FMRIB Crest

Mark Jenkinson

 University Crest

Publications


Journal Articles and Book Chapters

  1. Jenkinson M., Beckmann, C.F., Behrens, T.E., Woolrich, M.W., and Smith S.M.
    FSL
    NeuroImage, 2011 (in press).

  2. Kong, Y., Jenkinson, M., Andersson, J., Tracey, I., and Brooks, J.C.
    Assessment of Physiological Noise Modelling Methods for Functional Imaging of the Spinal Cord
    NeuroImage, 2011 (in press).

  3. Kincses, Z.T., Szabó, N., Valálik, I., Kopniczky, Z., Dézsi, L., Klivényi, P., Jenkinson, M., Király, A., Babos, M., Vörös, E., Barzó, P., Vécsei, L.
    Target identification for stereotactic thalamotomy using diffusion tractography
    PLoS ONE, 2011 (in press).

  4. Patenaude, B., Smith, S.M., Kennedy, D., and Jenkinson M.
    A Bayesian Model of Shape and Appearance for Subcortical Brain
    NeuroImage, 56(3):907-922, 2011.

  5. Sallet, J., Mars, R.B., Noonan, M.P., Andersson, J.L., O'Reilly, J.X., Jbabdi, S., Croxson, P.L., Jenkinson, M., Miller, K.L., and Rushworth, M.F.S.
    Social Network Size Affects Neural Circuits in Macaques
    Science, 697-700, 4 November 2011.

  6. Wartolowska, K., Hough, M.G., Jenkinson, M., Andersson, J., Wordsworth, P.B., and Tracey, I.
    Structural brain changes in rheumatoid arthritis
    Arthritis and Rheumatism, 2011 (in press).

  7. Tondelli, M., Wilcock, G.K., Nichelli, P., de Jager, C., Jenkinson, M., and Zamboni, G.
    Structural MRI changes detectable up to ten years before clinical Alzheimer's disease
    Neurobiology of Aging, 2011 (in press).

  8. Gelineau-Morel, R., Tomassini, V., Jenkinson, M., Johansen-Berg, H., Matthews, P.M., and Palace, J.
    The effect of hypointense white matter lesions on automated grey matter segmentation in multiple sclerosis
    Human Brain Mapping, 2011 (in press).

  9. Marcus, D., Harwell, J., Olsen, T., Hodge, M., Glasser, M., Prior, F., Jenkinson, M., Laumann, T., Curtiss, S., and Van Essen, D.
    Informatics and Data Mining Tools and Strategies for the Human Connectome Project
    Frontiers in Neuroinformatics, 5, 2011.

  10. Murphy, K., van Ginneken, B., Reinhardt, J.M., Kabus, S., Ding, K., Deng, X., Cao, K., Du, K., Christensen, G.E., Garcia, V., Vercauteren, T., Ayache, N., Commowick, O., Malandain, G., Glocker, B., Paragios, N., Navab, N., Gorbunova, V., Sporring, J., de Bruijne, M., Han, X., Heinrich, M.P., Schnabel, J.A., Jenkinson, M., Lorenz, C., Modat, M., McClelland, J.R., , Ourselin, S., Muenzing, S.E.A., Viergever, M.A., De Nigris, D., Collins, D.L., Arbel, T., Peroni, M., Li, R., Sharp, G.C., Schmidt-Richberg, A., Ehrhardt, J., Werner, R., Smeets, D., Loeckx, D., Song, G., Tustison, N., Avants, B., Gee, J.C., Staring, M., Klein, S., Stoel, B.C., Urschler, M., Werlberger, M., Vandemeulebroucke, J., Rit, S., Sarrut, D., and Pluim, J.P.W.
    Evaluation of Registration Methods on Thoracic CT: The EMPIRE10 Challenge
    IEEE Transactions on Medical Imaging, 30(11):1901-20, 2011.

  11. Battaglini, M., Jenkinson, M., and De Stefano, N.
    Evaluating and Reducing the Impact of White Matter Lesions on Brain Volume Measurements
    Human Brain Mapping, 2011 (in press).

  12. Miller, K., Stagg, C.J., Douaud, G., Jbabdi, S. Smith, S.M., Behrens, T.E., Jenkinson, M., Chance, S.A., Esiri, M.M., Voets, N.L., Jenkinson, N., Aziz, T.Z., Turner, M., Johansen-Berg, H., and McNab, J.A.
    Diffusion imaging of whole, post-mortem human brains on a clinical MRI scanner
    NeuroImage, 57(1):167-181, 2011.

  13. Nunes, R.G., Drobnjak, I., Clare, S., Jezzard, P., Jenkinson, M.
    Performance of single spin-echo and doubly refocused diffusion-weighted sequences in the presence of eddy current fields with multiple components
    Magnetic Resonance Imaging, 29(5):659-667, 2011.

  14. Bishop, C.A., Jenkinson, M., Declerck, J., and Merhof, D.
    Novel Fast Marching for Automated Segmentation of the Hippocampus (FMASH): Method and Validation on Clinical Data
    NeuroImage, 55(3):1009-1019, 2011.

  15. Kincses, Z.T., Ropele, S., Jenkinson, M., Khalil, M., Petrovic, K., Loitfelder, M., Langkammer, C., Aspeck, E., Wallner-Blazek, M., Fuchs, S., Jehna, M., Schmidt, R., Vecsei, L., Fazekas, F., and Enzinger, C.
    Lesion probability mapping to explain clinical deficits and cognitive performance in multiple sclerosis
    Multiple Sclerosis, 17(6):681-689, 2011.

  16. Tziortzi, A.C., Searle, G.E., Tzimopoulou, S., Salinas, C., Beaver, J.D., Jenkinson, M., Laruelle, M., Rabiner, E.A. and Gunn, R.N.
    Imaging dopamine receptors in humans with [11C]-(+)-PHNO: Dissection of D3 signal and anatomy
    NeuroImage, 54(1):264-277, 2011.

  17. Drobnjak, I., Pell, G., and Jenkinson, M.
    Simulating the effects of time-varying magnetic fields with a realistic simulated scanner
    Magnetic Resonance Imaging, 28(7):1014-21, 2010.

  18. Zarei, M., Patenaude, B., Damoiseaux, J., Morgese, C., Smith, S., Matthews, P.M., Barkhof, F., Rombouts, S., Sanz-Arigita, E. and Jenkinson, M.
    Combining Shape and Connectivity Analysis: An MRI study of Thalamic Degeneration in Alzheimer's Disease
    NeuroImage, 49(1):1-8, 2010.

  19. Gallichan, D., Andersson, J.L.R., Jenkinson, M., Robson, M.D., and Miller, K.L.
    Reducing distortions in Diffusion-weighted Echo Planar Imaging with a dual- echo blip-reversed sequence
    Magnetic Resonance in Medicine, 64(2):382-90, 2009.

  20. Babalola, K.O., Patenaude, B., Aljabar, P., Schnabel, J., Kennedy, D., Crum, W., Smith, S., Cootes, T., Jenkinson, M. and Rueckert, D.
    An evaluation of four automatic methods of segmenting the subcortical structures in the brain.
    NeuroImage, 47(4):1435-1447, 2009.

  21. Woolrich, M., Jbabdi, S., Patenaude, B., Chappell, M., Makni, S., Behrens, T., Beckmann, C., Jenkinson, M., Smith, S.M.
    Bayesian Analysis of Neuroimaging Data in FSL
    NeuroImage, 45(1S1):173-186, 2009.

  22. Klein, A., Andersson, J., Ardekani, B.A., Ashburner, J., Avants, B., Chiang, M-C., Christensen, G.E., Collins, L., Hellier, P., Jenkinson, M., Lepage, C., Rueckert, D., Song, J H., Thompson, P., Vercauteren, T.., Woods, R.P., Mann, J.J. and Parsey, R.V.
    Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration
    NeuroImage, 46(3):786-802, 2009.

  23. Harvey, A.K., Pattinson, K.T.S., Brooks, J.C.W., Mayhew, S.D., Jenkinson, M., and Wise, R.G.
    Brainstem Functional Magnetic Resonance Imaging: Disentangling Signal From Physiological Noise
    JMRI, 28(6):1337-44, 2008.

  24. Sun, D., Stuart, G.W., Jenkinson, M., Wood, S.J., McGorry, P.D., Velakoulis, D., van Erp, T.G.M., Thompson, P.M., Toga, A.W., Smith, D.J., Cannon, T.D., and Pantelis, C.
    Brain surface contraction mapped in first-episode schizophrenia: a longitudinal magnetic resonance imaging study
    Molecular Psychiatry, 14(10):976-986, 2008.

  25. Brooks, J., Beckmann, C.F., Miller, K.L., Wise, R.G., Porro, C.A., Tracey, I., and Jenkinson, M.
    Physiological noise modelling for spinal functional magnetic resonance imaging studies
    NeuroImage, 39(2):680-692, 2008.

  26. Smith, S.M., Johansen-Berg, H., Jenkinson, M., Rueckert, D., Nichols, T.E., Miller, K.L., Robson, M.D., Jones, D.K., Klein, J.C., Bartsch, A.J., and Behrens, T.E.J.
    A Protocol for Acquisition and Voxelwise Analysis of Multi-Subject Diffusion Data with Tract-Based Spatial Statistics
    Nature Protocols, 2(3):499-503, 2007.

  27. Bartsch, A.J., Homola, G., Biller, A., Smith, S.M., Weijers, H-G., Wiesbeck, G.A., Jenkinson, M., De Stefano, N., Solymosi, L., and Bendszus, M.
    Manifestations of early brain recovery associated with abstinence from alcoholism
    Brain, 130:36-47, 2007.

  28. Smith, S.M., Jenkinson, M., Beckmann, C.F., Miller, K.L., and Woolrich, M.W.
    Meaningful Design and Contrast Estimability in FMRI
    Neuroimage, 34(1), 127-136, 2007.

  29. Bannister, P.R., Brady, J.M. and Jenkinson, M.
    Integrating Temporal Information with a Non-rigid Method of Motion Correction for Functional Magnetic Resonance Images
    Image and Vision Computing, 25(2), 311-320, 2007.

  30. Smith, S.M., Rao, A., De Stefano, N., Jenkinson, M., Schott, J.M., Matthews, P.M., and Fox, N.C.
    Longitudinal and cross-sectional analysis of atrophy in Alzheimer's disease: Cross-validation of BSI, SIENA and SIENAX.
    NeuroImage, 36(4):1200-1206, 2007.

  31. Douaud, G., Smith, S., Jenkinson, M., Behrens, T., Johansen-Berg, H., Vickers, J., James, S., Voets, N., Watkins, K., Matthews, P.M., and James, A.
    Anatomically-related grey and white matter abnormalities in adolescent-onset schizophrenia.
    Brain, 130:2375-2386, 2007.

  32. Zarei, M., Johansen-Berg, H., Jenkinson, M., Ciccarelli, O., Thompson, A.J. and Matthews, P.M.
    Two-dimensional population map of cortical connections in the human internal capsule
    Journal of Magnetic Resonance Imaging, 25(1), 48-54, 2007.

  33. Drobnjak, I., Gavaghan, D., Suli, E., Pitt-Francis, J., and Jenkinson, M.
    Development of an FMRI Simulator for Modelling Realistic Rigid-Body Motion Artifacts
    Magnetic Resonance in Medicine, 52(6), 364-380, 2006.

  34. Smith, S.M., Jenkinson, M., Johansen-Berg, H., Rueckert, D., Nichols, T., Mackay, C., Watkins, K., Ciccarelli, O., Cader, M., Matthews, P., and Behrens, T.
    Tract-Based Spatial Statistics: Voxelwise Analysis of Multi-Subject Diffusion Data
    Neuroimage, 31(4), 1487-1505, 2006.

  35. Beckmann, C.F., Jenkinson, M., Woolrich, M.W., Behrens, T.E.J., Flitney, D.E.F., Devin, J.T., and Smith, S.M.
    Applying FSL to the FIAC Data: Model-Based and Model-Free Analysis of Voice and Sentence Repetition Priming
    Human Brain Mapping, 27(5), 380-391, 2006.

  36. Behrens, T.E.J., Jenkinson, M., Robson, M.D., Smith, S.M., and Johansen-Berg, H.
    A consistent relationship between local white matter architecture and functional specialisation in medial frontal cortex
    Neuroimage, 30(1), 220-227, 2006.

  37. Bridge, H., Clare, S., Jenkinson, M., Jezzard, P., Parker, A.J., and Matthews, P.M.
    Independent anatomical and functional measures of the V1/V2 boundary in human visual cortex
    Journal of Vision, 5(2), 93-102, 2005.

  38. Osterbauer, R.A., Matthews, P.M., Jenkinson, M., Beckmann, C.F., Hansen, P.C., and Calvert, G.A.
    The color of scents: chromatic stimuli modulate odor responses in the human brain
    J Neurophysiol, 93(6): 3434-3441, 2005.

  39. Smith, S., Beckmann, C., Ramnani, N., Woolrich, M., Bannister, P., Jenkinson, M., Matthews, P., and McGonigle, D.
    Variability in FMRI: A re-examination of intersession differences
    Human Brain Mapping, 24(3), 248-257, 2005.

  40. Jenkinson, M., Wilson, J., and Jezzard, P.
    A Perturbation Method for Magnetic Field Calculations of Non-Conductive Objects
    Magnetic Resonance in Medicine, 52(3), 471-477, 2004.

  41. Woolrich, M., Jenkinson, M., Brady, J. and Smith, S.
    Fully Bayesian spatio-temporal modelling of FMRI data
    IEEE Trans. on Medical Imaging, 23(2), 213-231, 2004.

  42. Woolrich, M.W., Behrens, T.E.J., Beckmann, C.F., Jenkinson, M. and Smith, S.M.
    Multi-Level Linear Modelling for FMRI Group Analysis Using Bayesian Inference
    Neuroimage, 21(4), 1732-1747, 2004.

  43. Smith, S.M., Jenkinson, M., Woolrich, M.W., Beckmann, C.F., Behrens, T.E.J., Johansen-Berg, H., Bannister, P.R., De Luca, M., Drobnjak, I., Flitney, D., Niazy, R., Saunders, J., Vickers, J., Zhang, Y., De Stefano, N., Brady, J.M. and Matthews, P.M.
    Advances in functional and structural MR image analysis and implementation as FSL
    Neuroimage, 23(S1), S208-S219, 2004.

  44. Jenkinson, M.
    A Fast, Automated, N-Dimensional Phase Unwrapping Algorithm
    Magnetic Resonance in Medicine, 49(1), 193-197, 2003.

  45. Walters, N., Egan, G., Kril, J.J., Kean, M., Waley, P., Jenkinson, M. and Watson, J.D.
    In vivo identification of human cortical areas using high-resolution MRI: an approach to cerebral structure-function correlation
    Proc Natl Acad Sci USA (PNAS), 100(5):2981-6, 2003.

  46. Beckmann, C.*, Jenkinson, M.* and Smith, S.
    General multi-level linear modelling for group analysis in FMRI
    NeuroImage, 20(2), 1052-1063, 2003.
    * the first two authors contributed equally

  47. Wilson, J. L., Jenkinson, M. and Jezzard, P.
    Protocol to Determine the Optimal Intra-Oral Passive Shim for Minimization of Susceptibility Artifact in Human Inferior Frontal Cortex
    NeuroImage, 19(4), 1802-1811, 2003.

  48. Behrens, T., Woolrich, M., Jenkinson, M., Johansen-Berg, H., Nunes, R., Clare, S., Matthews, P., Brady, J. and Smith, S.
    Characterisation and propagation of uncertainty in diffusion weighted MR imaging
    Magnetic Resonance in Medicine, 50(5), 1077-1088, 2003.

  49. Parry, A., Clare, S., Jenkinson, M., Smith, S.M., Palace, J. and Matthews PM.
    MRI brain T1 relaxation time changes in MS patients increase over time in both the white matter and the cortex
    In Journal of Neuroimaging, 13(3), 234-239, 2003.

  50. Jenkinson, M., Bannister, P., Brady, J. M. and Smith, S. M.
    Improved Optimisation for the Robust and Accurate Linear Registration and Motion Correction of Brain Images
    NeuroImage, 17(2), 825-841, 2002.

  51. Wilson, J. L., Jenkinson, M., de Araujo, I., Kringelbach, M. L., Rolls, E. T. and Jezzard, P.
    Fast, Fully Automated Global and Local Magnetic Field Optimisation for fMRI of the Human Brain
    NeuroImage, 17(2), 967-976, 2002.

  52. Wilson, J., Jenkinson, M. and Jezzard, P.
    Optimisation of Static Field Homogeneity in Human Brain Using Diamagnetic Passive Shims
    Magnetic Resonance in Medicine, 48(5), 906-914, 2002.

  53. Jenkinson, M. and Brady, J. M.
    A Saliency-Based Hierarchy for Local Symmetries
    Image and Vision Computing, 20(2), 85-101, 2002.

  54. Smith, S.M., Zhang, Y., Jenkinson, M., Chen, J., Matthews, P., Federico, A. and De Stefano, N.
    Accurate, robust and automated longitudinal and cross-sectional brain change analysis
    NeuroImage, 17(1), 479-489, 2002.

  55. Parry, A., Clare, S., Jenkinson, M., Smith, S. M., Palace, J. and Matthews, P. M.
    White matter and lesion T1 relaxation times increase in parallel and correlate with disability in multiple sclerosis
    In Journal of Neurology, 249 (9), 1279-1286, 2002.

  56. Jenkinson, M. and Smith, S. M.
    A Global Optimisation Method for Robust Affine Registration of Brain Images
    Medical Image Analysis, 5(2), 143-156, 2001.

  57. Smith, S. M., De Stefano, N., Jenkinson, M. and Matthews, P. M.
    Normalised accurate measurement of longitudinal brain change
    Journal of Computer Assisted Tomography, 25(3), 466-475, 2001.

  58. Jenkinson, M.
    Structural Imaging in fMRI: Registration, Atlases and Cortical Flattening
    Chapter in Functional Magnetic Resonance Imaging of the Brain: An Introductory Guide, Eds. P. Jezzard, P.M. Matthews and S.M. Smith, 2001, Oxford University Press

  59. Jenkinson, M. and Smith, S. M.
    The Role of Registration in Functional Magnetic Resonance Imaging
    Chapter 8 in Medical Image Registration, Ed. J. V. Hajnal, D. L. G. Hill and D. J. Hawkes June 2001, CRC Press

  60. Reddy, H., Narayanan, S., Arnoutelis, R., Jenkinson, M., Antel, J., Matthews, P.M. and Arnold, D.L.
    Evidence for Adaptive Functional Changes in the Cerebral Cortex with Axonal Injury from Multiple Sclerosis
    In Brain, 123(11):2314-2320, 2000.

  61. Lee, M., Reddy, H., Johansen-Berg, H., Pendlebury, S., Jenkinson, M., Smith, S., Palace, J. and Matthews, P.M.
    The Motor Cortex Shows Adaptive Functional Changes to Brain Injury from Multiple Sclerosis
    In Annals of Neurology, 47(5):606-613, 2000.

  62. Jenkinson, M.
    Saliency in Image Analysis
    D. Phil. Thesis, Robotics Research Group, Department of Engineering Science, University of Oxford, 1999.


Refereed Conference Proceedings

  1. Petrovic, A., Smith, S.M., Menke, R.A., and Jenkinson, M.
    Methods for Tractography-Driven Surface Registration of Brain Structures
    Lecture Notes in Computer Science, Medical Image Computing and Computer Assisted Intervention (MICCAI), 2009.

  2. Poynton, C., Jenkinson, M. and Wells, W.
    Atlas-based Improved Prediction of Magnetic Field Inhomogeneity for Distortion Correction of EPI data
    Lecture Notes in Computer Science, Medical Image Computing and Computer Assisted Intervention (MICCAI), 2009.

  3. Poynton, C., Jenkinson, M., Whalen, S., Golby A.J., and Wells, W.
    Fieldmap-Free Retrospective Registration and Distortion Correction for EPI-based Functional Imaging
    Lecture Notes in Computer Science, Medical Image Computing and Computer Assisted Intervention (MICCAI) 271-279, 2008.

  4. Babalola, K., Patenaude, B., Aljabar, P., Schnabel, J., Kennedy, D., Crum, W., Smith, S., Cootes, T., Jenkinson, M., and Rueckert, D.
    Comparison and Evaluation of Segmentation Techniques for Sub-cortical Structures in Brain MRI Lecture Notes in Computer Science, Medical Image Computing and Computer Assisted Intervention (MICCAI) 409-416, 2008.

  5. Andersson, J., Smith, S., and Jenkinson, M.
    FNIRT - FMRIB's Non-linear Image Registration Tool
    In Fourteenth Annual Meeting of the Organization for Human Brain Mapping - HBM, 2008.

  6. Drobnjak, I., Pell, G., and Jenkinson, M.
    Effects of current timing and local shimming in neuronal current imaging: experiment and simulation
    In Fourteenth Annual Meeting of the Organization for Human Brain Mapping - HBM, 2008.

  7. Patenaude, B., Smith, S., Kennedy, D., and Jenkinson, M.
    Improved Surface Models for FIRST
    In Fourteenth Annual Meeting of the Organization for Human Brain Mapping - HBM, 2008.

  8. Patenaude, B., Jenkinson, M., Damoiseaux, J., Smith, S., Matthews, P., Barkhof, F., Rombouts, S., Sanz-Arigita, E., and Zarei, M.
    Regional thalamic degeneration in Alzheimer's disease characterised by structural vertex- and diffusion tractography-based analyses
    In Fourteenth Annual Meeting of the Organization for Human Brain Mapping - HBM, 2008.

  9. Gallichan, D., Andersson, J.L., Jenkinson, M., Robson, M.D., and Miller, K.L.
    Reducing distortions in DW-EPI with a dual-echo blip-reversed sequence
    In Fourteenth Annual Meeting of the Organization for Human Brain Mapping - HBM, 2008.

  10. Douaud, G., Smith, S., Andersson, J., Jenkinson, M., Matthews, P., and James, A.
    Longitudinal structural and diffusion imaging in adolescent-onset schizophrenia: a delayed brain maturation story?
    In Fourteenth Annual Meeting of the Organization for Human Brain Mapping - HBM, 2008.

  11. Breeze, J., Patenaude, B., Frazier, J., Jenkinson, M., Smith, S., and Kennedy, D.
    Comparison of FSL-FIRST with Manual Segmentation of Subcortical Brain Volumes.
    In Fourteenth Annual Meeting of the Organization for Human Brain Mapping - HBM, 2008.

  12. Brooks, J., Harvey, A., Pattinson, K., Jenkinson, M., and Wise, R.
    Improved Physiological Noise Modelling for Brainstem Functional Imaging
    In Proc. Int. Soc. of Magnetic Resonance in Medicine, 2008.

  13. Drobnjak, I., Pell, G., and Jenkinson, M.,
    Neuronal Current Imaging: Sensitivity of Magnitude and Spatial Distribution to Changes in Current Timing
    In Proc. Int. Soc. of Magnetic Resonance in Medicine, 2008.

  14. Gallichan, D., Andersson, J.L.R., Jenkinson, M., Robson, M.D., and Miller, K.L.
    Reducing Distortions in DW-EPI with a Dual-Echo Blip-Reversed Sequence
    In Proc. Int. Soc. of Magnetic Resonance in Medicine, 2008.

  15. Zollei, L., Jenkinson, M., Timoner, S., and Wells, W.
    A marginalized MAP approach and EM optimization for pair-wise registration.
    Inf Process Med Imaging, 20:662-74, 2007.

  16. Patenaude, B., Smith, S., Kennedy, D., and Jenkinson, M.
    FIRST - FMRIB's Integrated Registration and Segmentation Tool.
    In Thirteenth Annual Meeting of the Organization for Human Brain Mapping - HBM, 2007.

  17. Battaglini, M., Smith, S.M., Douaud, G., Jenkinson, M., Stromillo, M.L., Federico, A., Matthews, P.M., and De Stefano, N.
    Voxel-Based Analysis of Global and Neocortical Progression of Brain Atrophy in RR MS
    In Proc. Int. Soc. of Magnetic Resonance in Medicine, 2007.

  18. Douaud, G., Jenkinson, M., Vickers, J., McLeish, K., Waldman, A., Dresner, A., Counsell, S., Khanban, A., Rueckert, D., Hill, D., Hajnal, J., and Smith, S.M.
    Smoking: A TBSS and VBM-style investigation of white matter integrity and grey matter volume.
    In Proc. Int. Soc. of Magnetic Resonance in Medicine, 2007.

  19. Douaud, G., Smith, S.M., Vickers, J., Voets, N., James, S., Jenkinson, M., Matthews, P.M., and James, A.
    Investigating structural abnormalities in adolescent-onset schizophrenic patients: A combined T1-weighted and diffusion-weighted study.
    In Proc. Int. Soc. of Magnetic Resonance in Medicine, 2007.

  20. Brooks, J.C., Jenkinson, M., Miller, K.L., Clare, S., and Tracey, I.
    Improved physiological noise modelling reveals expected pattern of spinal cord activation
    In Proc. Int. Soc. of Magnetic Resonance in Medicine, 2007.

  21. Smith, S.M., Rao, A., De Stefano, N., Jenkinson, M., Boyes, R.G., Schott, J.M., Matthews, P.M., and Fox, N.C.
    Relating Longitudinal and Cross-Sectional Analyses of Atrophy in Alzheimer's: BSI, SIENA and SIENAX
    In Proc. Int. Soc. of Magnetic Resonance in Medicine, 2007.

  22. Babalola, K.O., Cootes, T.F., Patenaude, B., Rao, A., and Jenkinson, M.
    Comparing the Similarity of Statistical Shape Models Using the Bhattacharya Metric
    Lecture Notes in Computer Science, Medical Image Computing and Computer Assisted Intervention (MICCAI), 142-150, 2006.

  23. Jenkinson, M.
    Constrained non-linear registration of EPI and structural images.
    In Twelfth Annual Meeting of the Organization for Human Brain Mapping - HBM, 2006.

  24. Brooks, J., Beckmann, C., Miller, K., Schweinhardt, P., Jenkinson, M., and Tracey, I.
    Independent component analysis (ICA) of physiological noise in spinal EPI images.
    In Twelfth Annual Meeting of the Organization for Human Brain Mapping, 2006.

  25. Brooks, J.C., Jenkinson, M., Clare, S., Beckmann, C., Miller, K., Schweinhardt, P., Wise, R., Gallichan, D., and Tracey, I.
    Strategies for modelling physiological noise in spinal EPI images.
    In Twelfth Annual Meeting of the Organization for Human Brain Mapping, 2006.

  26. Drobnjak, I., Beckmann, C.F., and Jenkinson, M.
    Quantification of motion-related artifacts in simulated fMRI data using ICA.
    In Proc. Int. Soc. of Magnetic Resonance in Medicine, page 2840, 2006.

  27. Hough, M.G., Jenkinson, M., Beckmann, C.F., and Smith, S.M.
    Comparison of the stability of sensitivity-matched thresholding techniques and the effect of removing structured noise.
    In Twelfth Annual Meeting of the Organization for Human Brain Mapping, 2006.

  28. Hough, M.G., Smith, S.M., Jenkinson, M., and Beckmann, C.F.
    Comparing DOF corrections for removing structured noise from FMRI time series.
    In Twelfth Annual Meeting of the Organization for Human Brain Mapping, 2006.

  29. Patenaude, B.M., Smith, S., Kennedy, D., and Jenkinson, M.
    Automated subcortical segmentation using statistical shape models.
    In Twelfth Annual Meeting of the Organization for Human Brain Mapping, 2006.

  30. Smith, S.M., Jenkinson, M., Johansen-Berg, H., Rueckert, D., Nichols, T.E., Mackay, C.E., Watkins, K.E., Ciccarelli, O., Cader, M.Z., Bartsch, A.J., Matthews, P.M., and Behrens, T.E.J.
    Voxel-based analysis of FA: TBSS.
    In Twelfth Annual Meeting of the Organization for Human Brain Mapping, 2006.

  31. Smith, S.M., Jenkinson, M., Johansen-Berg, H., Rueckert, D., Nichols, T.E., Mackay, C., Watkins, K.E., Ciccarelli, O., Cader, M.Z., Bartsch, A.J., Matthews, P.M., and Behrens, T.E.J.
    Tract-based spatial statistics: Voxelwise analysis of multi-subject diffusion data.
    In Proc. Int. Soc. of Magnetic Resonance in Medicine, page 443, 2006.

  32. Crum, W.R., Camara, O., Rueckert, D., Bhatia, K., Jenkinson, M. and Hill, D.L.G.
    Generalised Overlap Measures for Assessment of Pairwise and Groupwise Image Registration and Segmentation
    Lecture Notes in Computer Science, Medical Image Computing and Computer Assisted Intervention (MICCAI), 99-106, 2005.

  33. Jenkinson, M., Behrens, T.E.J., Woolrich, M.W., Crum, W.R., Hill, D.L.G., and Smith, S.M.
    A Bayesian Similarity Function for Segmentation using Anatomical, Shape-Based Models
    In Medical Image Understanding and Analysis (MIUA), 2005

  34. Jenkinson, M., Pechaud, M. and Smith, S.
    BET2 - MR-Based Estimation of Brain, Skull and Scalp Surfaces
    In Int. Conf. on Human Brain Mapping (HBM), 2005

  35. Nunes, R.G., Drobnjak, I., Clare, S., Jezzard, P., and Jenkinson, M.
    Quantitative simulation of affine registration for correction of eddy current distortions in diffusion-weighted images.
    In Int. Soc. of Magnetic Resonance in Medicine - ISMRM, 2005.

  36. Smith, S.M., Ning, F., Jenkinson, M., and Woolrich, M.
    Meaningful Contrast Estimability
    In Int. Conf. on Human Brain Mapping (HBM), 2005

  37. Behrens, T.E.J., Jenkinson, M., Robson, M., Smith, S.M., and Johansen-Berg, H.
    Diffusion Tensor Data Localises Functional Boundaries
    In Int. Soc. of Magnetic Resonance in Medicine - ISMRM2005

  38. Crum, W.R., Camara, O., Rueckert, D., Jenkinson, M. and Hill, D.L.G.
    Evaluating Atlas Segmentation of Multiple Structures Using Generalised Measures of Region Overlap
    In Medical Image Understanding and Analysis (MIUA), 2005

  39. Behrens, T.E.J., Jenkinson, M., Robson, M.D., Smith, S.M., and Johansen-Berg, H.
    A consistent relationship between local white matter architecture and functional specialisation in medial frontal cortex.
    In Eleventh Annual Meeting of the Organization for Human Brain Mapping, 2005.

  40. Drobnjak, I., Gavaghan, D., Suli, E., and Jenkinson, M.
    Application of an FMRI simulator in modeling the spin history effects.
    In Eleventh Annual Meeting of the Organization for Human Brain Mapping, 2005.

  41. Crum, W., Rueckert, D., Jenkinson, M., Kennedy, D. and Smith, S.
    A Framework For Detailed Objective Comparison of Non-Rigid Registration Algorithms in Neuroimaging
    Lecture Notes in Computer Science, Medical Image Computing and Computer Assisted Intervention (MICCAI), 679-686, 2004.

  42. Jenkinson, M.
    Improving the Registration of B0-distorted EPI Images using Calculated Cost Function Weights
    In Int. Conf. on Human Brain Mapping (HBM), 2004
        (download poster - ps)

  43. Drobnjak, I. and Jenkinson, M.
    FMRI simulation and its application in modelling the interaction of motion and B0-inhomogeneities
    In Int. Conf. on Human Brain Mapping (HBM), 2004

  44. The MIDAS Consortium: Boada, F., Collins, L., Drobnjak, I., Eddy, W., Evans, A., Griffin, M., Jenkinson, M., Noll, D., Pike, B., Shi, H., Shroff, D., Stenger, A., Worsley, K.
    MIDAS - A Multi-Site FMRI Simulator Consortium
    In Int. Conf. on Human Brain Mapping (HBM), 2004

  45. Drobnjak, I. and Jenkinson, M.
    Modelling FMRI motion artifacts using a simulated scanner
    In Int. Soc. of Magnetic Resonance in Medicine - ISMRM2004

  46. Non-rigid Motion Estimation and Spatio-temporal Realignment in FMRI
    Bannister, P.R., Brady, J.M., and Jenkinson, M.
    In 3rd IEEE Workshop on Articulated and Non-rigid Motion, IEEE Computer Society Conference on Computer Vision and Pattern Recognition - CVPR, Washinton D.C., June 2004

  47. TIGER: A New Model For Spatio-temporal Realignment Of FMRI Data
    Bannister, P.R., Brady, J.M., and Jenkinson, M.
    In Workshop on Computer Vision Approaches to Medical Image Analysis, 8th European Conference on Computer Vision - ECCV, Prague, May 2004

  48. Freire, L., Orchard, J., Jenkinson, M. and Mangin, J.F.
    Reducing activation-related bias in FMRI registration
    In 2nd International Conference on Medical Imaging and Augmented Reality, LNCS 3150, Beijing, China, August 2004

  49. Brodtmann, A., Puce, A., Jenkinson, M., Darby, D., and Donnan, G.A.
    Activated voxel counts correlate with brain volume measures on a group, not an individual, basis.
    In Tenth Annual Meeting of the Organization for Human Brain Mapping, 2004.

  50. Freire, L. and Jenkinson, M.
    A gradient-informed robust motion correction method for FMRI
    In 2nd Int. Workshop on Biomedical Image Registration, LNCS 2717, Springer-Verlag, pp. 377-386, Philadelphia, PA., USA, June 2003

  51. Wilson, J., Jenkinson, M. and Jezzard, P.
    Protocol to Determine the Optimal Intra-Oral Passive Shim for Susceptibility Minimization in Inferior Frontal Cortex
    In Int. Soc. of Magnetic Resonance in Medicine - ISMRM2003

  52. De Stefano, N., Jenkinson, M., Guidi, L., Bartolozzi, M.L., Federico, A., Smith, S.M.
    Voxel-Level Cross-Subject Statistical Analysis of Brain Atrophy in early Relapsing Remitting MS patients
    In Int. Soc. of Magnetic Resonance in Medicine - ISMRM2003

  53. Smith, S., Beckmann, C., Ramnani, N., Woolrich, M., Bannister, P., Jenkinson, M., Matthews, P. and McGonigle, D.
    Intersession variability in FMRI and the effect of different analysis methods
    In Int. Conf. on Human Brain Mapping (HBM), 2003

  54. Smith, S., Behrens, T., Jenkinson, M., Beckmann, C. and Woolrich, M.
    Multi-subject analysis: Specifying models
    In Int. Conf. on Human Brain Mapping (HBM), 2003

  55. Loftus, C., Jenkinson, M., Cunnington, R. and Egan, G.
    Optimizing temporal ICA of ERP data using spatial correlations
    In Int. Conf. on Human Brain Mapping (HBM), 2003

  56. Stuart, G., Sun, D., Jenkinson, M., Wood, S., Velakoulis, D., Yucel, M., McGorry, P. and Pantelis, C.
    Pattern of structural brain change in first episode psychosis, chronic schizophrenia and healthy controls
    In Int. Conf. on Human Brain Mapping (HBM), 2003

  57. Freire, L. and Jenkinson, M.
    A Gradient-informed Robust Motion Correction Method for FMRI
    In Int. Workshop on Biomedical Image Registration - WBIR, 2003.

  58. Jenkinson, M., Wilson, J. and Jezzard, P.
    Perturbation Calculation of B0 Field for Non-Conducting Materials
    In Int. Soc. of Magnetic Resonance in Medicine - ISMRM2002

  59. Jenkinson, M., Woolrich, M., Leibovici, D., Smith, S. M. and Beckmann, C.
    Group Analysis in FMRI using General Multi-Level Linear Modelling
    In Int. Conf. on Human Brain Mapping (HBM), 2002

  60. Bannister, P., Beckmann, C. and Jenkinson, M.
    Motion artefact decorrelation in FMRI analysis using ICA
    In Int. Soc. of Magnetic Resonance in Medicine - ISMRM2002

  61. Behrens, T., Jenkinson, M., Brady, J. and Smith, S.
    A probabilistic framework for estimating neural connectivity from diffusion weighted MRI
    In Int. Soc. of Magnetic Resonance in Medicine - ISMRM2002

  62. Behrens, T., Woolrich, M., Jenkinson, M., Brady, J. and Smith, S.
    Bayesian parameter estimation in diffusion weighted MRI
    In Int. Soc. of Magnetic Resonance in Medicine - ISMRM2002

  63. Wilson, J., Jenkinson, M. and Jezzard, P.
    A bit of a mouth full: susceptibility artifact reduction using diamagnetic passive shims
    In Int. Soc. of Magnetic Resonance in Medicine - ISMRM2002

  64. Bannister, P., Smith, S., Brady, M. and Jenkinson, M.
    Spatio-temporal realignment of FMRI data
    In Int. Conf. on Human Brain Mapping (HBM), 2002

  65. Behrens, T., Jenkinson, M., Woolrich, M., Brady, J. and Smith, S.
    Characterisation of uncertainty in diffusion weighted MRI
    In Int. Conf. on Human Brain Mapping (HBM), 2002

  66. Stuart, G., Abdalla, A., Jenkinson, M. and Pantelis, C.
    Global variation in brain structure and its relation to head shape
    In Int. Conf. on Human Brain Mapping (HBM), 2002

  67. Smith, S., Woolrich, M., Bannister, P., Beckmann, C., Behrens, T., Brady, M., Clare, S., De Luca, M., Flitney, D., Greve, D. and Jenkinson, M.
    FEAT - new developments
    In Int. Conf. on Human Brain Mapping (HBM), 2002

  68. Jenkinson, M.
    Improved Unwarping of EPI Volumes using Regularised B0 Maps
    In Int. Conf. on Human Brain Mapping (HBM), 2001
        (download poster - ps)

  69. Bannister, P. R. and Jenkinson, M.
    Robust affine motion correction in fMRI time series
    In Int. Conf. on Human Brain Mapping (HBM), 2001

  70. Bannister, P. R., Beckmann, C. F. and Jenkinson, M.
    Exploratory motion analysis in fMRI using ICA
    In Int. Conf. on Human Brain Mapping (HBM), 2001

  71. Smith, S., Zhang, Y., Jenkinson, M., Matthews, P. and De Stefano, N.
    SIENA: single and multiple time point brain atrophy analysis
    In Int. Conf. on Human Brain Mapping (HBM), 2001

  72. Smith, S., Bannister, P., Beckmann, C., Brady, M., Clare, S., Flitney, D., Hansen, P., Jenkinson, M., Leibovici, D., Ripley, B., Woolrich, M. and Zhang, Y.
    FSL: New tools for functional and structural brain image analysis
    In Int. Conf. on Human Brain Mapping (HBM), 2001

  73. Hall, D., Goncalves, M., Smith, S., Jezzard, P., Jenkinson, M. and Haggard, M.
    Venous contribution to high magnitude BOLD contrast activation
    In Int. Conf. on Human Brain Mapping (HBM), 2001

  74. Jenkinson, M. and Smith, S. M.
    Global optimisation for robust affine registration
    In Int. Conf. on Human Brain Mapping (HBM), 2000

  75. Smith, S., De Stefano, N., Jenkinson, M. and Matthews, P.
    SIENA - normalised accurate measurement of longitudinal brain change
    In Int. Conf. on Human Brain Mapping (HBM), 2000

  76. Smith, S. M. and Jenkinson, M..
    Accurate robust symmetry estimation
    Lecture Notes in Computer Science, Medical Image Computing and Computer Assisted Intervention (MICCAI), 308-317, 1999.

  77. Jenkinson, M. and Smith, S.M.
    An investigation of the robustness of registration methods
    In Int. Workshop on Biomedical Image Registration - WBIR, pages 200-210, 1999.

  78. Smith, S. M. and Jenkinson, M..
    Robust accurate symmetry plane estimation
    In Int. Workshop on Biomedical Image Registration - WBIR, pages 244-261, 1999.

  79. Smith, S. M. and Jenkinson, M..
    Accurate robust symmetry estimation
    In Medical Imaging Understanding and Analysis - MIUA 1999.