The 2012 Bristol MR Summer School...1.50–2.40 Cognitive neuroscience applications Pascal Belin 3.00–3.50 fMRI and computer modelling Paul Howard-Jones 3.50–4.40 MR spectroscopy

The 2012 Bristol MR Summer School

(unit code PSYCM0013 as part of the MSc in Neuropsychology curriculum)

Bristol, March 26 – 29, 2012

Biological Sciences Building

Lecture Room B75

Woodland Avenue

Bristol BS8 1UG

Module Director: Professor Risto Kauppinen

School of Experimental Psychology

CRICBristol

University of Bristol

[email protected]

DATE TIME TOPIC TEACHERMar-26 9.00 – 9.50 Basic NMR and MRI Risto Kauppinen

9.50 – 10.40 Structural MRI Mark Jenkinson 11.00-11.50 Image analysis Mark Jenkinson11.50 – 1.00 Lunch break1.00 – 1.50 BOLD signal Risto Kauppinen1.50 – 2.40 BOLD Physiology and fMRI Richard Wise……..3.00 – 3.50 fMRI analysis Jonathan Brooks3.50 -4.40 Brain-computer interface and MR David Linden…….5.00 – 5.50 ASL and CBV MRI David Thomas

27-Mar9.00 – 9.50 Diffusion MRI Derek Jones9.50 – 10.40 Combined fMRI and EEG Andy Bagshaw……..11.00 – 11.50 Spontaneous BOLD fluctuations Risto Kauppinen11.50 – 1.00 Lunch break1.00 – 1.50 Neurodevelopment Frances Cowan1.50 – 2.40 Cognitive neuroscience applications Pascal Belin…….3.00 – 3.50 fMRI and computer modelling Paul Howard-Jones3.50 – 4.40 MR spectroscopy Risto Kauppinen

28-Mar 9.00 – 9.50 Neuroimaging of Pain Jonathan Brooks9.50 – 10.40 MR of brain disorders in neonates Axel Heep……11.00 – 11.50 Neurodegeneration by MR Liz Coulthard11.50 – 1.00 Lunch break1.00 – 1.50 Neuro-vascular diseases by MR Rose Bosnell1.50 – 2.40 Neuropsychiatry and MR Steve Williams…….3.00 – 3.50 Neuroinflammatory disorders by MR Mara Cercignani3.50 – 4.40 MRS analysis Martin Wilson…….5.00 – 5.50 Neuro-oncology by MR Martin Wilson

For MSc Students only

29-Mar 9.00-11.45 Demo at CRICBristol Group I (Students 1-16)

12.15 -3.00 Demo at CRICBristol Group II (Students 17-33)

Dr. Andy Bagshaw

University of Birmingham

Lecture title: Combined fMRI and EEG

Relevant publications

Debener S, Ullsperger M, Siegel M, Engel AK. (2006) Single-trial EEG-fMRI reveals the dynamics of cognitive function. Trends Cogn Sci. 10(12):558-63.

Laufs H, Daunizeau J, Carmichael DW, Kleinschmidt A. (2008) Recent advances in recording electrophysiological data simultaneously with magnetic resonance imaging. Neuroimage.40(2):515-28

Professor Pascal Belin

University of Glasgow

Lecture title: Cognitive Neuroscience Applications for fMRI

Relevant publications:

Latinus M, Crabbe F, Belin P. (2011) Learning-induced changes in the cerebral processing of voice identity. Cereb Cortex. 21(12):2820-8.

Bestelmeyer PE, Latinus M, Bruckert L, Rouger J, Crabbe F, Belin P. .(2011) Implicitly Perceived Vocal Attractiveness Modulates Prefrontal Cortex Activity. Cereb Cortex. 2011 Aug 9.

Sammler D, Baird A, Valabrègue R, Clément S, Dupont S, Belin P, Samson S. (2010) The relationship of lyrics and tunes in the processing of unfamiliar songs: a functional magneticresonance adaptation study. J Neurosci. 30(10):3572-8.

Dr. Rose BosnellUniversity of Bristol

Lecture title: Neuro-Vascular Diseases by Magnetic Resonance


Thomalla G, Cheng B, Ebinger M, Hao Q, Tourdias T, Wu O, Kim JS, Breuer L, SingerOC, Warach S, Christensen S, Treszl A, Forkert ND, Galinovic I,Rosenkranz M,Engelhorn T, Köhrmann M, Endres M, Kang DW, Dousset V, Sorensen AG, Liebeskind DS,Fiebach JB, Fiehler J, Gerloff C; STIR and VISTAImaging Investigators (2011) DWI-FLAIR mismatch for the identification of patients with acute ischaemic stroke within 4·5 h of symptom onset (PRE-FLAIR): a multicentre observational study. Lancet Neurol. 10:978-86.

Muir KW, Buchan A, von Kummer R, Rother J, Baron JC. (2006) Imaging of acute stroke.Lancet Neurol. 5:755-68.

Nagel S, Herweh C, Köhrmann M, Huttner HB, Poli S, Hartmann M, Hähnel S, Steiner T, Ringleb P, Hacke W. (2011) MRI in patients with acute basilar artery occlusion - DWI lesionscoring is an independent predictor of outcome. Int J Stroke. 2011 Dec 8. doi: 10.1111/j.1747-4949.2011.00705.x.

Donnan GA, Baron JC, Ma H, Davis SM. (2009) Penumbral selection of patients for trials ofacute stroke therapy. Lancet Neurol.8:261-9.

Stagg CJ, Bachtiar V, O'Shea J, Allman C, Bosnell RA, Kischka U, Matthews PM, Johansen-Berg H. (2012) Cortical activation changes underlying stimulation-induced behavioural gains inchronic stroke. Brain. 135(Pt 1):276-84.

Dr. Jonathan BrooksUniversity of Bristol

Lecture title: fMRI Analysis:


(1) Huettel, Song, McCarthy "Functional Magnetic Resonance Imaging 2nd Ed." Sinauer (2009)

(2) Jezzard, Matthews, Smith "Functional MRI" Oxford University Press (2001)

(3) http://imaging.mrc-cbu.cam.ac.uk/imaging/PrinciplesStatistics

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

Dr. Jonathan BrooksUniversity of Bristol

Lecture title: Neuroimaging of Pain


(1) Craig, A. D. B. (2003). Pain mechanisms: labeled lines versus convergence in central processing. Annual Review of Neuroscience, 26, 1-30.

(2) Brooks, J., & Tracey, I. (2005). From nociception to pain perception: imaging the spinal and supraspinal pathways. Journal of Anatomy, 207(1), 19-33.

(3) Rodriguez-Raecke, R., Niemeier, A., Ihle, K., Ruether, W., & May, A. (2009). Brain gray matter decrease in chronic pain is the consequence and not the cause of pain. The Journal of Neuroscience. 29(44), 13746-13750.

(4) Eippert, F., Bingel, U., Schoell, E. D., Yacubian, J., Klinger, R., Lorenz, J., & Büchel, C. (2009). Activation of the opioidergic descending pain control system underlies placebo analgesia. Neuron, 63(4), 533-543.

Professor Mara CercignaniUniversity of Brighton

Lecture title: Neuroinflammatory Diseases by Magnetic Resonance


Stoll G, Bendszus M. New approaches to neuroimaging of central nervous system inflammation. Curr Opin Neurol. 2010: 23(3):282-6.

Stanisz GJ, Webb S, Munro CA, Pun T, Midha R. MR properties of excised neural tissue following experimentally induced inflammation. Magn Reson Med. 2004: 51(3):473-9.

Dousset V, Brochet B, Deloire MS, Lagoarde L, Barroso B, Caille JM, Petry KG. MR imaging of relapsing multiple sclerosis patients using ultra-small-particle iron oxide and compared with gadolinium. AJNR Am J Neuroradiol. 2006 May;27(5):1000-5.

Laule C, Vavasour IM, Kolind SH, Li DK, Traboulsee TL, Moore GR, MacKay AL. Magnetic resonance imaging of myelin. Neurotherapeutics. 2007 Jul;4(3):460-84.

Dr. Elizabeth CoulthardFrenchay Hospital, Bristol

Lecture title: Neurodegenerative Diseases by Magnetic Resonance


Malhotra P, Coulthard E, Husain M (2009) Role of posterior parietal cortex in maintaining attention to spatial locations over time. Brain 132(3): 645-660

Coulthard E, Husain M (2008). Inhibitory deficits in motor neglect. Journal of Neurology, Neurosurgery & Psychiatry. 79(12), 1401-1404

Coulthard E, Nachev P, Husain M (2008). Control over conflict during movement preparation: role of the posterior parietal cortex. Neuron. 58: 144-157

P. Nachev, E. Coulthard, R. Stolwyk, R. Jager, C. Kennard, L. Cipolotti, M. Husain (2008). Enantiomorphic Normalization of Focally Lesioned Brains. Neuroimage. 78:1038-1038

Dr. Frances Cowan

Imperial College London

Lecture title: Neonatal brain imaged by MRI


Cowan F, Rutherford M, Groenendaal F, Eken P, Mercuri E, Bydder GM, Meiners LC, Dubowitz LM, de Vries LS. (2003) Origin and timing of brain lesions in term infants with neonatal encephalopathy. Lancet. 361:736-42.

Rathbone R, Counsell SJ, Kapellou O, Dyet L, Kennea N, Hajnal J, Allsop JM, Cowan F, Edwards AD. (2011) Perinatal cortical growth and childhood neurocognitive abilities. Neurology. 77:1510-7.

Cowan FM, de Vries LS. (2005) The internal capsule in neonatal imaging. Semin Fetal Neonatal Med. 10:461-74.

Martinez-Biarge M, Diez-Sebastian J, Kapellou O, Gindner D, Allsop JM, Rutherford MA, Cowan FM. (2011) Predicting motor outcome and death in term hypoxic-ischemic encephalopathy. Neurology. 76:2055-61.

Dr. Paul Howard-JonesUniversity of Bristol

Lecture title: fMRI and Computer Modelling


Paul A. Howard-Jones, Rafal Bogacz, Jee H. Yoo, Ute Leonards, Skevi Demetriou (2010) The neural mechanisms of learning from competitors. Neuroimage, 53, pp. 790–799.

Birte U. Forstmann, Alfred Anwander, Andreas Schäfer, Jane Neumann, Scott Brown, Eric-Jan Wagenmakers, Rafal Bogacz, Robert Turner (2010) Cortico-Striatal Connections Predict Control over Speed and Accuracy in Perceptual Decision Making. Proceedings of the National Academy of Sciences of the USA, 107, pp. 15916–15920.

Dr. Mark JenkinsonUniversity of Oxford

Lecture title: Image Analysis


S.M. Smith BET: Brain Extraction Tool FMRIB technical Report TR00SMS2bhttp://www.fmrib.ox.ac.uk/analysis/research/bet/bet.pdf

J.L.R. Andersson, M Jenkinson, and S.M. Smith Non-linear registration aka Spatial normalization FMRIB Technial Report TR07JA2http://www.fmrib.ox.ac.uk/analysis/techrep/tr07ja2/tr07ja2.pdf

Good, CD and Johnsrude, IS and Ashburner, J. and Henson, RNA and Friston, KJ andFrackowiak, RSJ (2001) A voxel-based morphometric study of ageing in 465 normal adult human brains NeuroImage, 14(1):21-36.

Stephen M. Smith , Nicola De Stefano , Mark Jenkinson and Paul M. MatthewsMeasurement of Brain Change Over Time FMRIB Technical Report TR00SMS1 http://www.fmrib.ox.ac.uk/analysis/research/siena/siena.pdf

Y. Zhang, M. Brady, and S. Smith. (2001) 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.

Professor Derek K JonesCUBRICCardiff University

Lecture title: Diffusion Magnetic Resonance Imaging


1. Jones DK, Leemans A. Diffusion tensor imaging. Methods Mol Biol. 2011;71: 127-44

2. Jones DK. 2010. Precision and accuracy in diffusion tensor MRI. Top Magn Reson Imaging. 21: 87-99.

3. Jones DK, Cercignani M. 2010. 25 pitfalls in the analysis of diffusion tensor MRI data. NMR in Biomedicine 23:803-820.

4. Jones DK. 2010. Challenges and limitations of quantifying connectivity in the human brain in vivo with diffusion MRI. Imaging in Medicine 2: 341-355

5. Jones DK. 2008. Studying connections in the living human brain with diffusion MRI Cortex 44:936-52.

Professor Risto Kauppinen


Lecture title: Spontaneous BOLD fluctuations


Obrig H., Neufang M., Wenzel R., Kohl M. Steinbrink J., Einhauptl K., Villringer A. (2000) Speontaneous low frequency oscillations of cerebral hemodynamics and metabolism in human adults. NeuroImage 12: 623-9

Scholvinck M.L. Maier A., Ye F.Q. Duyn J.H., Leopold D.A. (2010) Neural basis of global resting-state fMRI activity. Proc Natl Acad Asi USA 107: 10238-43.

Kiviniemi V. (2008) Endogenous brain fluctuations and diagnostic imaging. Hum Brain Mapp29: 810-7.



Lecture title: Magnetic Resonance Spectroscopy


Kauppinen R.A. and Williams S.R. (1994) Nuclear magnetic resonance spectroscopy studies of the brain. Prog. Neurobiol. 44, 87-118.

Alger JR. (2010) Quantitative proton magnetic resonance spectroscopy and spectroscopic imaging of the brain: a didactic review. Top Magn Reson Imaging. 21:115-28.



Lecture title: BOLD signal


van Zijl P.C.M., Eleff S.E., Ulatowski J.A., Oja J.M.E., Ulug A.M., Traystman R.J. and Kauppinen R.A. (1998) Quantitative assessment of blood flow, blood volume and blood oxygenation by magnetic resonance imaging. Nature Med. 4, 159-167.

Dickson JD, Ash TW, Williams GB, Sukstanskii AL, Ansorge RE, Yablonskiy DA. (2011)Quantitative phenomenological model of the BOLD contrast mechanism. J Magn Reson.212:17-25.

Professor David Linden

University of Cardiff

Lecture title: Brain-Computer Interface and Magnetic Resonance


Weiskopf N. (2011) Real-time fMRI and its application to neurofeedback. Neuroimage. 2011 Oct 14.

Linden D. (2012) The challenges and promise of neuroimaging in psychiatry. Neuron 73:8-22

Dr. David Thomas

University College London

Lecture topic: Arterial Spin Labelling Flow Imaging


E.T. Petersen, I. Zimine, Y.C. Ho, X. Golay, Non-invasive measurement of perfusion: a critical review of arterial spin labelling techniques. Br. J. Radiol. 79, 688-701 (2006).

R.B. Buxton, L.R. Frank, E.C. Wong, B. Siewert, S. Warach, R.R. Edelman, A general kinetic model for quantitative perfusion imaging with arterial spin labelling. Magn Reson Med 40, 383-396 (1998).

H. Lu, M. Law, G. Johnson, Y. Ge, P.C. van Zijl, J.A. Helpern, Novel approach to the measurement of absolute cerebral blood volume using vascular-space-occupancy magnetic resonance imaging. Magn Reson. Med. 54, 1403-1411 (2005).

J.Hua, Q.Qin, J.J.Pekar, P.C.van Zijl, Measurement of absolute arterial cerebral blood volume in human brain without using a contrast agent. NMR Biomed. 24, 1313-1325 (2011).

Professor Stephen Williams

King’s College London

Lecture title: Neuropsychiatry and Magnetic Resonance


Kempton MJ, Salvador Z, Munafò MR, Geddes JR, Simmons A, Frangou S, Williams SC. Structural neuroimaging studies in major depressive disorder. Meta-analysis and comparison with bipolar disorder. Arch Gen Psychiatry. 2011 Jul;68(7):675-90.

Kempton MJ, Geddes JR, Ettinger U, Williams SC, Grasby PM. Meta-analysis, database, and meta-regression of 98 structural imaging studies in bipolar disorder. Arch Gen Psychiatry. 2008 Sep;65(9):1017-32.

Mitterschiffthaler MT, Ettinger U, Mehta MA, Mataix-Cols D, Williams SC. Applications of functional magnetic resonance imaging in psychiatry. J Magn Reson Imaging. 2006 Jun;23(6):851-61. Review.

Fu CH, Williams SC, Cleare AJ, Brammer MJ, Walsh ND, Kim J, Andrew CM, Pich EM, Williams PM, Reed LJ, Mitterschiffthaler MT, Suckling J, Bullmore ET. Attenuation of the neural response to sad faces in major depression by antidepressant treatment: a prospective, event-related functional magnetic resonance imaging study. Arch Gen Psychiatry. 2004 Sep;61(9):877-89.

Dr. Martin WilsonUniversity of Birmingham

Lecture title: MRS Data Analysis


Poullet, J. B., Sima, D. M. & Van Huffel, S. MRS signal quantitation: a review of time- and frequency-domain methods. J Magn Reson 195, 134-144, doi:10.1016/j.jmr.2008.09.005 (2008).

Wilson, M., Reynolds, G., Kauppinen, R. A., Arvanitis, T. N. & Peet, A. C. A constrained least-squares approach to the automated quantitation of in vivo (1)H magnetic resonance spectroscopy data. Magn Reson Med 65, 1-12, doi:10.1002/mrm.22579 (2011).

Ramadan, S. et al. Use of in vivo two-dimensional MR spectroscopy to compare the biochemistry of the human brain to that of glioblastoma. Radiology 259, 540-549, doi:10.1148/radiol.11101123 (2011).

Professor Richard Wise

University of Cardiff

Lecture title: BOLD Physiology

Relevant literature

Buxton RB, Uludag K, Dubowitz DJ, Liu TT. (2004) Modeling the hemodynamic response to brain activation. Neuroimage. 23 Suppl 1:S220-33.

Logothetis NK. (2008) What we can do and what we cannot do with fMRI. Nature. 453:869-78.

Iannetti GD, Wise RG.(2007) BOLD functional MRI in disease and pharmacological studies: room for improvement? Magn Reson Imaging. 25(6):978-88.

Documents

The 2012 Bristol MR Summer School...1.50–2.40 Cognitive neuroscience applications Pascal Belin 3.00–3.50 fMRI and computer modelling Paul Howard-Jones 3.50–4.40 MR spectroscopy