Topics and Reading Schedule for M285 - Functional Neuroimaging

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LEGEND & Notes
- Required Reading
- Required but not available on line. Contact Donnafaye Miranda to borrow and duplicate our file copy
- Not available in digital form at this time.
- Optional Reading.
All others are required and can be downloaded from this site and viewed with Acrobat Reader
We are legally required to limit access to the PDF files to educational uses. In practise, this means that you cannot download them unless you are using a UCLA IP address. If you are using your computer from home, you may set up proxy services by following the instructions at http://www.bol.ucla.edu/services/proxy/ I will honor all requests for non-proxy access, even for academic uses at other institutions, but you must send email to Mark Cohen
This syllabus can, and will, evolve during the course. Problems sets on this page are place holders only until assigned.

Please Complete Reading prior to Class.

Schedule
Week of	Tuesday	Thursday
9/30		MRI Basics Required readings Chapters 1 & 2 of Huettel, et al. The slides and figures for this talk can be found at: MRI Teaching Slides
10/5	MRI Basics (cont'd) MRI Teaching Slides Required readings: Chapters 3 through 5 of Huettel, et al. the Rochester MRI Web tutorial This is a link to a superb web-based tutorial. Highly recommended for anyone who wants to actually learn about MR physics Optional readings: Rapid Imaging Overview A summary of a few popular methods of fast imaging EPI Theory The principles of Echo-Planar Imaging Physical Foundations of MR Imaging What is magnetization? What is the relation between nuclear magnetism and radio? MR Basics General Physical Principles of Magnetic Resonance Contrast MRI Teaching Slides (old)	Neurovascular Coupling Guest Lecturer: Stephen Engel Neurovascular coupling teaching slides Problem Set 1 - Due 10/12 Required readings: Chapter 6 of Huettel "A model for the coupling between cerebral blood flow and oxygen metabolism during neural stimulation.", Buxton RB, Frank LR, J Cereb Blood Flow Metab 1997 Jan;17(1):64-72 [PDF] "Single-neuron activity and tissue oxygenation in the cerebral cortex." Thompson JK, Peterson MR, Freeman RD. Science. 2003 Feb 14;299(5609):1070-2. [PDF] A Primer on Convolution Optional readings: "Dynamics of blood flow and oxygenation changes during brain activation: the balloon model."Buxton, RB; Wong, EC; Frank, LR., Magnetic Resonance in Medicine, 1998 Jun, 39(6):855-64. [PDF] "Persistent resetting of the cerebral oxygen/glucose uptake ratio by brain activation: evidence obtained with the Kety-Schmidt technique." Madsen PL, Hasselbalch SG, Hagemann LP, Olsen KS, Bulow J, Holm S, et al. J Cereb Blood Flow Metab 1995; 15: 485-91. [PDF] "Neuron-to-astrocyte signaling is central to the dynamic control of brain microcirculation." Zonta, M, et al., Nat Neurosci. 2003 Jan;6(1):43-50 [PDF]
10/12	fMRI History of fMRI Flavors of fMRI Models of the fMRI signal fMRI Basics Slides Required Readings: Chapter 7 of Huettel et al. Neurophysiological investigation of the basis of the fMRI signal" Logothetis, N. K., Pauls, J., Augath, M., Trinath, T., Oeltermann, A. Nature 412:150-157. 2001 [PDF] Localization of Brain Function by Magnetic Resonance Imaging Added 10/12 : Some notes on Convolution Optional Readings: Basic Theoretical Models of BOLD Signal Change, RM Weisskoff, in Moonen and Bandettini, "Functional MRI" Springer, 1999	Experimental Design I: Concepts How can we map cognitive concepts onto brain activity? Subtractive Logic Conjunction Analysis Parametric and Factorial Designs Adaptation/Priming Designs The Concept of a "baseline" Experimental design teaching slides We had a special optional session on the Fourier transform. The notes to which are [here]. matlab: Fourier analysis of blocked designs Problem Set 2 - Due 10/21 Required readings: Chapter 11 of Huettel, et al. Friston, KJ; Price, CJ; Fletcher, P; Moore, C; Frackowiak, RS; Dolan, RJ. "The trouble with cognitive subtraction." Neuroimage, 1996 Oct, 4(2):97-104 [PDF] "Experimental Design for Brain fMRI" Aguirre, GK, D'Esposito, M. in Moonen and Bandettini, "Functional MRI" Springer, 1999 Optional Readings: "Searching for a baseline: functional imaging and the resting human brain." Gusnard DA, Raichle ME, Raichle ME. Nat Rev Neurosci. 2001 Oct;2(10):685-94. [PDF] Caplan D, Moo L. Cognitive conjunction and cognitive functions. Neuroimage. 2004 Feb;21(2):751-6. [PDF] Grill-Spector K, Malach R. fMR-adaptation: a tool for studying the functional properties of human cortical neurons. Acta Psychol (Amst). 2001 Apr;107(1-3):293-321. [PDF]
10/19	Analysis I: The General Linear Model Linear systems analysis The general linear model Matrix form Assumptions of the GLM Temporal autocorrelation pre-whitening Analysis I teaching slides Required Readings: Chapter 12 (p. 321-343) and Chapter 8 (p. 206-214) of Huettel et al. Tom Wickens' GLM basics from IPAM MBI 2004 [PDF] Optional Readings: Woolrich MW, Ripley BD, Brady M, Smith SM. Temporal autocorrelation in univariate linear modeling of FMRI data. Neuroimage. 2001 Dec;14(6):1370-86. [PDF]	Experimental Design II Blocked versus event-related designs Hybrid designs Design efficiency and optimization Modeling trial components Subject-paced designs Sparse sampling designs Experimental design II teaching slides Problem set 3 - due 10/28 Required readings: "Event-related Functional MRI" Buckner, RL and Braver, TS, in Moonen and Bandettini, "Functional MRI" Springer, 1999 Dale AM. Optimal experimental design for event-related fMRI. Hum Brain Mapp. 1999;8(2-3):109-14. [PDF] Optional readings: Zarahn E. Testing for neural responses during temporal components of trials with BOLD fMRI. Neuroimage. 2000 Jun;11(6 Pt 1):783-96. [PDF] Liu TT, Frank LR, Wong EC, Buxton RB. Detection power, estimation efficiency, and predictability in event-related fMRI. Neuroimage. 2001 Apr;13(4):759-73. [PDF]
10/26	NO CLASS Society for Neuroscience	Analysis II Multiple tests Gaussian random fields False discovery rate Nonparametric methods Bayesian models Modeling connectivity Analysis II teaching slides Problem set 4 - due 11/3 Required readings: Chapter 12 (p. 343-356) of Huettel et al. Genovese CR, Lazar NA, Nichols T. Thresholding of statistical maps in functional neuroimaging using the false discovery rate. Neuroimage. 2002 Apr;15(4):870-8. [PDF] Chris Genovese's Bayesian modeling slides from IPAM MBI 2004 [PDF] Optional readings: Petersson KM, Nichols TE, Poline JB, Holmes AP. Statistical limitations in functional neuroimaging. I. Non-inferential methods and statistical models. Philos Trans R Soc Lond B Biol Sci. 1999 Jul 29;354(1387):1239-60. [PDF] Petersson KM, Nichols TE, Poline JB, Holmes AP. Statistical limitations in functional neuroimaging. II. Signal detection and statistical inference. Philos Trans R Soc Lond B Biol Sci. 1999 Jul 29;354(1387):1261-81. [PDF] McIntosh. "Understanding neural interactions in learning and memory using functional neuroimaging" Annals of the New York Academy of Sciences 855:556-571 (1998). [PDF] Nichols T, Hayasaka S. Controlling the Familywise Error Rate in Functional Neuroimaging: A Comparative Review. Statistical Methods in Medical Research, 12(5): 419-446, 2003. [PDF]
11/2	Class Project Presentations and Continued Growth through Self-Criticism.
11/9	Physical and Physiological Limitations and Tradeoffs Sources and nature of noise in fMRI Determinants of fMRI signals Field strength Coil design Spatial and temporal resolution of fMRI Limitations teaching slides Required readings: Chapter 8 (p. 185-206) and Chapter 9 of Huettel et al. A collection of MR Artifacts Wayne Patola's MR artifacts Syrinx artifact paper Motion Artifacts D. J. McGonigle, A. M. Howseman, B. S. Athwal, K. J. Friston, R. S. J. Frackowiak, and A. P. Holmes, "Variability in fMRI: An Examination of Intersession Differences", NeuroImage 11, 708–734 2000. [PDF] Hajnal, JV., Myers R, Oatridge A, Schwieso JE., Young IR."Artifacts Due to Stimulus Correlated Motion in Functional Imaging of the Brain" Magnetic Resonance in Medicine 31(3):281. 1994 (Sorry, this is not available in PDF at this time.)	Scanner Demo We will bring in (at least) one of the student-designed projects and perform the experiment. This session takes place on Veteran's day (sorry). We would appreciate volunteers to participate.
11/16	Practical Data Processing In this session we will use available processing tools to extract functional data acquired in the demo, using FSL and AFNI. Data processing teaching slides Problem set 5 - due 11/23! Required readings: FSL Documentation AFNI documentation pages Bandettini, PA; Jesmanowicz, A; Wong, EC; Hyde, JS. Processing strategies for time-course data sets in functional MRI of the human brain. Magnetic Resonance in Medicine, 1993 Aug, 30(2):161-73 [PDF] Optional readings: Friston, K J; Holmes, A P; Worsley, K J; Poline, J-P; Frith, C D; Frackowiak, R S J. Statistical parametric maps in functional imaging: A general linear approach. Human Brain Mapping, v.2, n.4, 1994-1995:189-210 [PDF]	Quality control and data pre-processing Quality control and artifact detection Introduction to spatial processing Linear and nonlinear transforms Correction of spatial distortions B0 field mapping and unwarping Motion correction The problem of task-correlated motion Spin-history effects Including motion in the statistical model Slice timing correction Spatial smoothing why? why not? Preprocessing teaching slides Required readings: Chapter 10 of Huettel et al. Optional readings: Bullmore ET, Brammer MJ, Rabe-Hesketh S, Curtis VA, Morris RG, Williams SC, Sharma T, McGuire PK. Methods for diagnosis and treatment of stimulus-correlated motion in generic brain activation studies using fMRI. Hum Brain Mapp. 1999;7(1):38-48. [PDF] Friston KJ, Williams S, Howard R, Frackowiak RS, Turner R. Movement-related effects in fMRI time-series. Magn Reson Med. 1996 Mar;35(3):346-55. (may be replaced!) [PDF]
11/23	Spatial Normalization Guest Lecturer: Paul Thompson Atlases for neuroimaging Functional variability Methods for spatial normalization Volume-based methods Surface-based methods Region-of-interest methods Spatial normalization teaching slides Problem set 6 - due 12/2 Required readings: Brett M, Johnsrude IS, Owen AM. The problem of functional localization in the human brain. Nat Rev Neurosci. 2002 Mar;3(3):243-9. [PDF] Van Essen, DC; Drury, HA; Joshi, S; Miller, MI. Functional and structural mapping of human cerebral cortex: solutions are in the surfaces. Proceedings of the National Academy of Sciences of the United States of America, 1998 Feb 3, 95(3):788-95. [PDF] Thompson PM, Giedd JN, Woods RP, MacDonald D, Evans AC, Toga AW. "Growth patterns in the developing brain detected by using continuum mechanical tensor maps. Nature, 2000 404(9):190-193. [PDF] Michael M. Zeineh, Stephen A. Engel, Paul M. Thompson, Susan Y. Bookheimer. 'Dynamics of the Hippocampus During Encoding and Retrieval of Face-Name Pairs", Science 2003. 299(24):577-560. [PDF] Watson JDG, Myers R, Frackowiak RSJ, Hajnal JV, Woods RP, Mazziotta JC, Shipp S, Zeki S "Area V5 of the human brain: evidence from a combined study using positron emission tomography and magnetic resonance imaging." Cerebral Cortex 3, 79-94, 1993. [PDF???] Optional readings: Ashburner J, Friston, KJ. Image registration. in Moonen and Bandettini, "Functional MRI" Springer, 1999 [PDF] (A fairly mathy but very solid introduction to volume-based registration techniques) Amunts K, Schleicher A, Ditterich A, Zilles K. Broca's region: cytoarchitectonic asymmetry and developmental changes. J Comp Neurol. 2003 Oct 6;465(1):72-89. [PDF] Roger Woods' pages on spatial transformation models in AIR thompson, woods? *tbd*	Happy Thanksgiving!
11/30	Group Statistics Approaches to group analyses: region-based analyses summary statistics approach mixed-effects modeling Power analyses and sample size Group statistics teaching slides Required readings: Beckmann CF, Jenkinson M, Smith SM. General multilevel linear modeling for group analysis in FMRI. Neuroimage. 2003 Oct;20(2):1052-63. [PDF] Desmond JE, Glover GH. Estimating sample size in functional MRI (fMRI) neuroimaging studies: statistical power analyses. J Neurosci Methods. 2002 Aug 30;118(2):115-28. [PDF] Smith, S., Beckmann, C., Ramnani, N., Woolrich, M., Bannister, P., Jenkinson, M., Matthews, P., and McGonigle, D. (2004). Variability in FMRI: A re-examination of intersession differences. Human Brain Mapping, in press. [PDF] Optional readings: Friston KJ, Holmes AP, Worsley KJ. How many subjects constitute a study? Neuroimage. 1999 Jul;10(1):1-5. [PDF]	Other stuff This class session will introduce a number of novel methods of data analysis that are either model-free and attempt to expose latent variables in the data or are driven by non-traditional independent variables. Machine Learning Resting States Model-free analyses (PCA/ICA) Teaching slides Problem set 7 - due 12/9 Required readings: Resting states Biswal, et al., "Simultaneous Assessment of Flow and BOLD Signals in Resting-State Functional Connectivity Maps" NMR Biomed. 10:165 (1997) [PDF] Pattern recognition Haxby, et al., "Distributed and Overlapping Representations of Faces and Objects in Ventral Temporal Cortex" Science 293:2425 (2001). [PDF] Cox and Savoy. "Functional magnetic resonance imaging (fMRI) "brain reading": detecting and classifying distributed patterns of fMRI activity in human visual cortex", NeuroImage 19(2):261, (2003). [PDF] Model-free analyses FMRIB documentation of their Independent Components Analysis tool (MELODIC) [HTML] Optional readings: Machine learning T.M. Mitchell, R. Hutchinson, R.S. Niculescu, X. Wang, M. Just, S. Newman. "Learning to Decode Cognitive States from Brain Images" [PDF] PCA/ICA StatSoft's introduction to Principal Components Analysis The serious GFP (glutton for punishment) will read the original papers: McKeown, et al., "Analysis of fMRI dadta by blind separation into independent spatial components", Hum. Brain Mapp. 6:160 (1998) [PDF] Bell and Sejnowski, "An information maximisation approach to blind separation and blind deconvolution." Neural computation 7:1004 (1995) [PDF] Structural equation modeling StatSoft introduction to Structural Equations
12/7	Multimodal Imaging and leftovers Multimodal Integration (EEG/MEG, TMS) Direct Current Measurement Latest Tools in MRI (Parallel imaging, Diffusion Tractography, Arterial Spin Labeling) Future Areas of Growth Amusing New Literature Required readings: Chapter 15 of Huettel, et al. RI Goldman, JM Stern, J Engel, MS Cohen . "Simultaneous EEG and fMRI of the alpha rhythm." Neuroreport 2002; 13(18):2487-2492. [PDF]	Critiquing the Literature (picks and pans) This will be handled as a set of in class debates. See the assignment list for details. Illes J. Neuroethics in a new era of neuroimaging. AJNR Am J Neuroradiol. 2003 Oct;24(9):1739-4 Is there a brain region specialized uniquely for the perception of faces? Gauthier I, Tarr MJ, Anderson AW, Skudlarski P, Gore JC. Activation of the middle fusiform 'face area' increases with expertise in recognizing novel objects. Nat Neurosci. 1999 Jun;2(6):568-73. Kanwisher, N; McDermott, J; Chun, MM. The fusiform face area: a module in human extrastriate cortex specialized for face perception. Journal of Neuroscience, 1997 Jun 1, 17(11):4302-11. Does fMRI, particularly the initial dip in fMRI, enable resolution to the level of cortical columns? Kim DS, Duong TQ, Kim SG. High-resolution mapping of iso-orientation columns by fMRI. Nat Neurosci. 2000 Feb;3(2):164-9. Lindauer U, Royl G, Leithner C, Kuhl M, Gold L, Gethmann J, Kohl-Bareis M, Villringer A, Dirnagl U. No evidence for early decrease in blood oxygenation in rat whisker cortex in response to functional activation. Neuroimage. 2001 Jun;13(6 Pt 1):988-1001. What are the ethical limitations and boundaries to the use of fMRI? Phelps EA, O'Connor KJ, Cunningham WA, Funayama ES, Gatenby JC, Gore JC, Banaji MR. Performance on indirect measures of race evaluation predicts amygdala activation. J Cogn Neurosci. 2000 Sep;12(5):729-38. McClure SM, Li J, Tomlin D, Cypert KS, Montague LM, Montague PR. Neural correlates of behavioral preference for culturally familiar drinks. Neuron. 2004 Oct 14;44(2):379-87. Background reading: In Love?: You just lit up your medial insula Greene JD, Sommerville RB, Nystrom LE, Darley JM, Cohen JD. An fMRI investigation of emotional engagement in moral judgment. Science. 2001 Sep 14;293(5537):2105-8. [PDF] The Mind of a Killer - [movie] Brain Fingerprinting - Farwell Brain Fingerprinting Is there a brain region hyperspecialized to the perception of classes of objects? Haxby JV, Gobbini MI, Furey ML, Ishai A, Schouten JL, Pietrini P. Distributed and overlapping representations of faces and objects in ventral temporal cortex. Science. 2001 Sep 28;293(5539):2425-30. Chao LL, Haxby JV, Martin A. Attribute-based neural substrates in temporal cortex for perceiving and knowing about objects. Nat Neurosci. 1999 Oct;2(10):913-9. Finals handed out in class The Final is Found [HERE]
12/14	Finals due in class

Miscellaneous fMRI-related Reading, on line from prior course sessions.

An example of a complete fMRI study - Please read before class, if possible:

"Inattentional Blindness Versus Inattentional Amnesia for Fixated But Ignored Words" Geraint Rees, Charlotte Russell, Christopher D. Frith, and Jon Driver Science Dec 24 1999: 2504-2507. [Abstract] [Full Text] [PDF]

Data Analysis

Lange, N; Strother, SC; Anderson, JR; Nielsen, FA; Holmes, AP; Kolenda, T; Savoy, R; Hansen, LK. Plurality and resemblance in fMRI data analysis. Neuroimage, 1999 Sep, 10:282-303
"Statistical Procedures for Functional MRI" Lange, N. in Moonen and Bandettini, "Functional MRI" Springer, 1999 (Sort of a reference tool)

Experimental design

"Functional Imaging in Behavioral Neurology and Cognitive Neuropsychology." Aguirre, G.K., in T. E. Feinberg & M. J. Farah (Eds.), Behavioral Neurology and Cognitive Neuropsychology . (in press). New York: McGraw Hill. [PDF]

Clinical Applications in Psychiatry

Bullmore E, Brammer M, Williams SCR, et al (1999): Functional MR imaging of confounded hypofrontality. Human Brain Mapping 8:86-91.[PDF]
Callicott JH, Weinberger DR (1999): Neuropsychiatric dynamics: the study of mental illness using functional magnetic resonance imaging. Eur J Radiol 30:95-104.[PDF]
Perlstein WM, Carter CS, Noll DC, Cohen JD (2001): Relation of prefrontal cortex dysfunction to working memory and symptoms in schizophrenia. American Journal of Psychiatry 158:1105-13.[PDF]

Attention/Imagery

O'Craven, K. M., Rosen, B. R., Kwong, K. K., Treisman, A, Savoy, R. L. "Voluntary attention modulates fMRI activity in human MT-MST" Neuron 18:591, 1997 [PDF]
Cohen, MS, SM Kosslyn, HC Breiter, GJ DiGirolamo, WL Thompson, AK Anderson, SY Brookheimer, BR Rosen & JW Belliveau, Changes in cortical activity during mental rotation. A mapping study using functional MRI. Brain, 1996. 119(Pt 1): p. 89-100. [PDF]
Chen, W, T Kato, XH Zhu, S Ogawa, DW Tank & K Ugurbil, Human primary visual cortex and lateral geniculate nucleus activation during visual imagery. Neuroreport, 1998. 9(16): p. 3669-74. [PDF]
Goebel, R, D Khorram-Sefat, L Muckli, H Hacker & W Singer, The constructive nature of vision: direct evidence from functional magnetic resonance imaging studies of apparent motion and motion imagery. Eur J Neurosci, 1998. 10(5): p. 1563-73.
Luft, AR, M Skalej, A Stefanou, U Klose & K Voigt, Comparing motion- and imagery-related activation in the human cerebellum: a functional MRI study. Hum Brain Mapp, 1998. 6(2): p. 105-13. [PDF]
Le Bihan, D, R Turner, TA Zeffiro, CA Cuenod, P Jezzard & V Bonnerot, Activation of human primary visual cortex during visual recall: a magnetic resonance imaging study. Proc Natl Acad Sci U S A, 1993. 90(24): p. 11802-5. [PDF]

Vision

Sereno, MI; Dale, AM; Reppas, JB; Kwong, KK; Belliveau, JW; Brady, TJ; Rosen, BR; Tootell, RB. Borders of multiple visual areas in humans revealed by functional magnetic resonance imaging. Science 268:889-893, 1995. [PDF]
Mendola, JD; Dale, AM; Fischl, B; Liu, AK; Tootell, RB. The representation of illusory and real contours in human cortical visual areas revealed by functional magnetic resonance imaging. Journal of Neuroscience, 1999 Oct 1, 19(19):8560-72 [PDF]
Heeger, DJ; Boynton, GM; Demb, JB; Seidemann, E; Newsome, WT. Motion opponency in visual cortex. Journal of Neuroscience, 1999 Aug 15, 19(16):7162-74 [PDF]
Grill-Spector, K; Kushnir, T; Hendler, T; Malach, R. The dynamics of object-selective activation correlate with recognition performance in humans. Nature Neuroscience 2000 Aug, 3(8):837-43. [PDF]
Levy, I, Hasson, U., Avidan, G., Hendler, T., Malach, R. Center-periphery organization of human object areas Nature Neuroscience 4, 533 - 539 (May 2001) [PDF]
"Area V5 of the human brain: evidence from a combined study using positron emission tomography and magnetic resonance imaging." Watson, J. D., et al. Cerebral

Memory

Brewer, JB; Zhao, Z; Desmond, JE; Glover, GH; Gabrieli, JD. Making memories: brain activity that predicts how well visual experience will be remembered. Science, 1998 Aug 21, 281(5380):1185-7. [PDF]
Buckner, R.L, & Wheeler, M.E., The Cognitive Neuroscience of Remembering Nature Reviews Neuroscience 2, 624 - 634 (September 2001) (a PDF is expected)
D'Esposito, M; Postle, BR; Rypma, B. Prefrontal cortical contributions to working memory: evidence from event-related fMRI studies. Experimental Brain Research 2000 Jul, 133(1):3-11 [PDF]
Henson, RN; Rugg, MD; Shallice, T; Josephs, O; Dolan, RJ. Recollection and familiarity in recognition memory: an event-related functional magnetic resonance imaging study. Journal of Neuroscience, 1999 May 15, 19(10):3962-72 [PDF]
Zarahn, E; Aguirre, GK; D'Esposito, M. Temporal isolation of the neural correlates of spatial mnemonic processing with fMRI. Brain Research. Cognitive Brain Research, 1999 Jan, 7(3):255-68

Other

Cortex, 3:79-94, 1993
Binder, J.R., S.M. Rao, T.A. Hammeke, J.A. Frost, P.A. Bandettini, A. Jesmanowicz, and J.S. Hyde."Lateralized human brain language systems demonstrated by task subtraction functional magnetic resonance imaging". Arch Neurol. 52(6):593-601. 1995 [PDF]
Mirella Dapretto and Susan Y. Bookheimer, "Form and Content: Dissociating Syntax and Semantics in Sentence Comprehension". Neuron 1999 24: 427.
Wagner AD, Pare-Blagoev EJ, Clark J, Poldrack RA. "Recovering meaning: left prefrontal cortex guides controlled semantic retrieval." Neuron. 2001 Aug 2;31(2):329-38 [PDF]
Shaywitz BA, Shaywitz SE, Pugh KR, Constable RT, Skudlarski P, Fulbright RK, Bronen RA, Fletcher JM, Shankweiler DP, Katz L, et al, "Sex differences in the functional organization of the brain for language." Nature Feb 16;373(6515):607-9, 1995 [PDF]
Petersen, S.E., P.T. Fox, M.I. Posner, M. Mintun, and M.E. Raichle."Positron emission tomographic studies of the cortical anatomy of single-word processing". Nature. 331(6157):585-9. 1988
Engel, S; Zhang, X; Wandell, B. "Colour tuning in human visual cortex measured with functional magnetic resonance imaging" Nature, 1997 Jul 3, 388(6637):68-71. [PDF]
Wagner, AD; Schacter, DL; Rotte, M; Koutstaal, W; Maril, A; Dale, AM; Rosen, BR; Buckner, RL. Building memories: remembering and forgetting of verbal experiences as predicted by brain activity. Science, 1998 Aug 21, 281(5380):1188-91. [PDF]
"Event-related Functional MRI" Buckner, RL and Braver, TS, in Moonen and Bandettini, "Functional MRI" Springer, 1999

M285 - Functional Neuroimaging

Topics and Reading Schedule for M285 - Functional Neuroimaging

CLASS e-mail list <== broadcast e-mail to your classmates. Please do not abuse (SPAM).

Week of

Tuesday

Thursday

MRI Basics

Required readings

MRI Basics (cont'd)

Required readings:

Optional readings:

Neurovascular Coupling

Required readings:

Optional readings:

fMRI

Required Readings:

Optional Readings:

Experimental Design I: Concepts

Required readings:

Optional Readings:

Analysis I: The General Linear Model

Required Readings:

Optional Readings:

Experimental Design II

Experimental design II teaching slides Problem set 3 - due 10/28 Required readings:

Optional readings:

NO CLASS Society for Neuroscience

Analysis II

Analysis II teaching slides Problem set 4 - due 11/3 Required readings:

Optional readings:

Class Project Presentations and Continued Growth through Self-Criticism.

Physical and Physiological Limitations and Tradeoffs

Limitations teaching slides

Required readings:

Scanner Demo

Practical Data Processing

Data processing teaching slides Problem set 5 - due 11/23! Required readings:

Optional readings:

Quality control and data pre-processing

Preprocessing teaching slides Required readings:

Optional readings:

Spatial Normalization

Problem set 6 - due 12/2 Required readings:

Optional readings:

Happy Thanksgiving!

Group Statistics

Group statistics teaching slides Required readings:

Optional readings:

Other stuff

Teaching slides Problem set 7 - due 12/9

Required readings:

Optional readings:

Multimodal Imaging and leftovers

Required readings:

Critiquing the Literature (picks and pans)

Finals handed out in class

Miscellaneous fMRI-related Reading, on line from prior course sessions.

An example of a complete fMRI study - Please read before class, if possible:

Data Analysis

Experimental design

Clinical Applications in Psychiatry

Attention/Imagery

Vision

Memory

Other

Experimental design II teaching slides

Problem set 3 - due 10/28

Required readings:

NO CLASS
Society for Neuroscience

Analysis II teaching slides

Problem set 4 - due 11/3

Required readings:

Data processing teaching slides

Problem set 5 - due 11/23!

Required readings:

Preprocessing teaching slides

Required readings:

Problem set 6 - due 12/2

Required readings:

Group statistics teaching slides

Required readings:

Teaching slides

Problem set 7 - due 12/9

Critiquing the Literature
(picks and pans)