z. Nagy, N. Weiskopf, D.C. Alexander & C.A. Clark (2016). Microstructural parameter estimation in vivo using diffusion MRI and structured prior information. Magnetic Resonance in Medicine 75(4):1787–1796. [pdf (2034 KiB); PubMed; DOI direct link]

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; DOI direct link]

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. [PubMed; DOI direct link]

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; DOI direct link]

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; DOI direct link]

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; DOI direct link]

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. [PubMed; DOI direct link]

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; DOI direct link]

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; DOI direct link]

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. [DOI direct link]

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; DOI direct link]

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; DOI direct link]

J.D. Clayden, M. Dayan & C.A. Clark (2013). Principal networks. PLoS ONE 8(4):e60997. [pdf (1520 KiB); PubMed; DOI direct link]

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; DOI direct link]

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; DOI direct link]

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; DOI direct link]

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; DOI direct link]

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; DOI direct link]

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; DOI direct link]

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; 2016 updated version]

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; DOI direct link]

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; DOI direct link]

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; DOI direct link]

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; DOI direct link]

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; DOI direct link]

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; DOI direct link]

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; DOI direct link]

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; DOI direct link]

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; DOI direct link]

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; DOI direct link]

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. Young, K. Aquilina, C.A. Clark & J.D. Clayden (2022). Fibre tract segmentation for intraoperative diffusion MRI in neurosurgical patients using tract-specific orientation atlas and tumour deformation modelling. International Journal of Computer Assisted Radiology and Surgery 17:1559–1567. [DOI direct link]

S. Muñoz Maniega, M.E. Bastin, I.J. Deary, J.M. Wardlaw & J.D. Clayden (2017). Improved reference tracts for unsupervised brain white matter tractography. In M. Valdés Hernández & V. González-Castro (eds), Medical Image Understanding and Analysis (MIUA). Communications in Computer and Information Science, vol. 723, pp. 425–435. Springer, Cham. [pdf (1464 KiB); DOI direct link]

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. [DOI direct link]

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); DOI direct link]

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); DOI direct link]

Selected 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)]

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)]

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.