D. Alnæs, T. Kaufmann, G. Richard, E. Duff, M.H. Sneve, T. Endestad, J.E. Norvdvick, O.A. Andreassen, S.M. Smith, and L.T. Westlye.
Attentional load modulates large-scale functional brain connectivity beyond the core attention networks.
NeuroImage, 109:260-272, 2015.

J. Bijsterbosch, S. Smith, and S.J. Bishop.
Functional connectivity under anticipation of shock: correlates of trait anxious affect versus induced anxiety.
Journal of Cognitive Neuroscience, 27(9):1840-1853, 2015.

G.L. Colclough, M.J. Brookes, S.M. Smith, and M.W. Woolrich.
A symmetric multivariate leakage correction for MEG connectomes.
NeuroImage, 117:439-448, 2015.

E.P. Duff, W. Vennart, R. Wise, M.A. Howard, R.E. Harris, M. Lee, K. Wartolowska, V. Wanigasekera, F.J. Wilson, M. Whitlock, I. Tracey, M.W. Woolrich, and S.M. Smith.
Learning to identify CNS drug action and efficacy using multi-study fMRI data.
Science Translational Medicine, 7(274):274ra16, 2015.

L. Griffanti, O. Dipasquale, M.M. Laganà, R. Nemni, M. Clerici, S.M. Smith, G. Baselli, and F. Baglio.
Effective artifact removal in resting state fMRI data improves detection of DMN functional connectivity alteration in Alzheimer's disease.
Frontiers in Human Neuroscience, 9(449):10.3389/fnhum.2015.00449, 2015.

S.J. Harrison, M.W. Woolrich, E.C. Robinson, M.F. Glasser, C.F. Beckmann, M. Jenkinson, and S.M. Smith.
Large-scale Probabilistic Functional Modes from resting state fMRI.
NeuroImage, 109:217-231, 2015.

F. Jernerén, A.K. Elshorbagy, A. Oulhaj, S.M. Smith, H. Refsum, and A.D. Smith.
Brain atrophy in cognitively impaired elderly: the importance of long-chain omega-3 fatty acids and B-vitamin status in a randomized controlled trial.
American Journal of Clinical Nutrition, 102(1):215-221, 2015.

T. Kaufmann, K.C. Skåtun, D. Alnæs, N.T. Doan, E.P. Duff, S. Tønnesen, E. Roussos, T. Ueland, S.R. Aminoff, T.V. Lagerberg, I. Agartz, I.S. Melle, S.M. Smith, O.A. Andreassen, and L. Westlye.
Disintegration of sensorimotor brain networks in schizophrenia.
Schizophrenia Bulletin, 2015.
in press.

S. Smith, T. Nichols, D. Vidaurre, A. Winkler, T. Behrens, M. Glasser, K. Ugurbil, D. Barch, D. Van Essen, and K. Miller.
A positive-negative mode of population covariation links brain connectivity, demographics and behavior.
Nature Neuroscience, 2015.
in press.

A.M. Winkler, M.A. Webster, D. Vidaurre, T.E. Nichols, and S.M. Smith.
Multi-level block permutation.
NeuroImage, 2015.
in press.

A.P. Baker, M.J. Brookes, H.T. Luckhoo, I.A. Rezek, S.M. Smith, T.E.J. Behrens, P.J. Probert Smith, and M.W. Woolrich.
Fast transient networks in spontaneous human brain activity.
eLife, 3:e01867, 2014.

J. Bijsterbosch, S. Smith, S. Forster, O.P. John, and S. Bishop.
Resting state correlates of sub-dimensions of anxious affect.
Journal of Cognitive Neuroscience, 26(4):914-926, 2014.

M. Chiew, S.M. Smith, P.J. Koopmans, N.N. Graedel, T. Blumensath, and K.L. Miller.
k-t FASTER: Acceleration of FMRI data acquisition using low rank constraints.
Magnetic Resonance in Medicine, 74(2):353-364, 2014.

I.A. Clark, K.E. Niehaus, E.P. Duff, M.C. Di Simplicio, G.D. Clifford, S.M. Smith, C.E. Mackay, M.W. Woolrich, and E.A. Holmes.
First steps in using machine learning on fMRI data to predict intrusive memories of traumatic film footage.
Behaviour Research and Therapy, 62:37-46, 2014.

F.A. Cowdrey, N. Filippini, R. Park, S. Smith, and C. McCabe.
Increased resting state functional connectivity in recovered anorexia nervosa patients.
Human Brain Mapping, 35(2):483-91, 2014.

G. Douaud, A.R. Groves, C.K. Tamnes, L.T. Westlye, E. Duff, A. Engvig, K.B. Walhovd, A. James, A. Gass, A.U. Monsch, P.M. Matthews, A.M. Fjell, S.M. Smith, and H. Johansen-Berg.
A common brain network links development, aging and vulnerability to disease.
PNAS, 111(49):17648-17653, 2014.

N. Filippini, E. Zsoldos, R. Haapakoski, C.E. Sexton, A. Mahmood, Allan C.L., A. Topiwala, V. Valkanova, E.J. Brunner, M.J. Shipley, E. Auerbach, S. Moeller, K. Ugurbil, J. Xu, E. Yacoub, J. Andersson, J. Bijsterbosch, S. Clare, L. Griffanti, A.T. Hess, M. Jenkinson, K.L. Miller, G. Salimi-Khorshidi, S.N. Sotiropoulos, N.L. Voets, S.M. Smith, J.R. Geddes, A. Singh-Manoux, C.E. Mackay, M. Kivimäki, and K.P. Ebmeier.
Study protocol: the Whitehall II imaging sub-study.
BMC Psychiatry, 14:159, 2014.

L. Griffanti, G. Salimi-Khorshidi, C.F. Beckmann, E.J. Auerbach, G. Douaud, C.E. Sexton, E. Zsoldos, K. Ebmeier, N. Filippini, C.E. Mackay, S. Moeller, J.G. Xu, E. Yacoub, G. Baselli, K. Ugurbil, K.L. Miller, and S.M. Smith.
ICA-based artefact removal and accelerated fMRI acquisition for improved resting state network imaging.
NeuroImage, 95:232-247, 2014.

M. Mennes, M. Jenkinson, R. Valabregue, J.K. Buitelaar, C.F. Beckmann, and S. Smith.
Optimizing full-brain coverage in human brain MRI through population distributions of brain size.
NeuroImage, 98:513-520, 2014.

E.C. Robinson, S. Jbabdi, M.F. Glasser, J. Andersson, G.C. Burgess, M.P. Harms, S.M. Smith, D.C. Van Essen, and M. Jenkinson.
MSM: a new flexible framework for Multimodal Surface Matching.
NeuroImage, 100:414-426, 2014.

G. Salimi-Khorshidi, G. Douaud, C.F. Beckmann, M.F. Glasser, L. Griffanti, and S.M. Smith.
Automatic denoising of functional MRI data: Combining independent component analysis and hierarchical fusion of classifiers.
NeuroImage, 90:449-468, 2014.

S.M. Smith, A. Hyvärinen, G. Varoquaux, K.L. Miller, and C.F. Beckmann.
Group-PCA for very large fMRI datasets.
NeuroImage, 101:738-749, 2014.

C. Stagg, V. Bachtiar, U. Amadi, C. Gudberg, A. Ilie, C. Sampaio-Baptista, J. O'Shea, M. Woolrich, S. Smith, N. Fillipini, J. Near, and H. Johansen-Berg.
Local GABA concentration is related to network-level resting functional connectivity.
eLife, 3:e01465, 2014.

A.M. Winkler, G.R. Ridgway, M.A. Webster, S.M. Smith, and T.E. Nichols.
Permutation inference for the general linear model.
NeuroImage, 92:381-397, 2014.

D.M. Barch, G.C. Burgess, M.P. Harms, S.E. Petersen, B.L. Schlaggar, M. Corbetta, M.F. Glasser, S. Curtiss, S. Dixit, C. Feldt, D. Nolan, E. Bryant, T. Hartley, O. Footer, J.M. Bjork, R. Poldrack, S. Smith, H. Johansen-Berg, A.Z. Snyder, and Van Essen, D. - for the WU-Minn HCP Consortium.
Function in the Human Connectome: Task-fMRI and individual differences in behavior.
NeuroImage, 80:169-189, 2013.

T. Blumensath, S. Jbabdi, M.F. Glasser, D.C. Van Essen, K. Ugurbil, T.E. Behrens, and S.M. Smith.
Spatially constrained hierarchical parcellation of the brain with resting-state FMRI.
NeuroImage, 76:313-324, 2013.

M. de Groot, M.W. Vernooij, S. Klein, A. Ikram, F.M. Vos, S.M. Smith, W.J. Niessen, and J.L.R. Andersson.
Improving alignment in tract-based spatial statistics: evaluation and optimization of image registration.
NeuroImage, 76:400-411, 2013.

G. Douaud, R. Menke, A. Gass, A. Monsch, A. Rao, B. Whitcher, G. Zamboni, P. Matthews, M. Sollberger, and S. Smith.
Brain microstructure reveals early abnormalities more than two years prior to clinical progression from mild cognitive impairment to Alzheimer's disease.
Journal of Neuroscience, 33(5):2147-2155, 2013.

G. Douaud, H. Refsum, C.A. de Jager, R. Jacoby, T.E. Nichols, S.M. Smith, and A.D. Smith.
Preventing Alzheimer's disease-related gray matter atrophy by B-vitamin treatment.
PNAS, 110(23):9523-8, 2013.

M.F. Glasser, S.N. Sotiropoulos, J.A. Wilson, T.S. Coalson, B. Fischl, J.L. Andersson, J. Xu, S. Jbabdi, M. Webster, J.R. Polimeni, D.C. Van Essen, and Jenkinson, M. - for the WU-Minn HCP Consortium.
The minimal preprocessing pipelines for the Human Connectome Project.
NeuroImage, 80:105-124, 2013.

A. Hyvärinen and S.M. Smith.
Pairwise likelihood ratios for estimation of non-Gaussian structural equation models.
Journal of Machine Learning Research, 14:111-152, 2013.

S. Jbabdi, S.N. Sotiropoulos, and T. E. Behrens.
The topographic connectome.
Current Opinion in Neurobiology, 23(2):207-15, 2013.

S. Jbabdi, J.F. Lehman, S.N. Haber, and T. E. Behrens.
Human and monkey ventral prefrontal fibers use the same organizational principles to reach their targets: tracing versus tractography.
Journal of Neuroscience, 33(7):3190-201, 2013.

L. Larson-Prior, R. Oostenveld, S. Della Penna, G. Michalareas, F. Prior, A. Babajani-Feremi, J.-M. Schoffelen, L. Marzetti, F. de Pasquale, F. Di Pompeo, J. Stout, M. Woolrich, Q. Luo, R. Bucholz, P. Fries, V. Pizzella, G.L. Romani, M. Corbetta, and Snyder, A. - for the WU-Minn HCP Consortium.
Adding dynamics to the Human Connectome Project with MEG.
NeuroImage, 80:190-201, 2013.

D.S. Marcus, M.P. Harms, A.Z. Snyder, M. Jenkinson, J.A. Wilson, M.F. Glasser, D.M. Barch, K.A. Archie, G.C. Burgess, M. Ramaratnam, M. Hodge, W. Horton, R. Herrick, T. Olsen, M. McKay, M. House, M. Hileman, E. Reid, J. Harwell, T. Coalson, J. Schindler, J. Elam, S.W. Curtiss, and Van Essen, D. - for the WU-Minn HCP Consortium.
Human Connectome Project informatics: Quality control, database services, and data visualization.
NeuroImage, 80:202-219, 2013.

K.L. Ray, D.R. McKay, P.M. Fox, M.C. Riedel, A.M. Uecker, C.F. Beckmann, S.M. Smith, P.T. Fox, and A. Laird.
ICA model order selection of task co-activation networks.
Frontiers in Systems Neuroscience, 7(237):1-12, 2013.

S.M. Smith, J. Andersson, E.J. Auerbach, C.F. Beckmann, J. Bijsterbosch, G. Douaud, E. Duff, D.A. Feinberg, L. Griffanti, M.P. Harms, M. Kelly, T. Laumann, K.L. Miller, S. Moeller, S. Petersen, J. Power, G. Salimi-Khorshidi, A.Z. Snyder, A. Vu, M.W. Woolrich, J. Xu, E. Yacoub, K. Ugurbil, D.C. Van Essen, and Glasser, M. - for the WU-Minn HCP Consortium.
Resting-state fMRI in the Human Connectome Project.
NeuroImage, 80:144-168, 2013.

S.M. Smith, D. Vidaurre, C.F. Beckmann, M.F. Glasser, M. Jenkinson, K.L. Miller, T.E. Nichols, E. Robinson, G. Salimi-Khorshidi, M.W. Woolrich, D.M. Barch, K. Ugurbil, and D.C. Van Essen.
Functional connectomics from resting-state fMRI.
Trends in Cognitive Sciences, 17(12):666-682, 2013.

S.N. Sotiropoulos, S. Jbabdi, J. Xu, J.L. Andersson, S. Moeller, E.J. Auerbach, M.F. Glasser, M. Hernandez, G. Sapiro, M. Jenkinson, D. Feinberg, E. Yacoub, C. Lenglet, D.C. Van Essen, K. Ugurbil, and Behrens, T. - for the WU-Minn HCP Consortium.
Advances in diffusion MRI acquisition and processing in the Human Connectome Project.
NeuroImage, 80:125-143, 2013.

L. Tian, Y. Kong, J. Ren, G. Varoquaux, Y. Zang, and S. Smith.
Spatial vs. temporal features in ICA of resting-state fMRI - A quantitative and qualitative investigation in the context of response inhibition.
PLoS ONE, 8(6):e66572, 2013.

K. Ugurbil, J. Xu, E.J. Auerbach, S. Moeller, A. Vu, J.M. Duarte-Carvajalino, C. Lenglet, X. Wu, S. Schmitter, P.F. Van de Moortele, J. Strupp, G. Sapiro, F. De Martino, D. Wang, N. Harel, M. Garwood, L. Chen, D.A. Feinberg, S.M. Smith, K.L. Miller, S.N. Sotiropoulos, S. Jbabdi, J.L. Andersson, T.E.J. Behrens, M.F. Glasser, D.C. Van Essen, and Yacoub, E. - for the WU-Minn HCP Consortium.
Pushing spatial and temporal resolution for functional and diffusion MRI in the Human Connectome Project.
NeuroImage, 80:80-104, 2013.

D.C. Van Essen, S.M. Smith, D.M. Barch, T.E. Behrens, E. Yacoub, and Ugurbil, K. - for the WU-Minn HCP Consortium.
The WU-Minn Human Connectome Project: An overview.
NeuroImage, 80:62-79, 2013.

M. W. Woolrich and K. E. Stephan.
Biophysical network models and the human connectome.
Neuroimage, 80:330-338, Oct 2013.

J. Xu, S. Moeller, E.J. Auerbach, J. Strupp, S.M. Smith, D.A. Feinberg, E. Yacoub, and K. Ugurbil.
Evaluation of slice accelerations using multiband echo planar imaging at 3 Tesla.
NeuroImage, 83:991-1001, 2013.

G. Zamboni, G.K. Wilcock, G. Douaud, E. Drazich, E. McCulloch, N. Filippini, I. Tracey, J.C.W. Brooks, S.M. Smith, M. Jenkinson, and C.E. Mackay.
Resting functional connectivity reveals residual functional activity in Alzheimer's disease.
Biological Psychiatry, 74(5):375-83, 2013.

M. Battaglini, M. Jenkinson, and N. De Stefano.
Evaluating and reducing the impact of white matter lesions on brain volume measurements.
Human Brain Mapping, 33(9):2062-2071, 2012.

C.F. Beckmann.
Modelling with independent components.
NeuroImage, 62:891-901, 2012.

M.J. Donahue, H. Hoogduin, S.M. Smith, J.C.W. Siero, M. Chappell, N. Petridou, P. Jezzard, P.R. Luijten, and J. Hendrikse.
Spontaneous BOLD fMRI signal is modulated by behavioral state and correlates with evoked response in sensorimotor cortex: A 7.0 Tesla fMRI study.
Human Brain Mapping, 33(3):511-522, 2012.

E.P. Duff, A.J. Tractenberg, C.E. Mackay, M.A. Howard, F. Wilson, S.M. Smith, and M.W. Woolrich.
Task-driven ICA feature generation for accurate and interpretable prediction using FMRI.
NeuroImage, 60(1):189-203, 2012.

N. Filippini, L.D. Nickerson, C.F. Beckmann, K.P. Ebmeier, G.B. Frisoni, P.M. Matthews, S.M. Smith, and C.E. Mackay.
Age-related adaptations of brain function during a memory task are also present at rest.
NeuroImage, 59(4):3821-3828, 2012.

R. Gelineau-Morel, V. Tomassini, M. Jenkinson, H. Johansen-Berg, P. M. Matthews, and J. Palace.
The effect of hypointense white matter lesions on automated gray matter segmentation in multiple sclerosis.
Hum Brain Mapp, 33(12):2802-14, 2012.

A.R. Groves, S.M. Smith, A.M. Fjell, C.K. Tamnes, K.B. Walhovd, G. Douaud, M.W. Woolrich, and L.T. Westlye.
Benefits of multi-modal fusion analysis on a large-scale dataset: Life-span patterns of inter-subject variability in cortical morphometry and white matter microstructure.
NeuroImage, 63(1):365-380, 2012.

M.J. Hawrylycz, E.S. Lein, A.L. Guillozet-Bongaarts, E.H. Shen, L. Ng, J.A. Miller, L.N. van de Lagemaat, K.A. Smith, A. Ebbert, Z.L. Riley, C. Abajian, C.F. Beckmann, A. Bernard, D. Bertagnolli, A.F. Boe, P.M. Cartagena, M.M. Chakravarty, M. Chapin, J. Chong, R.A. Dalley, B.D. Daly, C. Dang, S. Datta, N. Dee, T.A. Dolbeare, V. Faber, D. Feng, D.R. Fowler, J. Goldy, B.W. Gregor, Z. Haradon, D.R. Haynor, J.G. Hohmann, S. Horvath, R.E. Howard, A. Jeromin, J.M. Jochim, M. Kinnunen, C. Lau, E.T. Lazarz, C. Lee, T.A. Lemon, L. Li, Y. Li, J.A. Morris, C.C. Overly, P.D. Parker, S.E. Parry, M. Reding, J.J. Royall, J. Schulkin, P.A. Sequeira, C.R. Slaughterbeck, S.C. Smith, A.J. Sodt, S. Sunkin, B.E. Swanson, M.P. Vawter, D. Williams, P. Wohnoutka, H.R. Zielke, D.H. Geschwind, P.R. Hof, S.M. Smith, C. Koch, S.G.N. Grant, and A.R. Jones.
An anatomically comprehensive atlas of the adult human brain transcriptome.
Nature, 489:391-399, 2012.

S. Jbabdi, Stamatios N. Sotiropoulos, Alexander M. Savio, Manuel Grana, and T. E. Behrens.
Model-based analysis of multishell diffusion MR data for tractography: How to get over fitting problems.
Magnetic Resonance in Medicine, 68(6):1846-55, 2012.

S. Jbabdi and T. E. Behrens.
Specialization: The connections have it.
Nature Neuroscience, 15(2):171-172, 2012.

M. Jenkinson, C.F. Beckmann, T.E.J. Behrens, M.W. Woolrich, and S.M. Smith.
NeuroImage, 62:782-790, 2012.

S.M. Smith, P.A. Bandettini, K.L. Miller, T.E.J. Behrens, K.J. Friston, O. David, T. Liu, M.W. Woolrich, and T.E. Nichols.
The danger of systematic bias in group-level FMRI-lag-based causality estimation.
NeuroImage, 59:1228-9, 2012.

S.M. Smith.
The future of FMRI connectivity.
NeuroImage, 62:1257-1266, 2012.

S.M. Smith, K.L. Miller, S. Moeller, J. Xu, E.J. Auerbach, M.W. Woolrich, C.F. Beckmann, M. Jenkinson, J. Andersson, M.F. Glasser, D. Van Essen, D. Feinberg, E. Yacoub, and K. Ugurbil.
Temporally-independent functional modes of spontaneous brain activity.
Proc Natl Acad Sci USA (PNAS), 109(8):3131-6, 2012.

M. Tondelli, G.K. Wilcock, P. Nichelli, C.A. De Jager, M. Jenkinson, and G. Zamboni.
Structural MRI changes detectable up to ten years before clinical Alzheimer's disease.
Neurobiology of Aging, 33(4):825.e25-825.e36, 2012.

A.J. Trachtenberg, N. Filippini, K.P. Ebmeier, S.M. Smith, F. Karpe, and C.E. Mackay.
The effects of APOE on the functional architecture of the resting brain.
NeuroImage, 59(1):565-572, 2012.

D.C. Van Essen, K. Ugurbil, E. Auerbach, D. Barch, T.E.J. Behrens, R. Bucholz, A. Chang, L. Chen, M. Corbetta, S.W. Curtiss, S. Della Penna, D. Feinberg, M.F. Glasser, N. Harel, A.C. Heath, L. Larson-Prior, D. Marcus, G. Michalareas, S. Moeller, R. Oostenveld, S.E. Petersen, F. Prior, B.L. Schlaggar, S.M. Smith, A.Z. Snyder, J. Xu, E. Yacoub, and WU-Minn HCP Consortium.
The Human Connectome Project: A data acquisition perspective.
NeuroImage, 62(4):2222-2231, 2012.

K. Wartolowska, M. G. Hough, M. Jenkinson, J. Andersson, B. P. Wordsworth, and I. Tracey.
Structural brain changes in rheumatoid arthritis.
Arthritis Rheum, 64(2):371-379, 2012.

K.E. Watkins, A. Cowey, A. Alexander, N. Fillipini, J. Kennedy, S.M. Smith, N. Ragge, and H. Bridge.
Language networks in anophthalmia: maintained hierarchy of processing in `visual' cortex.
Brain, 135(5):1566-1577, 2012.

M.W. Woolrich.
Bayesian inference in FMRI.
NeuroImage, 62:801-810, 2012.

C.A. Bishop, M. Jenkinson, J. Declerck, and D. Merhof.
Novel fast marching for automated segmentation of the hippocampus (fmash): Method and validation on clinical data.
NeuroImage, 55(3):1009-1019, 2011.

M.J. Brookes, M.W. Woolrich, H. Luckhoo, D. Price, J.R. Hale, M.C. Stephenson, G.R. Barnes, S.M. Smith, and P.G. Morris.
Investigating the electrophysiological basis of resting state networks using magnetoencephalography.
Proc Natl Acad Sci USA (PNAS), 108(40):16783-16788, 2011.

G. Douaud, S. Jbabdi, T. Behrens, R. Menke, A. Gass, A. Monsch, A. Rao, B. Whitcher, G. Kindlmann, P. Matthews, and S. Smith.
DTI measures in crossing-fibre areas: Increased diffusion anisotropy reveals early white matter alteration in MCI and mild Alzheimer's disease.
NeuroImage, 55(3):880-890, 2011.

N. Filippini, K.P. Ebmeier, B.J. MacIntosh, A.J. Trachtenberg, G.B. Frisoni, G.K. Wilcock, C.F. Beckmann, S.M. Smith, P.M. Matthews, and C.E. Mackay.
Differential effects of the APOE genotype on brain function across the lifespan.
NeuroImage, 54(1):602-610, 2011.

A.R. Groves, C.F. Beckmann, S.M. Smith, and M.W. Woolrich.
Linked independent component analysis for multimodal data fusion.
NeuroImage, 54(3):2198-2217, 2011.

ZT Kincses, S. Ropele, M. Jenkinson, M. Khalil, K. Petrovic, M. Loitfelder, C. Langkammer, E. Aspeck, M. Wallner-Blazek, S. Fuchs, et al.
Lesion probability mapping to explain clinical deficits and cognitive performance in multiple sclerosis.
Multiple Sclerosis Journal, 17(6):681-689, 2011.

A.R. Laird, P.M. Fox, S.B. Eickhoff, J.A. Turner, K.L. Ray, D.R. McKay, D.C. Glahn, C.F. Beckmann, S.M. Smith, and P.T. Fox.
Behavioral interpretations of intrinsic connectivity networks.
Journal of Cognitive Neuroscience, 23(12):4022-4037, 2011.

R. Leech, S. Kamourieh, C.F. Beckmann, and D.J. Sharp.
Fractionating the default mode network: Distinct contributions of the ventral and dorsal posterior cingulate cortex to cognitive control.
The Journal of Neuroscience, 31(9):3217-3224, 2011.

D.S. Marcus, J. Harwell, T. Olsen, M. Hodge, M.F. Glasser, F. Prior, M. Jenkinson, T. Laumann, S.W. Curtiss, and D.C. Van Essen.
Informatics and data mining tools and strategies for the Human Connectome Project.
Frontiers in Neuroinformatics, 5(4), 2011.

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

K. Murphy, B. van Ginneken, J.M. Reinhardt, S. Kabus, K. Ding, X. Deng, K. Cao, K. Du, G.E. Christensen, V. Garcia, T. Vercauteren, N. Ayache, O. Commowick, G. Malandain, B. Glocker, N. Paragios, N. Navab, V. Gorbunova, J. Sporring, M. de Bruijne, X. Han, M.P. Heinrich, J.A. Schnabel, M. Jenkinson, C. Lorenz, M. Modat, J.R. McClelland, S. , Ourselin, S.E.A. Muenzing, M.A. Viergever, D. De Nigris, D.L. Collins, T. Arbel, M. Peroni, R. Li, G.C. Sharp, A. Schmidt-Richberg, J. Ehrhardt, R. Werner, D. Smeets, D. Loeckx, G. Song, N. Tustison, B. Avants, J.C. Gee, M. Staring, S. Klein, B.C. Stoel, M. Urschler, M. Werlberger, J. Vandemeulebroucke, S. Rit, D. Sarrut, and J.P.W. Pluim.
Evaluation of registration methods on thoracic ct: The empire10 challenge.
IEEE transactions on medical imaging, 30(11):1901-1920, 2011.

R.G. Nunes, I. Drobnjak, S. Clare, P. Jezzard, and M. Jenkinson.
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.

B. Patenaude, S.M. Smith, D.N. Kennedy, and M. Jenkinson.
A Bayesian model of shape and appearance for subcortical brain segmentation.
NeuroImage, 56(3):907-922, 2011.

G. Salimi-Khorshidi, S.M. Smith, and T.E. Nichols.
Adjusting the effect of nonstationarity in cluster-based and TFCE inference.
NeuroImage, 54(3):2006-2019, 2011.

G. Salimi-Khorshidi, T.E. Nichols, S.M. Smith, and M.W. Woolrich.
Using Gaussian-process regression for meta-analytic neuroimaging inference based on sparse observations.
IEEE Trans. on Medical Imaging, 30(7):1401-1416, 2011.

J. Sallet, R. B. Mars, M. P. Noonan, J. L. Andersson, J. X. O'Reilly, S. Jbabdi, P. L. Croxson, M. Jenkinson, K. L. Miller, and M. F. Rushworth.
Social network size affects neural circuits in macaques.
Science, 334:697-700, Nov 2011.

S.M. Smith, K.L. Miller, G. Salimi-Khorshidi, M. Webster, C.F. Beckmann, T.E. Nichols, J.D. Ramsey, and M.W. Woolrich.
Network modelling methods for FMRI.
NeuroImage, 54:875-891, 2011.

A.C. Tziortzi, G.E. Searle, S. Tzimopoulou, C. Salinas, J.D. Beaver, M. Jenkinson, M. Laruelle, E.A. Rabiner, and R.N. Gunn.
Imaging dopamine receptors in humans with [11c]-(+)-phno: Dissection of d3 signal and anatomy.
Neuroimage, 54(1):264-277, 2011.

Anastasia Yendiki, Patricia Panneck, Priti Srinivasan, Allison Stevens, Lilla Zollei, Jean Augustinack, Ruopeng Wang, David Salat, Stefan Ehrlich, Tim Behrens, Saad Jbabdi, Randy Gollub, and Bruce Fischl.
Automated probabilistic reconstruction of white-matter pathways in health and disease using an atlas of the underlying anatomy.
Frontiers in Neuroinformatics, 5(00023), 2011.

B.B. Biswal, M. Mennes, X. Zuo, S. Gohel, C. Kelly, S.M. Smith, C.F. Beckmann, J.S. Adelstein, Others, and M.P. Milham.
Towards discovery science of human brain function.
Proc Natl Acad Sci USA (PNAS), 107(10):4734-9, 2010.

M Chappell, B MacIntosh, M Donahue, M Günther, P Jezzard, and MW Woolrich.
Separation of intravascular signal in multi-inversion time arterial spin labelling MRI.
Magnetic Resonance in Medicine, 63(5):1357-1365, 2010.

David M. Cole, Stephen M. Smith, and Christian F. Beckmann.
Advances and pitfalls in the analysis and interpretation of resting-state FMRI data.
Frontiers in Systems Neuroscience, 4(8):1-15, 2010.

I. Drobnjak, G.S. Pell, and M. Jenkinson.
Simulating the effects of time-varying magnetic fields with a realistic simulated scanner.
Magnetic Resonance Imaging, 28(7):1014-1021, 2010.

D.A. Feinberg, S. Moeller, S.M. Smith, E. Auerbach, S. Ramanna, M.F. Glasser, K.L. Miller, K. Ugurbil, and E. Yacoub.
Multiplexed echo planar imaging for sub-second whole brain FMRI and fast diffusion imaging.
PLoS ONE, 5(12):e15710, 2010.

D. Gallichan, J.L.R. Andersson, M. Jenkinson, M.D. Robson, and K.L. Miller.
Reducing distortions in diffusion-weighted echo planar imaging with a dual-echo blip-reversed sequence.
Magnetic Resonance in Medicine, 64(2):382-390, 2010.

A. Giorgio, K.E. Watkins, M. Chadwick, S. James, L. Winmill, G. Douaud, N. De Stefano, P.M. Matthews, S.M. Smith, H. Johansen-Berg, and A.C. James.
Longitudinal changes in grey and white matter during adolescence.
NeuroImage, 49(1):94-103, 2010.

A. Giorgio, L. Santelli, V. Tomassini, R. Bosnell, S. Smith, N. De Stefano, and H. Johansen-Berg.
Age-related changes in grey and white matter structure throughout adulthood.
NeuroImage, 51(3):943-951, 2010.

D.C. Glahn, A.M. Winkler, P. Kochunov, L. Almasy, R. Duggirala, M.A. Carless, J.C. Curran, R.L. Olvera, A.R. Laird, S.M. Smith, C.F. Beckmann, P.T. Fox, and J. Blangero.
Genetic control over the resting brain.
Proc Natl Acad Sci USA (PNAS), 107(3):1223-1228, 2010.

S. Jbabdi, T. E. Behrens, and S. M. Smith.
Crossing fibres in tract-based spatial statistics.
Neuroimage, 49:249-256, 2010.

P. Kochunov, D.C. Glahn, J.L. Lancaster, A.M. Winkler, S. Smith, P.M. Thompson, L. Almasy, R. Duggirala, P.T. Fox, and J. Blangero.
Genetics of microstructure of cerebral white matter using diffusion tensor imaging.
NeuroImage, 53(3):1109-1116, 2010.

B MacIntosh, N Filippini, M Chappell, , MW Woolrich, C Mackay, and P Jezzard.
Assessment of arterial arrival times derived from multiple inversion time pulsed arterial spin labeling MRI.
Magnetic Resonance in Medicine, 63:641-647, 2010.

K.L. Miller, S.M. Smith, and P. Jezzard.
Asymmetries of the balanced SSFP profile. Part II: White matter.
Magnetic Resonance in Medicine, 63:396-406, 2010.

S.D. Roosendaal, M.M. Schoonheim, H.E. Hulst, E.J. Sanz-Arigita, S.M. Smith, J.J.G. Geurts, and F. Barkhof.
Resting state networks change in clinically isolated syndrome.
Brain, 2010.

A.D. Smith, S.M. Smith, C.A. de Jager, P. Whitbread, C. Johnston, G. Agacinski, A. Oulhaj, K.M. Bradley, R. Jacoby, and H. Refsum.
Homocysteine-lowering by B vitamins slows the rate of accelerated brain atrophy in mild cognitive impairment. A randomized controlled trial.
PLoS ONE, 5(9):e12244, 2010.

M. Zarei, B. Patenaude, J. Damoiseaux, C. Morgese, S. Smith, P.M. Matthews, F. Barkhof, S. Rombouts, E. Sanz-Arigita, and M. Jenkinson.
Combining shape and connectivity analysis: An MRI study of thalamic degeneration in Alzheimer's disease.
NeuroImage, 49:1-8, 2010.

T. Arichi, A. Moraux, A. Melendez, V. Doria, M. Groppo, N. Merchant, S. Combs, E. Burdet, D.J. Larkman, Counsell S.J., C.F. Beckmann, and A.D. Edwards.
Somatosensory cortical activation identified by functional mri in preterm and term infants.
NeuroImage, 2009.

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

T. E. Behrens, L. T. Hunt, and M. F. Rushworth.
The computation of social behavior.
Science, 324:1160-1164, 2009.

E. D. Boorman, T. E. Behrens, M. W. Woolrich, and M. F. Rushworth.
How green is the grass on the other side? Frontopolar cortex and the evidence in favor of alternative courses of action.
Neuron, 62:733-743, 2009.

M.A. Chappell, A.R. Groves, B. Whitcher, and M.W. Woolrich.
Variational Bayesian inference for a nonlinear forward model.
Signal Processing, IEEE Transactions on, 57(1):223-236, 2009.

O. Ciccarelli, T.E. Behrens, H. Johansen-Berg, K. Talbot, R.W. Orrell, R.S. Howard, R.G. Nunes, D.H. Miller, P.M. Matthews, A.J. Thompson, and S.M. Smith.
Investigation of white matter pathology in ALS and PLS using tract-based spatial statistics.
Human Brain Mapping, 30(2):615-624, 2009.

P. L. Croxson, M. E. Walton, J. X. O'Reilly, T. E. Behrens, and M. F. Rushworth.
Effort-based cost-benefit valuation and the human brain.
J. Neurosci., 29:4531-4541, 2009.

J.S. Damoiseaux, S.M. Smith, M.P. Witter, E.J. Sanz-Arigita, F. Barkhof, P. Scheltens, C.J. Stam, M. Zarei, and S.A.R.B. Rombouts.
White matter tract integrity in aging and Alzheimer's disease.
Human Brain Mapping, 30(4):1051-1059, 2009.

G. Douaud, C. Mackay, J. Andersson, S. James, D. Quested, M. Kar Ray, J. Connell, N. Roberts, T.J. Crow, P.M. Matthews, S. Smith, and A. James.
Schizophrenia delays and alters maturation of the brain in adolescence.
Brain, 132:2437-2448, 2009.

N. Filippini, B.J. MacIntosh, M.G. Hough, G.M. Goodwin, G.B. Frisoni, S.M. Smith, P.M. Matthews, C.F. Beckmann, and C.E. Mackay.
Distinct patterns of brain activity in young carriers of the APOE-e4 allele.
Proc Natl Acad Sci USA (PNAS), 106:7209-7214, 2009.

N. Filippini, M. Zarei, C. F. Beckmann, S. Galluzzi, G. Borsci, C. Testa, M. Bonetti, A. Beltramello, R. Ghidoni, L. Benussi, G. Binetti, and G. B. Frisoni.
Regional atrophy of transcallosal prefrontal connections in cognitively normal APOE-$\epsilon$4 carriers.
Journal of Magnetic Resonance Imaging, 29(5):1021-1026, 2009.

Adrian R Groves, Michael A Chappell, and Mark W Woolrich.
Combined spatial and non-spatial prior for inference on MRI time-series.
NeuroImage, 45(3):795-809, 2009.

C. Habas, N. Kamdar, D. Nguyen, K.E. Keller, C.F. Beckmann, V. Menon, and M.D. Greicius.
Distinct cerebellar contributions to intrinsic connectivity networks.
Journal of Neuroscience, 29:8586-8594, 2009.

S. Haller, G.A. Homola, K. Scheffler, C.F. Beckmann, and A.J. Bartsch.
Background MR gradient noise and non-auditory BOLD activations: A data-driven perspective.
Brain Research, 1282:74-83, 2009.

S. Jbabdi, M.W. Woolrich, and T.E.J. Behrens.
Multiple-subjects connectivity-based parcellation using hierarchical Dirichlet process mixture models.
NeuroImage, 44(2):373-384, 2009.

Gordon L. Kindlmann, Raúl San José Estépar, Stephen M. Smith, and Carl-Fredrik Westin.
Sampling and visualizing creases with scale-space particles.
IEEE Trans. Visualization and Computer Graphics, 15(6):1415-1424, Nov/Dec 2009.

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

L. Mancini, O. Ciccarelli, F. Manfredonia, J.S. Thornton, F. Agosta, F. Barkhof, C.F. Beckmann, N. De Stefano, C. Enzinger, F. Fazekas, M. Filippi, A. Gass, J. G. Hirsch, H. Johansen-Berg, L. Kappos, T. Korteweg, S.C. Manson, S. Marino, P.M. Matthews, X. Montalban, J. Palace, C. Polman, M. Rocca, S. Ropele, A. Rovira, C. Wegner, K. Friston, A. Thompson, and T Yousry.
Short-term adaptation to a simple motor task: a physiological process preserved in multiple sclerosis.
NeuroImage, 45(2):500-511, 2009.

R.K. Niazy, C.F. Beckmann, J.M. Brady, and S.M. Smith.
Performance evaluation of ensemble empirical mode decomposition.
Advances in Adaptive Data Analysis, 1(2):231-242, 2009.

J.X. O'Reilly, C.F. Beckmann, V. Tomassini, N. Ramnani, and H. Johansen-Berg.
Distinct and overlapping functional zones in the cerebellum defined by resting state functional connectivity.
Cerebral Cortex, 2009.

M. Pyka, C.F. Beckmann, S. Schöning, S. Hauke, D. Heider, H. Kugel, V. Arolt, and C. Konrad.
Impact of working memory load on fmri resting state pattern in subsequent resting phases.
PLoS ONE, 4(9), 2009.

S.A.R.B. Rombouts, J.S. Damoiseaux, R. Goekoop, F. Barkhof, P. Scheltens, S.M. Smith, and C.F. Beckmann.
Model-free group analysis shows altered BOLD FMRI networks in dementia.
Human Brain Mapping, 30(1):256-266, 2009.

Gholamreza Salimi-Khorshidi, Stephen M Smith, John R Keltner, Tor D Wager, and Thomas E Nichols.
Meta-analysis of neuroimaging data: A comparison of image-based and coordinate-based pooling of studies.
NeuroImage, 45(3):810-823, Jan 2009.

S.M. Smith and T.E. Nichols.
Threshold-free cluster enhancement: Addressing problems of smoothing, threshold dependence and localisation in cluster inference.
NeuroImage, 44(1):83-98, 2009.

S.M. Smith, P.T. Fox, K.L. Miller, D.C. Glahn, P.M. Fox, C.E. Mackay, N. Filippini, K.E. Watkins, R. Toro, A.R. Laird, and C.F. Beckmann.
Correspondence of the brain's functional architecture during activation and rest.
Proc Natl Acad Sci USA (PNAS), 106(31):13040-13045, 2009.

C. J. Stagg, J. O'Shea, Z. T. Kincses, M. Woolrich, P. M. Matthews, and H. Johansen-Berg.
Modulation of movement-associated cortical activation by transcranial direct current stimulation.
Eur. J. Neurosci., 30:1412-1423, Oct 2009.

Voets N.L., Adcock J.E., Stacey R., Hart Y., Carpenter K., Matthews P.M., and Beckmann C.F.
Functional and structural changes in the memory network associated with left temporal lobe epilepsy.
Human Brain Mapping, 2009.

M.W. Woolrich, S. Jbabdi, B. Patenaude, M. Chappell, S. Makni, T. Behrens, C. Beckmann, M. Jenkinson, and S.M. Smith.
Bayesian analysis of neuroimaging data in FSL.
NeuroImage, 45:S173-186, 2009.

M. Zarei, J. Damoiseaux, C. Morgese, C. Beckmann, S. Smith, P.M. Matthews, P. Scheltens, S. Rombouts, and F. Barkhof.
Regional white matter integrity differentiates between vascular dementia and Alzheimer's disease.
Stroke, 40:773-779, 2009.

J.L.R. Andersson.
Maximum a posteriori estimation of diffusion tensor parameters using a Rician noise model: Why, how and but.
NeuroImage, 42:1340-1356, 2008.

M. Battaglini, S.M. Smith, S. Brogi, and N. De Stefano.
Enhanced brain extraction improves the accuracy of brain atrophy estimation.
NeuroImage, 40(2):583-589, 2008.

T.E.J. Behrens, L.T. Hunt, M.W. Woolrich, and M.F.S. Rushworth.
Associative learning of social value.
Nature, 456:245-249, 2008.

R. Bosnell, C. Wegner, Z.T. Kincses, Y. Korteweg, F. Agosta, O. Ciccarelli, N. De Stefano, A. Gass, J. Hirsch, H. Johansen-Berg, L. Kappos, F. Barkhof, L. Mancini, F. Manfredonia, S. Marino, D.H. Miller, X. Montalban, J. Palace, M. Rocca, S. Ropele, A. Rovira, S. Smith, A. Thompson, J. Thornton, T. Yousry, B. Whitcher, M. Filippi, and P.M. Matthews.
Reproducibility of fMRI in the clinical setting: Implications for trial designs.
NeuroImage, 42(2):603-610, 2008.

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

D. K. Campbell-Meiklejohn, M. W. Woolrich, R. E. Passingham, and R. D. Rogers.
Knowing when to stop: the brain mechanisms of chasing losses.
Biol. Psychiatry, 63:293-300, 2008.

J.S. Damoiseaux, C.F. Beckmann, E.J. Sanz Arigita, F. Barkhof, P. Scheltens, C.J. Stam, S.M. Smith, and S.A.R.B. Rombouts.
Reduced resting-state brain activity in the 'default network' in normal aging.
Cerebral Cortex, 18(8):1856-1864, 2008.

M.A. Eckert, N.V. Kamdar, C.E. Chang, C.F. Beckmann, M.D. Greicius, and V. Menon.
A cross-modal system linking primary auditory and visual cortices: Evidence from intrinsic fmri connectivity analysis.
Human Brain Mapping, 29:848-857, 2008.

A. Giorgio, K.E. Watkins, G. Douaud, A.C. James, S. James, N. De Stefano, P.M. Matthews, S.M. Smith, and H. Johansen-Berg.
Changes in white matter microstructure during adolescence.
NeuroImage, 39(1):52-61, 2008.

A. Giorgio, M. Battaglini, S.M. Smith, and N. De Stefano.
Brain atrophy assessment in multiple sclerosis: Importance and limitations.
Neuroimaging Clinics of North America, 18(4):675-686, 2008.

A.K. Harvey, K.T.S. Pattinson, J.C.W. Brooks, S.D. Mayhew, M. Jenkinson, and R.G. Wise.
Brainstem functional magnetic resonance imaging: disentangling signal from physiological noise.
Journal of Magnetic Resonance Imaging, 28(6):1337-1344, 2008.

Z.T. Kincses, H. Johansen-Berg, V. Tomassini, R. Bosnell, P.M. Matthews, and C.F. Beckmann.
Model-free characterisation of brain functional networks for motor sequence learning usign fMRI.
NeuroImage, 39:1950-1958, 2008.

S. Makni, C. Beckmann, S. Smith, and M. Woolrich.
Bayesian deconvolution of FMRI data using bilinear dynamical systems.
NeuroImage, 42:1381-1396, 2008.

S.C. Manson, C. Wegner, M. Filippi, F. Barkhof, C. Beckmann, O. Ciccarelli, N. De Stefano, C. Enzinger, F. Fazekas, F. Agosta, A. Gass, J. Hirsch, H. Johansen-Berg, L. Kappos, T. Korteweg, C. Polman, L. Mancini, F. Manfredonia, S. Marino, D.H. Miller, X. Montalban, J. Palace, M. Rocca, S. Ropele, A. Rovira, S. Smith, A. Thompson, J. Thornton, T. Yousry, J.A. Frank, and P.M. Matthews.
Impairment of movement-associated brain deactivation in multiple sclerosis: Further evidence for a functional pathology of interhemispheric neuronal inhibition.
Experimental Brain Research, 187:25-31, 2008.

B.K. Puri, G.M. Bydder, M.S. Manku, A. Clarke, A.D. Waldman, and C.F. Beckmann.
Reduction in cerebral atrophy associated with ethyl-eicosapentaenoic acid treatment in patients with huntington's disease.
J IntMedRes, 36:896-905, 2008.

J.K. Rilling, M.F. Glasser, T.M. Preuss, X. Ma, T. Zhao, X. Hu, and T.E.J. Behrens.
The evolution of the arcuate fasiculus revealed with comparative DTI.
Nature Neuroscience, 11:426-428, 2008.

P. H. Rudebeck, T. E. Behrens, S. W. Kennerley, M. G. Baxter, M. J. Buckley, M. E. Walton, and M. F. Rushworth.
Frontal cortex subregions play distinct roles in choices between actions and stimuli.
J. Neurosci., 28:13775-13785, Dec 2008.

M. F. Rushworth and T. E. Behrens.
Choice, uncertainty and value in prefrontal and cingulate cortex.
Nat. Neurosci., 11:389-397, Apr 2008.

D. Sun, GW Stuart, M. Jenkinson, SJ Wood, PD McGorry, D. Velakoulis, TGM van Erp, PM Thompson, AW Toga, DJ Smith, et al.
Brain surface contraction mapped in first-episode schizophrenia: a longitudinal magnetic resonance imaging study.
Molecular Psychiatry, 14(10):976-986, 2008.

N. Voets, M. Hough, G. Douaud, P.M. Matthews, A. James, L. Winmill, P. Webster, and S.M. Smith.
Evidence for abnormalities of cortical development in adolescent-onset schizophrenia.
NeuroImage, 43:665-675, 2008.

A. Vogiatzoglou, H. Refsum, C. Johnston, S.M. Smith, K.M. Bradley, C. de Jager, M.M. Budge, and A.D. Smith.
Vitamin B12 status and rate of brain volume loss in community-dwelling elderly.
Neurology, 71:826-832, 2008.

K.E. Watkins, S.M. Smith, S. Davis, and P. Howell.
Structural and functional abnormalities of the motor system in developmental stuttering.
Brain, 131:50-59, 2008.

C. Wegner, M. Filippi, T. Korteweg, C. Beckmann, O. Ciccarelli, N. De Stefano, C. Enzinger, F. Fazekas, F. Agosta, A. Gass, J. Hirsch, H. Johansen-Berg, L. Kappos, F. Barkhof, C. Polman, L. Mancini, F. Manfredonia, S. Marino, D.H. Miller, X. Montalban, J. Palace, M. Rocca, S. Ropele, A. Rovira, S. Smith, A. Thompson, J. Thornton, T. Yousry, and P.M. Matthews.
Relating functional changes during hand movement to clinical parameters in patients with multiple sclerosis in a multi-centre fMRI study.
European Journal of Radiology, 15:113-122, 2008.

M. Woolrich.
Robust group analysis using outlier inference.
NeuroImage, 41(2):286-301, 2008.

A.R. Aron, T.E. Behrens, S. Smith, M.J. Frank, and R.A. Poldrack.
Triangulating a cognitive control network using diffusion-weighted MRI and functional MRI.
Journal of Neuroscience, 27(14):3743-3752, 2007.

P.R. Bannister, J.M. Brady, and M. Jenkinson.
Integrating temporal information with a non-rigid method of motion correction for functional magnetic resonance images.
Image and Vision Computing, 25(3):311-320, 2007.

A.J. Bartsch, G. Homola, A. Biller, S.M. Smith, H-G. Weijers, G.A. Wiesbeck, M. Jenkinson, N. De Stefano, L. Solymosi, and M. Bendszus.
Manifestations of early brain recovery associated with abstinence from alcoholism.
Brain, 130(1):36-47, 2007.

A.J. Bartsch, G.H. Homola, S. Thesen, P. Sahmer, R. Keim, C.F. Beckmann, A. Biller, C. Knaus, and M. Bendszus.
Scanning for the scanner: FMRI of audition by read-out omissions from echo-planar imaging.
NeuroImage, 35(1):234-243, 2007.

T.E.J. Behrens, H. Johansen-Berg, S. Jbabdi, M.F.S. Rushworth, and M.W. Woolrich.
Probabilistic diffusion tractography with multiple fibre orientations. What can we gain?
NeuroImage, 23:144-155, 2007.

T. E. Behrens, M. W. Woolrich, M. E. Walton, and M. F. Rushworth.
Learning the value of information in an uncertain world.
Nat. Neurosci., 10:1214-1221, 2007.

S. Cader, H. Johansen-Berg, M. Wylezinska, J. Palace, T.E. Behrens, S. Smith, and P.M. Matthews.
Discordant white matter N-acetylasparate and diffusion MRI measures suggest that chronic metabolic dysfunction contributes to axonal pathology in multiple sclerosis.
NeuroImage, 36(1):19-27, 2007.

N. De Stefano, M. Battaglini, and S.M. Smith.
Measuring brain atrophy in multiple sclerosis.
J Neuroimaging, 17s1:10-15S, 2007.

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

B. Jasperse, P. Valsasina, V. Neacsu, D.L. Knol, N. De Stefano, C. Enzinger, S.M. Smith, S. Ropele, T. Korteweg, A. Giorgio, V. Anderson, C.H. Polman, M. Filippi, D.H. Miller, M. Rovaris, F. Barkhof, H. Vrenken, and MAGNIMS.
Inter-center agreement of brain atrophy measurement in Multiple Sclerosis patients using manually edited SIENAX and SIENA.
Journal of Magnetic Resonance Imaging, 26:881-885, 2007.

B. Jasperse, H. Vrenken, E. Sanz-Arigita, V. de Groot, S.M. Smith, C.H. Polman, and F. Barkhof.
Regional brain atrophy development is related to specific aspects of clinical dysfunction in Multiple Sclerosis.
NeuroImage, 38(3):529-537, 2007.

S. Jbabdi, M.W. Woolrich, J.L. Andersson, and T.E.J. Behrens.
A Bayesian framework for global tractography.
NeuroImage, 37(1):116-129, 2007.

H. Johansen-Berg, V. Della-Maggiore, T.E.J. Behrens, S.M. Smith, and T. Paus.
Integrity of white matter in the corpus callosum correlates with bimanual co-ordination skills.
NeuroImage, 36 Supp. 2:T16-21, 2007.

J. Klein, T.E.J. Behrens, C.E. Mackay, M.D. Robson, and H. Johansen-Berg.
Connectivity-based parcellation of human cortex using diffusion MRI: Establishing reproducibility, validity and observer-independence in BA 44/45 and SMA/pre-SMA.
NeuroImage, 34(1):204-211, 2007.

P. Kochunov, P.M. Thompson, J.L. Lancaster, G. Bartzokis, S. Smith, T. Coyle, D.R. Royall, A. Laird, and P.T. Fox.
Relationship between white matter fractional anisotropy and other indices of cerebral health in normal aging: Tract-Based Spatial Statistics study of aging.
NeuroImage, 35(2):478-487, 2007.

K.L. Miller, S.M. Smith, P. Jezzard, G.C. Wiggins, and C.J. Wiggins.
Signal and noise characteristics of SSFP FMRI: A comparison with GRE at multiple field strengths.
NeuroImage, 37:1227-1236, 2007.

K.L. Miller, D.P. Bulte, H. Devlin, M.D. Robson, R.G. Wise, M.W. Woolrich, P. Jezzard, and T.E.J. Behrens.
Evidence for a vascular contribution to diffusion FMRI at high b-value.
Proc Natl Acad Sci USA (PNAS), 104:20967-20972, 2007.

S.M. Smith, M. Jenkinson, C.F. Beckmann, K.L. Miller, and M. Woolrich.
Meaningful design and contrast estimability in FMRI.
NeuroImage, 34(1):127-136, 2007.

S.M. Smith, H. Johansen-Berg, M. Jenkinson, D. Rueckert, T.E. Nichols, K.L. Miller, M.D. Robson, D.K. Jones, J.C. Klein, A.J. Bartsch, and T.E.J. Behrens.
Acquisition and voxelwise analysis of multi-subject diffusion data with Tract-Based Spatial Statistics.
Nature Protocols, 2(3):499-503, 2007.

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

M.E. Walton, P.L. Croxson, T.E.J. Behrens, S.W. Kennerley, and M.F.S Rushworth.
Adaptive decision making and value in the anterior cingulate cortex.
NeuroImage, 36 Supp. 2:T142-154, 2007.

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

C.F. Beckmann, M.J. Jenkinson, M.W. Woolrich, T.E.J. Behrens, D.E. Flitney, J.T. Devlin, and S.M. Smith.
Applying FSL to the FIAC data: Model-based and model-free analysis of voice and sentence repetition priming.
Human Brain Mapping, 27:380-391, 2006.

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

J.S. Damoiseaux, S.A.R.B. Rombouts, F. Barkhof, P. Scheltens, C.J. Stam, S.M. Smith, and C.F. Beckmann.
Consistent resting-state networks across healthy subjects.
Proc Natl Acad Sci USA, 103(37):13848-13853, 2006.

I. Drobnjak, D. Gavaghan, E. Suli, J. Pitt-Francis, and M. Jenkinson.
Development of a functional magnetic resonance imaging simulator for modelling realistic rigid-body motion artifacts.
Magnetic Resonance in Medicine, 56(2):364-380, 2006.

C. Enzinger, S. Smith, F. Fazekas, G. Drevin, S. Ropele, T. Nichols, T. Behrens, R. Schmidt, and P.M. Matthews.
Lesion probability maps of white matter hyperintensities in elderly individuals.
Journal of Neurology, 253(8):1064-70, 2006.

E. Heiervang, T.E.J. Behrens, C.E. Mackay, M.D. Robson, and H. Johansen-Berg.
Between session reproducibility and between subject variability of diffusion MR and tractography measures.
NeuroImage, 33(3):867-877, 2006.

S.W. Kennerley, M.E. Walton, T.E.J Behrens, M.J. Buckley, and M.F.S. Rushworth.
Optimal decision making and the anterior cingulate cortex.
Nature Neuroscience, 9(7):940-947, 2006.

S. D. Mayhew, G. D. Iannetti, M. W. Woolrich, and R. G. Wise.
Automated single-trial measurement of amplitude and latency of laser-evoked potentials (LEPs) using multiple linear regression.
Clin Neurophysiol, 117:1331-1344, Jun 2006.

K.L. Miller, S.M. Smith, P. Jezzard, and J.M. Pauly.
High-resolution FMRI at 1.5T using balanced SSFP.
Magnetic Resonance in Medicine, 55(1):161-170, 2006.

S.M. Smith, M. Jenkinson, H. Johansen-Berg, D. Rueckert, T.E. Nichols, C.E. Mackay, K.E. Watkins, O. Ciccarelli, M.Z. Cader, P.M. Matthews, and T.E.J. Behrens.
Tract-based spatial statistics: Voxelwise analysis of multi-subject diffusion data.
NeuroImage, 31:1487-1505, 2006.

G. Winterer, F. Musso, C.F. Beckmann, V. Mattay, M.F. Egan, D.W. Jones, J.H. Callicott, R. Coppola, and D.R. Weinberger.
Instability of prefrontal signal processing in schizophrenia.
American Journal of Psychiatry, 163:1960-1968, 2006.

M. Woolrich, P. Chiarelli, J. Perthen, and T.T. Liu.
Bayesian inference of haemodynamic changes in functional ASL data.
Magnetic Resonance in Medicine, 56:891-906, 2006.

M. Woolrich and T. Behrens.
Variational Bayes inference of spatial mixture models for segmentation.
IEEE Trans. on Medical Imaging, 25(10):1380-1391, 2006.

M. Zarei, H. Johansen-Berg, S. Smith, O. Ciccarelli, A.J. Thompson, and P.M. Matthews.
Functional anatomy of interhemispheric cortical connections in the human brain.
J Anat., 209:311-320, 2006.

C.F. Beckmann and S.M. Smith.
Tensorial extensions of independent component analysis for multisubject FMRI analysis.
NeuroImage, 25(1):294-311, 2005.

C.F. Beckmann, M. De Luca, J.T. Devlin, and S.M. Smith.
Investigations into resting-state connectivity using independent component analysis.
Philosophical Transactions of the Royal Society, 360(1457):1001-1013, 2005.

T.E.J. Behrens and H. Johansen-Berg.
Relating connectional architecture to grey matter function using diffusion imaging.
Philosophical Transactions of the Royal Society B, 360:903-911, 2005.

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

S.P. David, M.R. Munafò, H. Johansen-Berg, S.M. Smith, R.D. Rogers, P.M. Matthews, and R.T. Walton.
Ventral striatum/nucleus accumbens activation to smoking-related pictorial cues in smokers and nonsmokers: A functional magnetic resonance imaging study.
Biol Psychiatry, 58:488-494, 2005.

M. De Luca, C.F. Beckmann, N. De Stefano, P.M. Matthews, and S.M. Smith.
FMRI resting state networks define distinct modes of long-distance interactions in the human brain.
NeuroImage, 29(4):1359-1367, 2005.

M. De Luca, S. Smith, N. De Stefano, A. Federico, and P.M. Matthews.
Blood oxygenation level dependent contrast resting state networks are relevant to functional activity in the neocortical sensorimotor system.
Experimental Brain Research, 167(4):587-594, 2005.

C. Enzinger, F. Fazekas, P.M. Matthews, S. Ropele, H. Schmidt, S. Smith, and R. Schmidt.
Risk factors for progression of brain atrophy in aging. Six-year follow-up of normal subjects.
Neurology, 64:1704-1711, 2005.

G.D. Iannetti, R.K. Niazy, R.G. Wise, P. Jezzard, J.C.W. Brooks, L. Zambreanu, W. Vennart, P.M. Matthews, and I. Tracey.
Simultaneous recording of laser-evoked brain potentials and continuous, high-field functional magnetic resonance imaging in humans.
NeuroImage, 28(3):708-719, 2005.

H. Johansen-Berg, T.E.J Behrens, E.L. Sillery, O. Ciccarelli, C.A.M. Wheeler-Kingshott, A.J. Thompson, S.M. Smith, and P.M. Matthews.
Functional-anatomical validation and individual variation of diffusion tractography-based segmentation of the human thalamus.
Cerebral Cortex, 15:31-39, 2005.

R.K. Niazy, C.F. Beckmann, G.D. Iannetti, J.M. Brady, and S.M. Smith.
Removal of FMRI environment artifacts from EEG data using optimal basis sets.
NeuroImage, 28(3):720-737, November 2005.

C.N.L. Olivers, S. Smith, P. Matthews, and G.W. Humphreys.
Prioritizing new over old: An fMRI study of the preview search task.
Human Brain Mapping, 24(1):69-78, 2005.

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

R. Schmidt, S. Ropele, C. Enzinger, K. Petrovic, S. Smith, H. Schmidt, P.M. Matthews, and F. Fazekas.
White matter lesion progression, brain atrophy, and cognitive decline: The Austrian stroke prevention study.
Annals of Neurology, 58(4):610-616, October 2005.

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

M.W. Woolrich, T.E.J. Behrens, C.F. Beckmann, and S.M. Smith.
Mixture models with adaptive spatial regularisation for segmentation with an application to FMRI data.
IEEE Trans. on Medical Imaging, 24(1):1-11, 2005.

C.F. Beckmann and S.M. Smith.
Probabilistic independent component analysis for functional magnetic resonance imaging.
IEEE Trans. on Medical Imaging, 23(2):137-152, 2004.

J.T. Chen, S. Narayanan, D.L. Collins, S.M. Smith, P.M. Matthews, and D.L. Arnold.
Relating neocortical pathology to disability progression in multiple sclerosis using MRI.
NeuroImage, 23(3):1168-1175, 2004.

C. Enzinger, S. Ropele, S. Smith, S. Strasser-Fuchs, B. Poltrum, H. Schmidt, P.M. Matthews, and F. Fazekas.
Accelerated evolution of brain atrophy and black holes in MS patients with APOE-e4.
Annals of Neurology, 55(4):563-569, 2004.

M. Filippi, M. Rovaris, M. Inglese, F. Barkhof, N. De Stefano, S. Smith, and P.G. Comi.
Interferon beta-1a for brain tissue loss in patients at presentation with syndromes suggestive of multiple sclerosis: A randomised, double-blind, placebo-controlled trial.
Lancet, 364(9444):1489-1496, 2004.

S.M. Gobel, H. Johansen-Berg, T.E.J. Behrens, and M.F.S. Rushworth.
Parietal activation during number comparison is not number specific.
J Cogn Neurosci., 16:1536-51, 2004.

M. Jenkinson, J. Wilson, and P. Jezzard.
A perturbation method for magnetic field calculations of non-conductive objects.
Magnetic Resonance in Medicine, 52(3):471-477, 2004.

H. Johansen-Berg, T.E.J. Behrens, M.D. Robson, I. Drobnjak, M.F.S. Rushworth, J.M. Brady, S.M. Smith, D.J. Higham, and P.M. Matthews.
Changes in connectivity profiles define functionally distinct regions in human medial frontal cortex.
Proc Natl Acad Sci U S A, 101(36):13335-13340, 2004.

Narender Ramnani, Timothy E J Behrens, Will Penny, and Paul M Matthews.
New approaches for exploring anatomical and functional connectivity in the human brain.
Biol Psychiatry, 56(9):613-619, Nov 2004.

R.D. Rogers, N. Ramnani, C. Mackay, J.L. Wilson, P. Jezzard, C.S. Carter, and S.M. Smith.
Distinct portions of anterior cingulate cortex and medial prefrontal cortex are activated by reward processing in separable phases of decision-making cognition.
Biological Psychiatry, 55(6):594-602, March 2004.

S. Saini, N. De Stefano, S. Smith, L. Guidi, M.P. Amato, A. Federico, and P.M. Matthews.
Altered cerebellar functional connectivity mediates potential adaptive plasticity in patients with multiple sclerosis.
Journal of Neurology Neurosurgery and Psychiatry, 75:840-846, 2004.

S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews.
Advances in functional and structural MR image analysis and implementation as FSL.
NeuroImage, 23(S1):208-219, 2004.

S.M. Smith.
Overview of fMRI analysis.
British Journal of Radiology, 77:S167-175, 2004.

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

M.W. Woolrich, T.E.J. Behrens, C.F. Beckmann, M. Jenkinson, and S.M. Smith.
Multi-level linear modelling for FMRI group analysis using Bayesian inference.
NeuroImage, 21(4):1732-1747, 2004.

M.W. Woolrich, T.E.J. Behrens, and S.M. Smith.
Constrained linear basis sets for HRF modelling using Variational Bayes.
NeuroImage, 21(4):1748-1761, 2004.

C.F. Beckmann, M. Jenkinson, and S.M. Smith.
General multi-level linear modelling for group analysis in FMRI.
NeuroImage, 20:1052-1063, 2003.

T.E.J. Behrens, H. Johansen-Berg, M.W. Woolrich, S.M. Smith, C.A.M. Wheeler-Kingshott, P.A. Boulby, G.J. Barker, E.L. Sillery, K. Sheehan, O. Ciccarelli, A.J. Thompson, J.M. Brady, and P.M. Matthews.
Non-invasive mapping of connections between human thalamus and cortex using diffusion imaging.
Nature Neuroscience, 6(7):750-757, 2003.

T.E.J. Behrens, M.W. Woolrich, M. Jenkinson, H. Johansen-Berg, R.G. Nunes, S. Clare, P.M. Matthews, J.M. Brady, and S.M. Smith.
Characterization and propagation of uncertainty in diffusion-weighted MR imaging.
Magn Reson Med, 50(5):1077-1088, 2003.

N. De Stefano, P.M Matthews, M. Filippi, F. Agosta, M. De Luca, M.L. Bartolozzi, L. Guidi, A. Ghezzi, E. Montanari, A. Cifelli, A. Federico, and S.M. Smith.
Evidence of early cortical atrophy in MS.
Neurology, 60:1157-1162, 2003.

J. T. Devlin, J. Raley, E. Tunbridge, K. Lanary, A. Floyer-Lea, C. Narain, I. Cohen, T.E.J Behrens, P. Jezzard, P. M. Matthews, and D. R. Moore.
Functional asymmetry for auditiory processing in human primary auditory cortex.
J Neurosci., 23(37):11516-11522, 2003.

M. Jenkinson.
A fast, automated, n-dimensional phase unwrapping algorithm.
Magnetic Resonance in Medicine, 49(1):193-197, 2003.

H. Johansen-Berg.
Motor physiology: a brain of two halves,.
Current Biology, 13:R802-804, 2004.

J.L. Marchini and S.M. Smith.
On bias in the estimation of autocorrelations for fMRI voxel time-series analysis.
NeuroImage, 18(1):83-90, 2003.

P.M. Matthews, J. Adcock, Y. Chen, S. Fu, J.T. Devlin, M.F.S. Rushworth, S. Smith, C. Beckmann, and S. Iversen.
Towards understanding language organisation in the brain using fMRI.
Human Brain Mapping, 18(3):239-247, 2003.

A. Parry, S. Clare, M. Jenkinson, S.M. Smith, J. Palace, and P.M. Matthews.
MRI brain T1 relaxation time changes in MS patients increase over time in both the white matter and the cortex.
Journal of Neuroimaging, 13(3):234-9, 2003.

A.M.M. Parry, R.B. Scott, J. Palace, S. Smith, and P.M. Matthews.
Potentially adaptive functional changes in cognitive processing for patients with multiple sclerosis and their acute modulation by rivastigmine.
Brain, 126(12):2750-2760, 2003.

N. Walters, G. Egan, J.J. Kril, M. Kean, P. Waley, M. Jenkinson, and J.D. Watson.
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.

J. L. Wilson, M. Jenkinson, and P. Jezzard.
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.

S.J. Bantick, R.G. Wise, A. Ploghaus, S. Clare, S.M. Smith, and I. Tracey.
Imaging how attention modulates pain in humans using functional MRI.
Brain, 125(2):310-319, 2002.

Y. Chen, S. Fu, S.D. Iversen, S.M. Smith, and P.M. Matthews.
Testing for dual brain processing routes in reading: A direct contrast of Chinese character and Pinyin reading using fMRI.
Journal of Cognitive Neuroscience, 14(7):1088-1098, 2002.

N. De Stefano, S. Narayanan, S.J. Francis, S. Smith, M. Mortilla, M.L. Tartaglia, M.C. Bartolozzi, L. Guidi, A. Federico, and D.L. Arnold.
Diffuse axonal and tissue injury in patients with multiple sclerosis with low cerebral lesion load and no disability.
Arch. Neurol., 59(10):1565-71, 2002.

S. Fu, Y. Chen, S. Smith, S. Iversen, and P. Matthews.
Effects of word form on brain processing of written chinese.
NeuroImage, 17:1538-1548, 2002.

D. Hall, M. Gonçalves, S. Smith, P. Jezzard, M. Haggard, and J. Kornak.
A method for determining venous contribution to BOLD contrast functional activation.
Magnetic Resonance Imaging, 20(10):695-706, 2002.

M. Jenkinson, P.R. Bannister, J.M. Brady, and S.M. Smith.
Improved optimisation for the robust and accurate linear registration and motion correction of brain images.
NeuroImage, 17(2):825-841, 2002.

M. Jenkinson and J. M Brady.
A saliency-based hierarchy for local symmetries.
Image and Vision Computing, 20(2):85-101, 2002.

H. Johansen-Berg, H. Dawes, C. Guy, S.M. Smith, D.T. Wade, and P.M. Matthews.
Correlation between motor improvements and altered fMRI activity after rehabilitive therapy.
Brain, 125:2731--42, 2002.

A.C.H. Lee, T.W. Robbins, S. Smith, G.A. Calvert, I. Tracey, P. Matthews, and A.M. Owen.
Evidence for asymmetric frontal-lobe involvement in episodic memory from functional magnetic resonance imaging and patients with unilateral frontal-lobe excisions.
Neuropsychologia, 40(13):2420-2437, 2002.

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

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

S.M. Smith.
Fast robust automated brain extraction.
Human Brain Mapping, 17(3):143-155, November 2002.

K.A. Smith, A. Ploghaus, P. Cowen, J.M. McCleery, G.M. Goodwin, S. Smith, I. Tracey, and P.M. Matthews.
Cerebellar responses during anticipation of noxious stimuli in subjects recovered from depression.
British Journal of Psychiatry, 181:411-415, 2002.

V.L. Stevenson, S.M. Smith, P.M. Matthews, D.H. Miller, and A.J. Thompson.
Monitoring disease activity and progression in primary progressive multiple sclerosis using MRI: sub-voxel registration to identify lesion changes and to detect cerebral atrophy.
Journal of Neurology, 249(2):171-177, 2002.

I. Tracey, A. Ploghaus, J.S. Gati, S. Clare, S. Smith, R.S. Menon, and P.M. Matthews.
Imaging attentional modulation of pain in the periaqueductal gray in humans.
Journal of Neuroscience, 22(7):2748-2752, 2002.

J. L. Wilson, M. Jenkinson, I. de Araujo, M. L. Kringelbach, E . T. Rolls, and P. Jezzard.
Fast, fully automated global and local magnetic field optimisation for fmri of the human brain.
NeuroImage, 17(2):967-976, 2002.

J. Wilson, M. Jenkinson, and P. Jezzard.
Optimisation of static field homogeneity in human brain using diamagnetic passive shims.
Magnetic Resonance in Medicine, 48:906-914, 2002.

N. Evangelou, D. Konz, M.M. Esiri, S. Smith, J. Palace, and P.M. Matthews.
Size-selective neuronal changes in the anterior optic pathways suggest a differential susceptibility to injury in multiple sclerosis.
Brain, 124(9):1813-1820, 2001.

M. Jenkinson and S.M. Smith.
A global optimisation method for robust affine registration of brain images.
Medical Image Analysis, 5(2):143-156, 2001.

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

M.W. Woolrich, B.D. Ripley, J.M. Brady, and S.M. Smith.
Temporal autocorrelation in univariate linear modelling of FMRI data.
NeuroImage, 14(6):1370-1386, 2001.

Y. Zhang, M. Brady, and S. Smith.
Segmentation of brain MR images through a hidden Markov random field model and the expectation maximization algorithm.
IEEE Trans. on Medical Imaging, 20(1):45-57, 2001.

N. Evangelou, D. Konz, M.M. Esiri, S. Smith, J. Palace, and P.M. Matthews.
Regional axonal loss in the corpus callosum correlates with cerebral white matter lesion volume and distribution in multiple sclerosis.
Brain, 123(9):1845-1849, 2000.

H. Johansen-Berg, V. Christensen, M. Woolrich, and P.M. Matthews.
Attention to touch modulates activity in both primary and secondary somatosensory areas.
Neuroreport, 11(6):1237--41, 2000.

M. Lee, H. Reddy, H. Johansen-Berg, S. Pendlebury, M. Jenkinson, S. Smith, J. Palace, and P.M. Matthews.
The motor cortex shows adaptive functional changes to brain injury from multiple sclerosis.
Annals of Neurology, 47(5):606-613, 2000.

R. Pineiro, S.T. Pendlebury, S. Smith, D. Flitney, A.M. Blamire, P. Styles, and P.M. Matthews.
Relating MRI changes to motor deficit after ischemic stroke by segmentation of functional motor pathways.
Stroke, 31(1):672-9, March 2000.

H. Reddy, S. Narayanan, R. Arnoutelis, M. Jenkinson, J. Antel, PM Matthews, and DL Arnold.
Evidence for adaptive functional changes in the cerebral cortex with axonal injury from multiple sclerosis.
Brain, 123(11):2314-2320, 2000.

P.M. Hayton, M. Brady, S.M. Smith, and N. Moore.
A non-rigid registration algorithm for dynamic breast MR images.
Artificial Intelligence, 114:125-156, 1999.

M.A. Lee, S. Smith, J. Palace, S. Narayanan, N. Silver, L. Minicucci, M. Filippi, D.H. Miller, D.L. Arnold, and P.M. Matthews.
Spatial mapping of T2 and gadolinium-enhancing T1 lesion volumes in MS: Evidence for distinct mechanisms of lesion genesis?
Brain, 122:1261-1270, 1999.

M.A. Lee, S. Smith, J. Palace, and P.M. Matthews.
Defining multiple sclerosis disease activity using MRI T$_2$-weighted difference imaging.
Brain, 121:2095--2102, 1998.

S.M. Smith and J.M. Brady.
SUSAN - a new approach to low level image processing.
International Journal of Computer Vision, 23(1):45-78, May 1997.

S.M. Smith, G. Kindlmann, and S. Jbabdi.
Tract-based spatial statistics and other approaches for cross-subject comparison of local diffusion MRI parameters.
In A. Toga, editor, Brain Mapping: An Encyclopedic Reference. Academic Press: Elsevier, 2015.

S.M. Smith and G. Kindlmann.
Cross-subject comparison of local diffusion MRI parameters.
In H. Johansen-Berg and T. Behrens, editors, Imaging brain pathways - Diffusion MRI: from quantitative measurement to in-vivo neuroanatomy. Elsevier, 2009.

M.W. Woolrich, C.F. Beckmann, T.E. Nichols, and S.M. Smith.
Statistical analysis of fMRI data.
In M. Filippi, editor, fMRI Techniques and Protocols. Springer-Verlag, 2009.

M. Jenkinson.
Registration, atlases and cortical flattening.
In P. Jezzard, P.M. Matthews, and S.M. Smith, editors, Functional MRI: An Introduction to Methods. OUP, Oxford, 2001.

M. Jenkinson and S.M. Smith.
The role of registration in functional magnetic resonance imaging.
In J. Hajnal, D.J. Hawkes, and D. Hill, editors, Medical Image Registration, chapter 8. CRC Press, 2001.

S.M. Smith.
Overview of fMRI analysis.
In P. Jezzard, P.M. Matthews, and S.M. Smith, editors, Functional MRI: An Introduction to Methods. OUP, Oxford, 2001.

S.M. Smith.
Preparing fMRI data for statistical analysis.
In P. Jezzard, P.M. Matthews, and S.M. Smith, editors, Functional MRI: An Introduction to Methods. OUP, Oxford, 2001.

P. Jezzard, P.M. Matthews, and S.M. Smith, editors.
Functional MRI: An Introduction to Methods.
OUP, Oxford, 2001.

Stephen Smith 2015-09-02