Research Topics
Species | Stephen M SmithSummaryAffiliation: University of Oxford Country: UK Publications
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Detail Information
Publications
Variability in fMRI: a re-examination of inter-session differencesStephen M Smith
Oxford Centre for Functional Magnetic Resonance Imaging of the Brain FMRIB, Department of Clinical Neurology, Oxford University, John Radcliffe Hospital, Headington, Oxford, United Kingdom
Hum Brain Mapp 24:248-57. 2005..Finally, we show that the use of different first-level preprocessing, time-series statistics, and registration analysis methodologies can give significantly different inter-session analysis results...- Tract-based spatial statistics: voxelwise analysis of multi-subject diffusion dataStephen M Smith
Oxford University Centre for Functional MRI of the Brain FMRIB, Dept Clinical Neurology, University of Oxford, UK
Neuroimage 31:1487-505. 2006..TBSS aims to improve the sensitivity, objectivity and interpretability of analysis of multi-subject diffusion imaging studies. We describe TBSS in detail and present example TBSS results from several diffusion imaging studies... - Acquisition and voxelwise analysis of multi-subject diffusion data with tract-based spatial statisticsStephen M Smith
Oxford University Centre for Functional Magnetic Resonance Imaging of the Brain, Oxford, UK
Nat Protoc 2:499-503. 2007..In this protocol, we describe the MRI data acquisition and analysis protocols required for TBSS studies of localized change in brain connectivity across multiple subjects... 
Threshold-free cluster enhancement: addressing problems of smoothing, threshold dependence and localisation in cluster inferenceStephen M Smith
FMRIB Oxford University Centre for Functional MRI of the Brain, Department of Clinical Neurology, University of Oxford, Oxford, UK
Neuroimage 44:83-98. 2009..We also show an example on a real imaging dataset, suggesting that TFCE does indeed provide not just improved sensitivity, but richer and more interpretable output than cluster-based thresholding...- The future of FMRI connectivityStephen M Smith
Oxford University Centre for Functional MRI of the Brain, UK
Neuroimage 62:1257-66. 2012.... 
Temporally-independent functional modes of spontaneous brain activityStephen M Smith
Oxford Centre for Functional Magnetic Resonance Imaging of the Brain, University of Oxford, Oxford OX3 9DU, United Kingdom
Proc Natl Acad Sci U S A 109:3131-6. 2012..These functionally distinct modes of spontaneous brain activity are, in general, quite different from resting-state networks previously reported, and may have greater biological interpretability...- Normalized accurate measurement of longitudinal brain changeS M Smith
Oxford Centre for Functional Magnetic Resonance Imaging of the Brain, Department of Clinical Neurology, University of Oxford, John Radcliffe Hospital, England
J Comput Assist Tomogr 25:466-75. 2001..New methods of change analysis attempt to improve robustness, accuracy, and extent of automation. A fully automated method has been developed that achieves high estimation accuracy... - Network modelling methods for FMRIStephen M Smith
FMRIB Oxford University Centre for Functional MRI of the Brain, Department of Clinical Neurology, University of Oxford, Oxford, UK
Neuroimage 54:875-91. 2011.... - Advances in functional and structural MR image analysis and implementation as FSLStephen M Smith
Oxford Centre for Functional Magnetic Resonance Imaging of the Brain FMRIB, Department of Clinical Neurology, John Radcliffe Hospital, Oxford University, Headington, Oxford OX3 9DU, UK
Neuroimage 23:S208-19. 2004..The majority of the research laid out in this paper has been implemented as freely available software tools within FMRIB's Software Library (FSL)... - Correspondence of the brain's functional architecture during activation and restStephen M Smith
Centre for Functional MRI of the Brain, University of Oxford, Oxford OX3 9DU, United Kingdom
Proc Natl Acad Sci U S A 106:13040-5. 2009..We conclude that the full repertoire of functional networks utilized by the brain in action is continuously and dynamically "active" even when at "rest.".. - Longitudinal and cross-sectional analysis of atrophy in Alzheimer's disease: cross-validation of BSI, SIENA and SIENAXStephen M Smith
Oxford University Centre for Functional MRI of the Brain FMRIB, Oxford, UK
Neuroimage 36:1200-6. 2007..We also compare the SIENA longitudinal measure with atrophy state estimated by SIENAX using just the earliest scan taken from each subject. We show strong correspondence and similar sensitivity to atrophy between all 3 measures... - Fast robust automated brain extractionStephen M Smith
Oxford Centre for Functional Magnetic Resonance Imaging of the Brain, Department of Clinical Neurology, Oxford University, John Radcliffe Hospital, Headington, Oxford, United Kingdom
Hum Brain Mapp 17:143-55. 2002..We describe the new method and give examples of results and the results of extensive quantitative testing against "gold-standard" hand segmentations, and two other popular automated methods... - The danger of systematic bias in group-level FMRI-lag-based causality estimationS M Smith
Oxford Centre for Functional MRI of the Brain FMRIB, Nuffield Department of Clinical Neurosciences, Oxford University, UK
Neuroimage 59:1228-9. 2012..While many statements in the paper (e.g., the final two sentences) do refer to this problem, we fear that the overriding message that many readers may take from the paper could cause misunderstanding... - Applying FSL to the FIAC data: model-based and model-free analysis of voice and sentence repetition primingChristian F Beckmann
Oxford Centre for Functional Magnetic Resonance Imaging of the Brain FMRIB, University of Oxford, Oxford, UK
Hum Brain Mapp 27:380-91. 2006..These results suggest that both are processed in a single underlying system without any significant asymmetries for content vs. voice processing... - Multilevel linear modelling for FMRI group analysis using Bayesian inferenceMark W Woolrich
Oxford Centre for Functional Magnetic Resonance Imaging of the Brain, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
Neuroimage 21:1732-47. 2004..We also demonstrate that we can infer on the top level of multilevel hierarchies by inferring on the levels of the hierarchy separately and passing summary statistics of a noncentral multivariate t distribution between them... - Constrained linear basis sets for HRF modelling using Variational BayesMark W Woolrich
Oxford Centre for Functional Magnetic Resonance Imaging of the Brain, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
Neuroimage 21:1748-61. 2004..We use spatial mixture modelling to produce final probabilities of activation and demonstrate increased sensitivity on an FMRI dataset... - Adjusting the neuroimaging statistical inferences for nonstationarityGholamreza Salimi-Khorshidi
Centre for Functional MRI of the Brain FMRIB, University of Oxford, Oxford, UK
Med Image Comput Comput Assist Interv 12:992-9. 2009.... - Adjusting the effect of nonstationarity in cluster-based and TFCE inferenceGholamreza Salimi-Khorshidi
Centre for Functional MRI of the Brain FMRIB, University of Oxford, Oxford, UK
Neuroimage 54:2006-19. 2011..We also find that adjusting for local smoothness via a separate resampling procedure is more effective at removing nonstationarity than an adjustment via a random field theory based smoothness estimator... - Mixture models with adaptive spatial regularization for segmentation with an application to FMRI dataMark W Woolrich
Oxford Centre for Functional Magnetic Resonance Imaging of the Brain, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
IEEE Trans Med Imaging 24:1-11. 2005..We examine the behavior of this model when applied to artificial data with different spatial characteristics, and to functional magnetic resonance imaging SPMs... - Fully Bayesian spatio-temporal modeling of FMRI dataMark W Woolrich
Oxford Centre for Functional Magnetic Resonance Imaging of the Brain, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
IEEE Trans Med Imaging 23:213-31. 2004.... - Accurate, robust, and automated longitudinal and cross-sectional brain change analysisStephen M Smith
Oxford Centre for Functional Magnetic Resonance Imaging of the Brain, Department of Clinical Neurology, FMRIB, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, United Kingdom
Neuroimage 17:479-89. 2002..The methods provide easy manual review of their output by the automatic production of summary images which show the results of the brain extraction, registration, tissue segmentation, and final atrophy estimation... - Asymmetries of the balanced SSFP profile. Part II: white matterKarla L Miller
Centre for Functional MRI of the Brain, University of Oxford, Oxford, UK
Magn Reson Med 63:396-406. 2010..These results are discussed in the context of previous work studying gradient-recalled echo (GRE) signal behavior in white matter, and it is suggested that these two techniques are detecting closely related phenomena... - Language networks in anophthalmia: maintained hierarchy of processing in 'visual' cortexKate E Watkins
Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, UK
Brain 135:1566-77. 2012.... - Diffusion imaging of whole, post-mortem human brains on a clinical MRI scannerKarla L Miller
FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
Neuroimage 57:167-81. 2011..Despite these alterations, diffusion tractography of several major tracts is successfully demonstrated at both resolutions. We also report novel findings of cortical anisotropy and partial volume effects... - Using Gaussian-process regression for meta-analytic neuroimaging inference based on sparse observationsGholamreza Salimi-Khorshidi
FMRIB Centre, University of Oxford, Oxford, UK
IEEE Trans Med Imaging 30:1401-16. 2011..Our results show that GPR outperforms existing CBMA techniques and is capable of more accurately reproducing the (usually unavailable) full-image analysis results... - FSLMark Jenkinson
FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, UK
Neuroimage 62:782-90. 2012..We hope that some of this content might be of interest to users of FSL, and also maybe to new research groups considering creating, releasing and supporting new software packages for brain image analysis... - Spontaneous blood oxygenation level-dependent fMRI signal is modulated by behavioral state and correlates with evoked response in sensorimotor cortex: a 7.0-T fMRI studyManus J Donahue
Department of Clinical Neurology, FMRIB Centre, University of Oxford, Oxford, UK
Hum Brain Mapp 33:511-22. 2012..81; P = 0.03), suggesting that spontaneous signal synchrony may be a predictor of evoked BOLD response magnitude and may account for intersubject variability in sensorimotor cortex... - Functional-anatomical validation and individual variation of diffusion tractography-based segmentation of the human thalamusHeidi Johansen-Berg
Centre for Functional Magnetic Resonance Imaging of the Brain, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
Cereb Cortex 15:31-9. 2005..This provides a tool for specific localization of functional activations or lesions to putative thalamic nuclei... - Tools of the trade: psychophysiological interactions and functional connectivityJill X O'Reilly
FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
Soc Cogn Affect Neurosci 7:604-9. 2012..In this tutorial, we aim to give a simple conceptual explanation of how PPI analysis works, in order to assist readers in planning and interpreting their own PPI experiments... - Probabilistic independent component analysis for functional magnetic resonance imagingChristian F Beckmann
Medical Vision Laboratory, Department of Engineering Science and the Oxford Centre for Functional Magnetic Resonance Imaging of the Brain, University of Oxford, Oxford OX3 9DU, UK
IEEE Trans Med Imaging 23:137-52. 2004..The performance of our approach is illustrated and evaluated on real and artificial FMRI data, and compared to the spatio-temporal accuracy of results obtained from classical ICA and GLM analyses... - A Bayesian model of shape and appearance for subcortical brain segmentationBrian Patenaude
FMRIB Centre, Department of Clinical Neurology, University of Oxford, Oxford, UK
Neuroimage 56:907-22. 2011..7 and 0.9 are obtained with this method, which is comparable or better than other automated methods. An implementation of this method, called FIRST, is currently distributed with the freely-available FSL package... - Signal and noise characteristics of SSFP FMRI: a comparison with GRE at multiple field strengthsKarla L Miller
Centre for Functional MRI of the Brain FMRIB, University of Oxford, Oxford, UK, and A A Martinos Center, Massachusetts General Hospital, Charlestown, USA
Neuroimage 37:1227-36. 2007..In addition, the temporal noise properties are significantly different, with important implications for SSFP FMRI sequence optimisation... - Ventral striatum/nucleus accumbens activation to smoking-related pictorial cues in smokers and nonsmokers: a functional magnetic resonance imaging studySean P David
Cancer Research United Kingdom General Practice Research Group, Department of Clinical Pharmacology, University of Oxford, Radcliffe Infirmary, UK
Biol Psychiatry 58:488-94. 2005..Converging evidence from several theories of the development of incentive-sensitization to smoking-related environmental stimuli suggests that the ventral striatum plays an important role in the processing of smoking-related cue reactivity... - General multilevel linear modeling for group analysis in FMRIChristian F Beckmann
Oxford Centre for Functional Magnetic Resonance Imaging of the Brain, Department of Clinical Neurology, University of Oxford, Oxford, OX3 9DU, UK
Neuroimage 20:1052-63. 2003.... - Resting-state FMRI single subject cortical parcellation based on region growingThomas Blumensath
Oxford Centre for Functional MRI of the Brain FMRIB Centre, University of Oxford, Oxford, UK
Med Image Comput Comput Assist Interv 15:188-95. 2012.... - Investigations into resting-state connectivity using independent component analysisChristian F Beckmann
Oxford Centre for Functional Magnetic Resonance Imaging of the Brain FMRIB, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
Philos Trans R Soc Lond B Biol Sci 360:1001-13. 2005..We show that these networks exhibit high spatial consistency across subjects and closely resemble discrete cortical functional networks such as visual cortical areas or sensory-motor cortex... - Spatially constrained hierarchical parcellation of the brain with resting-state fMRIThomas Blumensath
FMRIB, University of Oxford, Oxford, UK ISVR Signal Processing and Control Group, University of Southampton, Southampton, UK Electronic address
Neuroimage 76:313-24. 2013..Connectivity-derived parcellation borders are less well matched to borders derived from cortical myelination and from cytoarchitectonic atlases, but this may reflect inherent differences in the data... - High-resolution FMRI at 1.5T using balanced SSFPKarla L Miller
Oxford Centre for Functional MRI of the Brain, FMRIB, Oxford University, UK
Magn Reson Med 55:161-70. 2006..5 T. Currently, the major limitation of BOSS FMRI is its sensitivity to temporal and spatial field drift... - Crossing fibres in tract-based spatial statisticsSaad Jbabdi
Oxford Centre for Functional Magnetic Resonance Imaging of the Brain, John Radcliffe Hospital, University of Oxford, Oxford, UK
Neuroimage 49:249-56. 2010..We show how this framework applies to the parameters of a crossing fibre model and discuss its implications for voxelwise analysis of the white matter... - Integrity of white matter in the corpus callosum correlates with bimanual co-ordination skillsHeidi Johansen-Berg
Oxford Centre for Functional MRI of the Brain, John Radcliffe Hospital, Headington, Oxford, OX3 0HS, UK
Neuroimage 36:T16-21. 2007..This provides further evidence for the role of medial wall motor areas in bimanual co-ordination and supports the idea that variation in brain structure reflects inter-individual differences in skilled performance... - Distinct patterns of brain activity in young carriers of the APOE-epsilon4 alleleNicola Filippini
University Department of Psychiatry, University of Oxford, Oxford OX3 9DU, United Kingdom
Proc Natl Acad Sci U S A 106:7209-14. 2009..The APOE epsilon4 allele modulates brain function decades before any clinical or neurophysiological expression of neurodegenerative processes... - Structural and functional abnormalities of the motor system in developmental stutteringKate E Watkins
Department of Experimental Psychology, University of Oxford, Oxford, UK
Brain 131:50-9. 2008.... - Bayesian analysis of neuroimaging data in FSLMark W Woolrich
University of Oxford Centre for Functional MRI of the Brain, UK
Neuroimage 45:S173-86. 2009..Finally, we mention some analysis scenarios where Bayesian methods are impractical, and briefly discuss some practical approaches that we have taken in these cases... - Methods for tractography-driven surface registration of brain structuresAleksandar Petrović
Centre for Functional MRI of the Brain FMRIB, University of Oxford
Med Image Comput Comput Assist Interv 12:705-12. 2009..The results suggest differences in thalamic connectivity predominantly in the medial dorsal parts of the left thalamus... - Distinct portions of anterior cingulate cortex and medial prefrontal cortex are activated by reward processing in separable phases of decision-making cognitionRobert D Rogers
University Department of Psychiatry, Warneford Hospital, Oxford, United Kingdom
Biol Psychiatry 55:594-602. 2004.... - Meta-analysis of neuroimaging data: a comparison of image-based and coordinate-based pooling of studiesGholamreza Salimi-Khorshidi
Centre for Functional MRI of the Brain FMRIB, University of Oxford, Oxford, UK
Neuroimage 45:810-23. 2009..To make IBMA analyses practical, however, the neuroimaging field needs to develop an effective mechanism for sharing image data, including whole-brain images of both effect estimates and their standard errors... - Benefits of multi-modal fusion analysis on a large-scale dataset: life-span patterns of inter-subject variability in cortical morphometry and white matter microstructureAdrian R Groves
FMRIB Oxford Centre for Functional Magnetic Resonance Imaging of the Brain, Nuffield Department of Clinical Neurosciences, University of Oxford, OX3 9DU, UK
Neuroimage 63:365-80. 2012..This exploratory approach automatically generates models to explain structure in the data, and may prove especially powerful for large-scale studies, where the population variability can be explored in increased detail... - Correlation between motor improvements and altered fMRI activity after rehabilitative therapyHeidi Johansen-Berg
Oxford Centre for Functional Magnetic Resonance Imaging of the Brain, John Radcliffe Hospital and Rivermead Rehabilitation Centre, Oxford, UK
Brain 125:2731-42. 2002..Our results suggest that activity changes in sensorimotor regions are associated with successful motor rehabilitation... - Homocysteine-lowering by B vitamins slows the rate of accelerated brain atrophy in mild cognitive impairment: a randomized controlled trialA David Smith
Oxford Project to Investigate Memory and Ageing, University of Oxford, Oxford, United Kingdom
PLoS ONE 5:e12244. 2010..Homocysteine is a risk factor for brain atrophy, cognitive impairment and dementia. Plasma concentrations of homocysteine can be lowered by dietary administration of B vitamins... - On bias in the estimation of autocorrelations for fMRI voxel time-series analysisJonathan L Marchini
Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
Neuroimage 18:83-90. 2003..In fact estimates of the model parameters and their standard errors are seen to be so accurate that we conclude that bias correction is unnecessary... - Relationships of brain white matter microstructure with clinical and MR measures in relapsing-remitting multiple sclerosisAntonio Giorgio
Centre for Functional MRI of the Brain, University of Oxford, Oxford, UK
J Magn Reson Imaging 31:309-16. 2010.... - What is the most interesting part of the brain?Timothy E J Behrens
Functional MRI of the Brain Centre, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
Trends Cogn Sci 17:2-4. 2013..We tested this unstated hypothesis by regressing the journal impact factor against both the pattern of brain activity and the experimental keywords across thousands of brain imaging studies. We found the results to be illuminating... - Imaging how attention modulates pain in humans using functional MRISusanna J Bantick
Oxford University Department of Clinical Neurology, Centre for Functional Magnetic Resonance Imaging of the Brain, John Radcliffe Hospital, Headington, Oxford, UK
Brain 125:310-9. 2002..In contrast, many areas of the pain matrix (i.e. thalamus, insula, cognitive division of the ACC) displayed reduced activation, supporting the behavioural results of reduced pain perception... - Regional brain atrophy development is related to specific aspects of clinical dysfunction in multiple sclerosisBas Jasperse
Department of Neurology, VU University Medical Center, Boelelaan 1117, PO Box 7057, 1007 MB, Amsterdam, The Netherlands
Neuroimage 38:529-37. 2007.... - Concurrent numerical simulation of flow and blood clotting using the lattice Boltzmann techniqueJorg Bernsdorf
C and C Research Laboratories, NEC Europe Ltd, Rathausallee 10, Sankt Augustin, Germany
Int J Bioinform Res Appl 2:371-80. 2006..The applied numerical scheme is the lattice Boltzmann technique, which proved to be highly efficient particularly for transient flows and complex or varying geometries... - Monitoring disease activity and progression in primary progressive multiple sclerosis using MRI: sub-voxel registration to identify lesion changes and to detect cerebral atrophyValerie L Stevenson
NMR Research Unit, Institute of Neurology, London
J Neurol 249:171-7. 2002.... - Intercenter agreement of brain atrophy measurement in multiple sclerosis patients using manually-edited SIENA and SIENAXBas Jasperse
Department of Neurology, VU University Medical Center, Amsterdam, The Netherlands
J Magn Reson Imaging 26:881-5. 2007.... - Influence of noninvasive peripheral arterial blood pressure measurements on assessment of dynamic cerebral autoregulationEmily L Sammons
Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
J Appl Physiol 103:369-75. 2007.... - Manifestations of early brain recovery associated with abstinence from alcoholismAndreas J Bartsch
University of Wurzburg, Department of Neuroradiology, Wurzburg, Germany
Brain 130:36-47. 2007..Further understanding of the precise mechanisms of this recovery may become a valuable model of brain regeneration with relevance for other disorders... - Sensitivity and specificity of the blankenship FCE system's indicators of submaximal effortPerry N Brubaker
North Georgia College and State University, Dahlonega, GA, USA
J Orthop Sports Phys Ther 37:161-8. 2007..Single-blinded, randomized, posttest only design... - Recordings from single neocortical nerve terminals reveal a nonselective cation channel activated by decreases in extracellular calciumStephen M Smith
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, CA 94305, USA
Neuron 41:243-56. 2004..Activation of NSC channels by falls in [Ca(2+)](o) would be expected during periods of high activity in the neocortex and may modulate the excitability of the presynaptic terminal... - Vasopressin inhibits glutamate release via two distinct modes in the brainstemTimothy W Bailey
Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, Oregon 97239 3098, USA
J Neurosci 26:6131-42. 2006..Thus, AVP regulates NTS neurons by two distinct novel and state-dependent mechanisms: one, an analog, graded presynaptic inhibition of terminal glutamate release and the other, a binary, extraterminal block of conducted excitation... - Enhanced brain extraction improves the accuracy of brain atrophy estimationMarco Battaglini
Department of Neurological and Behavioural Sciences, University of Siena, Italy
Neuroimage 40:583-9. 2008..Multicentre studies monitoring brain atrophy in clinical trials may receive benefit by using this unbiased, fully automated procedure... - Are baroreflex events detected by invasive and non-invasive techniques coincident?Stephen M Smith
Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
Clin Physiol Funct Imaging 28:262-9. 2008..Non-invasive, compared with intra-arterial estimates of BRS by sequence analysis are not influenced by coincidence of sequences if acceptance of sequences is based on the correlation coefficient criteria (>0.85)... - Modulation of neuronal voltage-activated calcium and sodium channels by polyamines and pHWenyan Chen
Division of Pulmonary and Critical Care Medicine, Oregon Health and Science University, Portland, Oregon, USA
Channels (Austin) 1:281-90. 2007..Many of the observed effects can be explained by a model incorporating polyamine binding, H(+) binding and surface charge screening... - Measuring brain atrophy in multiple sclerosisNicola De Stefano
Department of Neurological and Behavioural Sciences, University of Siena, Italy
J Neuroimaging 17:10S-15S. 2007..It represents one of most promising in vivo measures of neuroaxonal degeneration in MS, and it should be used extensively in the future to assess and monitor pathological evolution and treatment efficacy in this disease...