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Postgraduate research: Methods Research and Infrastructure

Neuroimaging forms a key part of the Unit's endeavour, with a number of imaging modalities in regular use. Projects are available for those who wish to work on the methods that permit measurement of the brain. Successful candidates will enjoy generating new ideas in this exciting and rapidly developing field, be able to explain complex ideas in a clear way, and have a background that might include maths, physics or engineering. Knowledge of neuroimaging or neuroscience would be advantageous but is not always essential. See also: Methods research pages

Magnetic resonance imaging (MRI) acquisition and analysis

Installed in 2006, the Imaging Facility at the end of the garden contains a research-dedicated 3T Siemens Tim Trio, used for measuring:

  • Brain activity through changes in blood flow, volume and oxygenation (BOLD EPI)
  • Brain anatomy, in particular, delimiting grey and white matter (MPRAGE)
  • White matter tract integrity and direction (DTI)

There is substantial scope for the development of new acquisition methods. A Siemens collaboration agreement is in place that permits the development of new pulse sequences. An extensive computing system is available for analysis, with software packages from (amongst others) London (SPM), Oxford (FSL) and Boston (MNE) in regular use.

Example past projects are:

  • The development of a dual-echo gradient/spin echo sequence to recover signal in areas with dropout.
  • The development of real-time "dynamically adaptive imaging"
  • The use of field-mapping to characterise and correct for the effects of magnetic field inhomogenenities on the imaging process
  • The development of MVPA machine learning techniques to characterise information within brain regions
  • The use of effective connectivity of fMRI data

Potential supervisors in this field include:

Rik Henson, Niko Kriegeskorte, James Rowe

Magnetoencephalography (MEG) & Electroencephalography (EEG)

Elekta Neuromag Vectorview MEG facility was installed in 2007, providing 306 superconducting (SQUID) magnetic sensors (102 triplets comprising a magnetometer, a latitudinal gradiometer and a longitudinal gradiometer) for non-invasive real-time recordings of magnetic fields generated by the brain's electric activity. In addition to the MEG channels, concurrent recording of 124 electric (EEG) channels is possible with subsequent integration of MEG and EEG data into a single analysis stream. Additional stand-alone 64-channel EEG (Neuroscan) laboratory is available, with a pending installation of 128-channel active electrode system. There is a substantial scope for developing MEG/EEG analysis methods (e.g. source analysis, statistic mapping etc), for which a collaboration agreement with Elekta Neuromag exists, as well as for methodological exploration of MEG/EEG clinical applications, which is currently done in collaboration with Elekta Neuromag, GSK and Addenbrookes Hospital.

Example past projects are:

  • Development of Bayesian algorithms for the fusion of fMRI and MEG/EEG data
  • Methods for evaluating connectivity between localised MEG/EEG sources
  • Work on source localisation with minimum norm
  • Localising spatiotemporal patterns of brain activation and their relationship to cognitive processes based on MEG/EEG recordings

Potential supervisors in this field include:

Olaf Hauk, Rik Henson, Yury Shtyrov.

Peer reviewed publications

  • Avril, S., Huntley, J.M., Cusack, R. (2009) In-Vivo measurements of blood viscosity and wall stiffness in the carotid using PC-MRI. European Journal of Computational Mechanics, Vol 18, N°1, pp. 9-20.
  • Chen, C.C, Henson, R.N. Stephan, K.E, Kilner, J.M. & Friston, K. J. (2009) Forward and backward connections in the brain: A DCM study of functional asymmetries. Neuroimage, 45, 453-462.
  • CUSACK, R., BRETT, M. & OSSWALD, K. (2003) An evaluation of the use of magnetic field maps to undistort echo-planar images NeuroImage 18(1), 127-142.
  • CUSACK, R., CUMMING, N., BOR, D., NORRIS, D. & LYZENGA, J. (2005) Automated post-hoc noise cancellation tool for audio recordings acquired in an MRI scanner Human Brain Mapping 24(4), 299-304.
  • CUSACK, R., MITCHELL, D., Beauregard, D.A., Salfity, M.F. & Huntley, J.M. (under revision) "Individual differences in vein structure predict variation in BOLD activation."
  • CUSACK, R., Russell, B., COX, S.M.L., de PANFILIS, C., SCHWARZBAUER, C. & Ansorge, R. (2005) An evaluation of the use of passive shimming to improve frontal sensitivity in fMRI, NeuroImage 24(1), 82-91.
  • Datta, A.K., CUSACK, R., HAWKINS, K., Heutink, J., Rorden, C., Robertson, I. and MANLY, T. (2007) The P300 as a marker of warning attention and error propensity Computational Intelligence and Neuroscience:93968.
  • De Panfilis, C. & SCHWARZBAUER, C. (2005) Positive or negative Blips? The effect of the phase encoding scheme on susceptibiliy-induced signal losses in blipped EPI. Neuroimage 25, 112-21.
  • Delahunta, S., BARNARD, P., NIMMO-SMITH, I., POTTS, J. & RAMPONI, C. (2006) Densities of Agreement: making visible some intangible properties of dance, Dance Theatre Journal, 21(3), 17-23
  • Deichmann, R., SCHWARZBAUER, C., & Turner, R. (2004) Optimisation of the 3D MDEFT sequence for anatomical brain imaging: technical implications at 1.5 and 3 T. Neuroimage 21: 757-767.
  • DUNCAN, J., Parr, A., WOOLGAR, A., THOMPSON, R., Bright, P., Cox, S., BISHOP, S. & NIMMO-SMITH, I. (2008) Goal neglect and Spearman's g: Competing parts of a complex task, JEP: General, 137(1) 131-148
  • DUNN, B.D., DALGLEISH, T., LAWRENCE, A.D., CUSACK, R. & Ogilvie, A. (2004) Categoric emotions in response to emotional stimuli in depression: self-report and psychophysiology Journal of Abnormal Psychology 113(4): 654-60.
  • EMSLIE H., Wilson F.C., Burden V., NIMMO-SMITH I. and WILSON B. (submitted). Detecting Selective Executive Impairments Using the Behavioural Assessment of Dysexecutive Syndrome for Children (BADS-C).
  • Friston, K., Harrison, L., Daunizeau, J., Kiebel, S., Phillips, C., Trujillo-Barreto, N., HENSON, R., Flandin, G. & Mattout, J. (2008) Multiple sparse priors for the M/EEG inverse problem. Neuroimage, 39, 1104-1120.
  • Friston, K., HENSON, R., Phillips, C. & Mattout, J. (2006). Bayesian estimation of evoked and induced responses. Human Brain Mapping, 27, 722-735.
  • Guadagno, J.V., Jones, P.S., Aigbirhio, F.I., Wang, D., Fryer, T.D., Day, D.J. & Antoun, N., NIMMO-SMITH, I., Warburton, E.A. & Baron, J.C. (2008) Selective Neuronal
  • Individual Scientific Programmes, Methods Group 2:5:14
  • Loss in rescued penumbra relates to initial hypoperfusion, Brain, 130(10), 2494-2507
  • HAUK, O. (2004) Keep it simple: a case for using classical minimum norm estimation in the analysis of EEG and MEG data. Neuroimage, 21, 1612-1621.
  • HAUK, O., DAVIS, M.H., FORD, M., PULVERMÜLLER, F. & MARSLEN-WILSON, W.D. (2006) The time course of visual word recognition as revealed by linear regression analysis of ERP data. Neuroimage, 30, 1383-1400.
  • Henson, R.N., Flandin, G. & Friston, K.J. & Mattout, J. (submitted).A Parametric Empirical Bayesian framework for fMRI-constrained MEG/EEG source reconstruction
  • Henson, R.N., Mouchlianitis, E. & Friston, K.J. (2009). MEG and EEG data fusion: Simultaneous localisation of face-evoked responses. /Neuroimage, 47/, 581-589.
  • Henson, R.N., Mattout, J., Phillips, C. & Friston, K.J. (2009). Selecting forward models for MEG source-reconstruction using model-evidence. /Neuroimage, 46,/ 168-176.
  • Henson, R.N. Mattout, J, Singh, K, Barnes, G, Hillebrand, A. & Friston, K.J. (2007). Population-level inferences for distributed MEG source localisation under multiple constraints: Application to face-evoked fields. /Neuroimage, 38/, 422-438.
  • Hill, K., Mann, L., Laws, K.R., Stephenson, C.M.E., NIMMO-SMITH, I. & McKenna, P.J. (2004) Hypofrontality in Schizophrenia: A Meta-Analysis of Functional Imaging Studies, Acta Psychiatrica Scandinavica, 110, 1-14
  • Kherif, F., Poline, J.B., Mériaux, S., Benali, H., Flandin, G. and BRETT, M. (2003). Group analysis in functional neuroimaging: selecting subjects using similarity measures. NeuroImage, Volume 20(4), 2197-2208.
  • Kilner, J.M., Mattout, J., HENSON, R. & Friston, K.J. (2005). Hemodynamic correlates of EEG: A heuristic. Neuroimage, 28, 280-286.
  • LEE, A.C., BANDELOW, S., SCHWARZBAUER, C., HENSON, R.N. & GRAHAM, K.S. (2006) Perirhinal cortex activity during visual object discrimination: an event-related fMRI study. Neuroimage 33, 362-73.
  • LONG, C.J., NIMMO-SMITH, I., Baguley, D.M., O'Driscoll, M., Ramsden, R., Otto, S.R., Axon, P.R. & CARLYON, R.P. (2005) Optimizing the Clinical Fit of Auditory Brainstem Implants, Ear and Hearing, 26(3), 251-262.
  • MARCEL, A., Postma, P., CUSACK, R., Mackintosh, B, NIMMO-SMITH, I, VUCKOVICH, J. & Cox, S (2006) Is Susceptibility to Perceptual Migration and Fusion Modality-Specific or Multimodal?, Neuropsychologia, 44(5), 693-710.
  • MARCEL, A., Postma, P., Gillmeister, H., Cox, S., Rorden, C., NIMMO-SMITH, I. & MACKINTOSH, B. (2004) Migration and Fusion of Tactile Sensation - Premorbid Susceptibility to Allochiria, Neglect and Extinction?, Neuropsychologia, 42(13), 1749-1767.
  • MARCEL, A.J., Tegner, R. & NIMMO-SMITH, I. (2004) Anosognosia for plegia: specificity, extension, partiality and disunity of bodily unawareness. Cortex, 40(1), 19-40.
  • Marklund, O., Huntley, J.M., & CUSACK, R. (2007) Robust Unwrapping Algorithm for 3-D Phase Volumes of Arbitrary Shape Containing Knotted Phase Singularity Loops, Applied Optics 46, 085601.
  • McCarthy, R., Blackwell, A., deLahunta, S., Wing, A., Hollands, K, BARNARD, P, NIMMO-SMITH, I. & Marcel, A. (2006) Bodies Meet Minds: Choreography and Cognition, Leonardo, 39(5), 475-477.
  • MOHR, B., Endrass, T., HAUK, O. & PULVERMÜLLER, F. (2007) ERP correlates of the bilateral redundancy gain for words. Neuropsychologia, 45, 2114-2124.
  • MOHR, B., Endrass, T., Rockstroh, B. & PULVERMÜLLER, F. (2008) Hemispheric cooperation – A crucial factor in schizophrenia? Neurophysiological evidence. Neuroimage, 41, 1102-1110.
  • MOSCOSO DEL PRADO MARTIN, F., HAUK, O. & PULVERMÜLLER, F. (2006) Category specificity in the processing of color-related and form-related words: An ERP study. Neuroimage, 29, 29-37.
  • Individual Scientific Programmes, Methods Group 2:5:15
  • Muggleton, N., Postma, P., MOUTSOPOULOU, K., NIMMO-SMITH, I., Marcel, A. & Walsh, V. (2006) TMS over right posterior parietal cortex induces neglect in a scene-based frame of reference, Neuropsychologia, 44(7), 1222-1229.
  • NIMMO-SMITH, I., MARCEL, A.J. & Tegner, R. (2005) A diagnostic test of unawareness of bilateral motor task abilities in anosognosia for hemiplegia., Journal of Neurology, Neurosurgery & Psychiatry, 76, 1167-1169.
  • PASSAMONTI, L., ROWE, J.B., SCHWARZBAUER, C., EWBANK, M., VON DEM HAGEN E. & CALDER, A.J. (in press) Visually induced appetite: identifying the neural basis of a risk factor for overeating. Journal of Neuroscience.
  • PULVERMULLER, F., Shtyrov, Y. & Ilmoniemi, R. 2003: Spatio-temporal patterns of neural language processing: an MEG study using Minimum-Norm Current Estimates. /Neuroimage,/ *20*, 159-172
  • PULVERMULLER, F., & Shtyrov, Y. 2006. Language outside the focus of attention: the mismatch negativity as a tool for studying higher cognitive processes. /Progress in Neurobiology, /*79 (1),* 49-71
  • PULVERMULLER, F. & Shtyrov, Y. 2009. Spatio-temporal signatures of large-scale synfire chains for speech as revealed by MEG. /Cerebral Cortex, /*19*/ /(1), 79-88
  • RAMPONI, C., BARNARD, P.J. & NIMMO-SMITH, I. (2004) Recollection Deficits in Dysphoric Mood: An Effect of Schematic Models and Executive Mode? Memory, 12(5), 655-670
  • Salfity, M.F., Huntley, J.M., Graves, M.J., Marklund, O., CUSACK, R. & Beauregard, D. (2006a) Extending the dynamic range of phase contrast magnetic resonance velocity imaging using advanced higher-dimension unwrapping algorithms, J. Royal Soc. Interface, 3(8), 415-27.
  • Salfity, M.F., Ruiz, P.D., Huntely, J.M., Graves, M.J., CUSACK, R., & Beauregard, D. (2006b) Branch cut surface placement for unwrapping of undersampled three-dimensional phase data: application to magnetic resonance imaging arterial flow mapping. Applied Optics. 45: 2711-22.
  • Salvador, R., Suckling, J., SCHWARZBAUER, C. & Bullmore, E.T. (2005) Undirected graphs of frequency-dependent functional connectivity in whole brain networks. Philos Trans R Soc Lond B Biol Sci. 360, 937-46.
  • Saxe R., BRETT M., Kanwisher N. (2006) Divide and conquer: A defense of functional localizers. Neuroimage, 30:1088-1096.
  • SCHWARZBAUER, C., DAVIS, M.H., Rodd J. & Johnsrude, I. (2006a) Interleaved silent steady state (ISSS) imaging: Applications to event-related auditory fMRI. Neuroimage 29, 774-82.
  • SCOUTEN, A. & SCHWARZBAUER, C. (2008) Paced respiration with end-expiration technique offers superior BOLD signal repeatability for breath-hold studies. Neuroimage 43, 250-57.
  • SIGALA, N., Kusunoki, M., NIMMO-SMITH, I., Gaffan, D., DUNCAN, J. (2008) Hierarchical coding for sequential task events in the monkey prefrontal cortex, Proc Natl Acad Sci USA, 105(33), 11969-11974.
  • Turner, D.C., Aitken, M.R., Shanks, D.R., Sahakian, B.J., Robbins, T.W., SCHWARZBAUER, C. & Fletcher, P.C. (2004) The Role of the Lateral Frontal Cortex in Causal Associative Learning: Exploring Preventative and Super-learning. Cereb Cortex. 14, 872-80.
  • Wilkins, A., Sihra, N. & NIMMO-SMITH, I. (2005) Technical Note: How precise do precision tints have to be? Ophthalmic and Physiological Optics, 25, 269–276
  • Wilson, F.C., EMSLIE, H., Burden, V., NIMMO-SMITH, I., WILSON, B. (2004) Behavioural Assessment of the Dysexecutive Syndrome for Children (BADS-C): Utility in clinical practice? Brain Impairment, 5(1), 109