University of California, San Diego

Cognitive Science 279: Electrophysiology of Cognition

Spring Quarter 2013
Tu/Th 11:00-12:20 pm; CSB 180

(to Marta Kutas' courses)

Instructor: Prof. Marta Kutas
Office: CSB 155
Phone: 858-534-7450

Course Description and Goals

This course surveys the theory and practice of using recordings of electrical activity of the brain to study cognition and behavior. It explores what brain-waves reveal about normal and abnormal perception, processing, decision-making, memory, preparation, and comprehension. The course aims to give students: (1) knowledge (at both a technical and inferential level) of how electrophysiological techniques can be used to address issues in cognitive science, (2) practice with critically reading and evaluating research reports and reviews in the area, and (3) experience in developing research questions, designing experiments to test those questions, and writing research proposals.

On completion of this course, students should be able to:

  • demonstrate a basic level of competence with the technical and theoretical aspects of electrophysiological recordings
  • identify and explain how electrophysiological methods have contributed to our current understanding of various aspects of cognition
  • analyze and evaluate primary research reports in the area
  • develop an interesting and important research question
  • outline a research proposal that documents how that question might be addressed using electrophysiological methods


In brief, 50% of a student's grade will be based on his/her performance on two exams (midterm and final, each worth 25% of the final grade); exam questions will be derived from both the assigned readings and from lecture material. The remaining 50% of the grade will be based on the quality of a research proposal or a thoughtful literature review (5% for a 2-page version of the proposal; 20% for oral presentation, and 25% for the final 7-10 page proposal). In that paper, the student will be required to either (1) conduct a scholarly review of the ERP literature in an area of interest, concluding with a clear synthetic/analytic summary, or (2) review the literature in an area of interest, develop a research question based on the review, and design an experiment, using electrophysiological methods (alone or in combination with others), to test that question (ideas and readings for domains available upon request). Note that writing does count in the evaluation of the paper: students are expected to be able to write clearly and in a manner that is stylistically appropriate for a scientific paper. Accurate and appropriate documentation of sources is essential; plagiarism in any form will not be tolerated.

Problem Sets

Six problem sets are posted to guide reading of the articles. These are designed to help you consolidate the information covered in the readings and in lecture. Note that some of the questions in the problem set will re-appear on the exams. Other questions will resemble those on the exams, and thus can serve as a study guide.

Problem Set 1
Problem Set 2
Problem Set 3
Problem Set 4
Problem Set 5
Problem Set 6

Midterm = 25% (Thursday 5/2)

Research Proposal = 50%

5% for first proposal-related 2-page paper (due Thursday 5/21)

20% oral presentation of research proposal to class (last two classes 6/4 or 6/6)

25% for final (7-10 page) proposal (due no later than 4 pm, Thursday 6/6)

Final Exam = 25% (Tuesday, June 11, 11:30-2:30 PM; CSB 180)

The midterm and final exam will be similar both in format and in content to the problem sets. The exam will include short answer and essay questions based on material presented in the readings and in lecture.

Required readings will be posted online

When reading review articles keep the following questions in mind:

  • What are the issues that the author takes to be central to his/her area?
  • What are some advantages of electrophysiological techniques for addressing those issues?
  • How have electrophysiological techniques been used in this area to date?
    • what are typical designs for experiments in this area?
    • what aspects of the electrophysiological signal have been focused on?
    • what insights about cognition/physiology have been obtained?

When reading experimental reports keep the following questions in mind:

  • What is the general goal of the study? What is the specific hypothesis being tested? (Note that these are two separate questions.)
  • How does the experimental design address the question?
  • What are possible outcomes of the experiment and what would each mean?
  • What was the actual outcome?
  • What are the authors conclusions? Are there alternative explanations?
  • What are some further questions and how might you address them?


Cohen, D., and Cuffin, N.B. (1991). EEG Versus MEG Localization Accuracy: Theory and Experiment, Brain Topography, Vol 4(2), pp. 95-103.

Liu, A.K., Dale, A.M., and Belliveau, J.W. (2002). Monte Carlo Simulation Studies of EEG and MEG Localization Accuracy, Human Brain Mapping, Vol 16, pp. 47-62.

Irimia, A., Acar, Z.A., Hagler, D.J., Dale, A.M., Huang, M.X., and Halgren, E., Cortical Lead Fields of Electroencephalographic and Magnetoencephalographic Sensors, Submitted.

Halgren E. (2008). Considerations in Source Estimation of the P3, In: Ikeda I, Inoue Y, eds. Event-related Potentials in Patients with Epilepsy: from Current State to Future Prospects, Paris: John Libbey Eurotext, pp. 71-87.

Dehghani, N., Cash, S.S., Halgren, E. (2010). Emergence of Synchronous EEG Spindles From Asynchronous MEG Spindles, Human Brain Mapping, in print.

Dehghani, M., Cash, S.S., Chen, C.C., Hagler, D.J., Huang, M., Dale, A.M., Halgren, E. (2010). Divergent Cortical Generators of MEG and EEG during Human Sleep Spindles Suggested by Distributed Source Modeling, PLoS ONE,, 5(7), pp. 1-11.

Dehghani, N., Cash, S.S., Rossetti, A.O., Chen, C.C., and Halgren, E. (2010). Magnetoencephalography Demonstrates Multiple Asynchronous Generators During Human Sleep Spindles, Journal of Neurophysiology, 104, pp. 179-188.

Hamalainen, M., and Hari, R. (2004). Magnetoencephalographic (MEG) Characterization of Dynamic Brain Activation, Brain Mapping: The Methods, 2nd Edition, Toga et al. (eds).

Course Schedule and Readings

Readings that are designated required constitute the core material for the class and, along with information presented in the lectures, will form the basis for exam questions. Readings designated recommended provide additional examples of how electrophysiological methods have been used to address issues in a given topic area. It is suggested that students complete the recommended readings in one or more areas of interest to assist them in developing their research proposal. Note that to help the student prepare the final paper, the end of the reader contains additional information about what to include in a research report and about the documentation of references.

TUESDAY, APRIL 2 - slides

Physiological Basis of EEG, ERPs, and MEG
THURSDAY, APRIL 4 - slides

(review) Allison, T., Wood, C. C., and McCarthy, G. (1986). The central nervous system. In M. G. H. Coles, E. Donchin, and S. Porges (Eds.), Psychophysiology: systems, processes, and applications (pp. 5-25). New York: Guilford Press. (Note: Try not to become too bogged down by details; instead, read at a global level with the goal of getting a sense of the kind of electrical events happening in the body and when and how those can be picked up experimentally.)

(Luck book) Appendix: Basic Principles of Electricity. In An Introduction to the Event-related potential technique, S. J. Luck, MIT Press, Cambridge, 2005.

(Luck book) Chapter 1: Introduction to ERPs and Their Neural Origins

(Luck book): Chapter 7: ERP localization

(review) Dale, A.M., and Halgren, E. Spatiotemporal mapping of brain activity by integration of multiple imaging modalities, Current Opinion in Neurobiology, Special Issue: Cognitive neuroscience. Vol 11(2), Apr 2001, pp. 202-208

Technical aspects
TUESDAY, APRIL 9 - slides

(Luck book) Chapter 3: Basic principles of ERP recording

(Luck book) Chapter 4: Averaging, Artifact Rejection, and Artifact Correction

(review) Kutas-lab material provides another perspective and some more depth

Inferential aspects, measurement, and overview of ERP components
THURSDAY, APRIL 11 - slides

(review) Kutas, M. and Dale, A. (1997). Electrical and magnetic readings of mental functions, In M. D. Rugg (Ed.), Cognitive Neuroscience (pp. 197-242). (Note: Only pages 214-242 are required for this class.)

(review) Munte, T.F., Urbach, T.P., Duzel, E. and Kutas, M. (2000). Chapter 7. Event related brain potentials in the study of human cognition and neuropsychology, In F. Boller, J. Grafman and G. Rizzolatti (Eds) Handbook of Neuropsychology (Note: Only pgs. 11-16 on "Input process".)

(report) Vogel, E. K., Luck, S. J., & Shapiro, K. L. (1998). Electrophysiological evidence for a postperceptual locus of suppression during the attentional blink. Journal of Experimental Psychology: Human Perception and Performance, 24, 1656-1674.

Recommended (examples of the use of ERPs to address a variety of different types of questions):
(review) Kutas, M. (1991). Prophesies come true: what's new in event-related brain potential (ERP) research since 1984. In C. Barber and M. J. Taylor (Eds.) Evoked Potential Review No. 4 pp. 73-91. Nottingham, England: IEPS Publications.

Anticipation, preparation, movement, responses, and errors
TUESDAY, APRIL 16 - slides
THURSDAY, APRIL 18 - slides
TUESDAY, APRIL 23 - slides

(report) Walter, W.G, Cooper, R., Aldridge, J., V.J., McCallum, W.C., & Winter, A.L. (1964). Contingent Negative Variation: An electric sign of motor association and expectancy in the human brain. Nature, 203: 380-384.

(review) Coles, M.G.H. (1989). Modern mind-brain reading: psychophysiology, physiology and cognition. Psychophysiology, 26, 251-269.

(report) Nieuwenhuis, S., Ridderinkhof, R., Blom, J., Band, G.P.H., and Kok, A. (2001). Error-related brain potentials are differentially related to awareness of response errors: Evidence from an antisaccade task. Psychophysiology, 38:752-760.

(report) Osman, A., Bashore, T.R., Coles, M.G.H., Donchin, E., and Meyer, D.E. (1992). On the transmission of partial information: inferences from movement-related brain potentials. Journal of Experimental Psychology: Human Perception and Performance, 18, 217-232.

THURSDAY, APRIL 25 - slides
TUESDAY, APRIL 30 - slides

(report) Hillyard, S. A., Hink, R. F., Schwent, V. L., and Picton, T. W. (1973). Electrical signs of selective attention in the human brain. Science, 182, 177-180.

(review) Hillyard, S.A. (1985). Electrophysiology of human selective attention. Trends in Neurosciences, 8(9), 400-405.

(review) Hopfinger, J. B., Luck, S. J., & Hillyard, S. A. (2004). Selective attention: Electrophysiological and neuromagnetic studies. In M. S. Gazzaniga (Ed.), The Cognitive Neurosciences, Volume 3 pp. 561-574. Cambridge, MA: MIT Press.

(review) Naatanen, R., Tervaniemi, M., Sussman, E., Paavilainen, P., and Winkler, I. (2001). "Primitive Intelligence" in the auditory cortex, Trends in Neurosciences, 24(5), 283-288.

(tutorial review) Woodman, G.F. (2010). A brief introduction to the use of event-related potentials of perception and attention. Attention, Perception, & Psychophysics, 72(8), 2031-2046.


Information Processing
TUESDAY, MAY 7 - slides
THURSDAY, MAY 9 - slides
TUESDAY, MAY 14 - slides

(report) Sutton, S., Tueting, P., Zubin, J., and John, E. R. (1967). Information delivery and the sensory evoked potential. Science, 155, 1436-1439.

(report) Kutas, M., McCarthy, G., and Donchin, E. (1977). Augmenting mental chronometry: the P300 as a measure of stimulus evaluation time. Science, 197, 792-795.

(review) Donchin, E. (1981). Surprise!.Surprise? Psychophysiology, 18, 493-513.

(report) Luck, S.J. (1998). Sources of dual-task interference: Evidence from human electrophysiology. Psychological Science, 9(3): 223-227.

THURSDAY, MAY 16 - slides
TUESDAY, MAY 21 - slides

(report) Gonsalves and Paller, K.A. (2000). Neural events that underlie remembering something that never happened. Nature Neuroscience, 3(13): 1316-1321.

(review) Rosler, F, Heil, M., and Hennighausen, E. (1994). Slow potentials during long-term memory retrieval. In H-J. Heinze, T. Munte and G. R. Mangun (Eds.), Cognitive Electrophysiology (pp. 149-168). Boston: Birkhauser.

(review) Muente, T.F., Urbach, T.P., Duzel, E., & Kutas, M. (2000). Chapter 7. Event-related potentials in the study of human cognition and neuropsychology, in Handbook of Neuropsychology, Vol. 1, 2nd edition, F. Boller and J. Grafman (Eds), Elsevier, (section on memory only).

(review) Rugg, M.D., Curran, T. (2007). Event-related potentials and recognition memory. Trends in Cognitive Science, 11, 251-257.

All students should hand in a short (~2 page) paper that describes: (1) the topic area you have picked for your final paper, (2) a summary of your background literature (include references at the end), and (3) the question you will ask and/or hypothesis you will test.

THURSDAY, MAY 23 - slides
TUESDAY, MAY 28 - slides

(report) Kutas, M. and Hillyard, S. A. (1980). Reading senseless sentences: brain potentials reflect semantic incongruity. Science, 207, 203-208.

(review) Kutas, M., & Schmitt, B. (2003). Language in microvolts in Mind Brain and Language, M.T. Banich & M. Mack (Eds), Lawrence Erlbaum, 171-210.

(review) Federmeier, K. D., Kluender, R., & Kutas, M. (2003). Aligning linguistic and brain views on language comprehension in Cognitive Electrophysiology of Mind and Brain, A.M. Proverbio and A. Zani (Eds), Academic Press. 143-168.

(review) Osterhout, L., McLaughlin, J. & Bersick, J. (1997). Event-related brain potentials and human language, Trends in Cognitive Sciences, 1(6). 203-209.

(report) Nieuwland, M.S. and van Berkum, J.A. (2006). When peanuts fall in love: N400 evidence for the power of discourse. Journal of Cognitive Neuroscience, 18:7, 1098-1111.

(report) van Turennout, M., Hagoort, P., and Brown, C. (1998). Brain activity during speaking: from syntax to phonology in 40 milliseconds. Science, 280, 572-574.

(review) Kutas, M. & Federmeier, K.D. (2011). Thirty years and counting: Finding Meaning in the N400 component of the Event-Related Brain Potential, Annual Review of Psychology, 62:621-647.

(report) Hagoort, P., Hald, L, Bastiaansen, M., & Petersson, K.M. (2004). Integration of word meaning and world knowledge in language comprehension. Science, 304, 438-440.

(report) DeLong, K., Urbach, T., & Kutas, M. (2005). Probabilistic word pre-activation during language comprehension inferred from electrical brain activity. Nature Neuroscience, 8(8), 1117-1121.

(report) Roehm, D., Schlesewsky, M., Bornkessel, I., Frisch, S., and Haider, H. (2004). Fractionating language comprehension via frequency characteristics of the human EEG. Neuroreport, 15(3), 409-412.

Neural Plasticity
THURSDAY, MAY 30 - slides

(report) Neville, H. J. and Lawson, D. (1987). Attention to central and peripheral visual space in a movement detection task. III. Separate effects of auditory deprivation and acquisition of a visual language. Brain Research, 405, 284-294.

(report) Muente, T.F., Kohlmetz, C, Nager, W., Altenmueller, E. (2001). Superior auditory spatial tuning in conductors, Nature, 409 N6820:580

(report) Roder, B. Teder-Salejarvi, W. Sterr, A., Rosler, F, Hillyard, S.A., & Neville, H.J. (1999). Improved auditory spatial tuning in blind humans, Nature, 400, 162-166.

(report) McLaughlin, J., Osterhout, L., & Kim, A. (2004). Neural correlates of second-language word learning: minimal instruction produces rapid change. Nature Neuroscience, 7(7), 703-704.

Oral Presentations of Student Research Proposals


Readings to assist with preparation of final paper (highly recommended and available on website):

Luck, S. J. Ten simple rules for designing ERP experiments. In T. C. Handy (Ed.), Event-Related Potentials: A Methods Handbook (pp. 17-32). Cambridge, MA: MIT Press.

Picton, T. W., Bentin, S., Berg, P., Donchin, E., Hillyard, S. A., Johnson, R. Jr., Miller, G. A., Ritter, W., Ruchkin, D. S., Rugg, M. D., and Taylor, M. J. (2000). Guidelines for using human event-related potentials to study cognition: recording standards and publication criteria. Psychophysiology, 37, 127-152.

See also Purdue Online Writing lab for some good pointers on APA style and research papers.

TUESDAY, JUNE 11, 11:30am-2:30pm, CSB 180

Final Paper Guidelines

The basic structure of your paper should be an introductory section followed by a methods section. The introductory section will outline the issue and its importance, provide a literature review, and present your hypothesis, design, and predictions. The methods section will describe how you plan to collect your data and should be of sufficient detail that I could take your paper and, using only the information there, walk into the lab and perform your experiment.

More specifically, your introductory section should include:

(1) a statement of the question or issue to be addressed and why it is important/interesting:

unacceptable: I am interested in schizophrenia and language processing because I have a friend with schizophrenia. (the topic is way too broad and there isn't any question/issue here; rationale should be general and objective, not personal)

acceptable: Schizophrenia is a late-onset psychological disorder that affects approximately xx% of the population. One hallmark of the disease is disordered language processing, as in this example . . . . One current theory states that language processing may be disordered in schizophrenia, not because of any defect in language processing per se, but because these patients' semantic memory has an abnormal structure . . . (reference)

(2) an indication of why ERPs might be useful for addressing the issue:

unacceptable: ERPs will be used to study schizophrenia because they measure brain activity and have good temporal resolution. (these are general strengths of ERPs, but it isn't clear why they matter here)

acceptable: One difficulty with using behavioral measures to look at semantic memory organization in schizophrenia is that these patients often have difficulty understanding and following task instructions. Using ERPs, however, one can get a measure of semantic memory organization, via semantic priming, without the need for the patient to perform a task requiring overt responses.

(3) a brief overview of the ERP literature relevant to the topic (some behavioral literature is okay too if it is needed to justify the design and predictions):

unacceptable: I found 15 references on ERPs and schizophrenia. Here they are in no particular order . . . (include only those references that you need to justify your design and predictions; it should be perfectly clear to your reader why you are mentioning each study that you do, and the review should have a logical organization)

acceptable: We know from previous ERP research that semantic priming is associated with a reduction in a negativity peaking around 400 ms post-stimulus onset with a central/posterior distribution (N400) (REFERENCE1). We also know that, in general, schizophrenia is associated with somewhat smaller, later N400s (REFERENCE2). One previous ERP study of semantic priming inschizophrenia used materials consisting of . . .. They found . . . (REFERENCE3).

(4) your specific hypothesis

unacceptable: If schizophrenia affects language processing then the ERPs should show it. (probably true, but way too general; there is no mention of a dependent measure, of a task or situation, of how the dependent measure might be expected to change, etc.)

acceptable: If part of the language disorder in schizophrenia arises from differences in how semantic memory is organized in these patients, then we would expect to see differences in the amplitude of the N400 elicited by semantically-related and unrelated words in a priming task when measured in schizophrenics as compared with normal control subjects.

(5) an outline of your task and measure

unacceptable: I will have schizophrenics read sentences on the computer screen and look at the N400. (what kind of sentences? why? what part of the sentence will you look at the ERPs to? why?)

acceptable: Schizophrenics and matched control subjects will be asked to read for comprehension pairs of words presented one word at a time in the center of a computer screen. Some pairs will consist of semantically related items (e.g., honey-sugar) and others will consist of semantically unrelated items (e.g., chair-carrot). The amplitude of the N400 response to the second (target) word of each pair will be measured and compared across conditions.

(6) a description of the possible outcomes and what they might mean

unacceptable: I expect the ERP responses to be different in schizophrenics. (doesn't say how the ERP responses are expected to change; doesn't say what that would lead you to conclude; doesn't say what you would conclude if they turned out not to be different)

acceptable: Based on previous research, I know that control subjects should elicit a smaller N400 amplitude to the target preceded by a related as compared with an unrelated word. If the organization of semantic memory is different in schizophrenics, such that items that are related for normal controls are not related for schizophrenics and vice versa, then these patients might not show this semantic priming effect -- i.e., there may be no N400 difference between related and unrelated items. Thus, if I get this result I would conclude that . . . However, if schizophrenics show a normal semantic priming effect, then I will conclude that . . . If schizophrenics show a semantic priming effect, but one that is somehow different (later/smaller/etc.), this might mean that . . .

Your methods section should include detailed, organized descriptions of:

(1) the subject population(s) and their characteristics

(2) the stimulus materials and what will be controlled for

(3) the procedure by which the stimuli will be presented and the subjects' task, including:

  • the timing of the stimuli
  • what the subjects were told about the task
  • what the subject actually had to do and how s/he had to respond

(4) how the EEG data will be collected, including:

  • the number and arrangement of the electrodes
  • what kind of reference will be used
  • the sampling rate
  • filtering/gain associated with amplification

(5) how artifacts will be dealt with (prevention and removal)

(6) how stimuli will be grouped for averaging (what are the relevant dimensions of the experiment) and what kind of time-locking will be used

(7) what aspect(s) of the ERP will be analyzed for each condition

(8) how any special issues or problems related to the task, subject population, nature of the ERP response expected, etc. will be dealt with, if applicable.

Your writing should be clear, concise, and appropriate in style for a research paper. The logic of the paper's organization should be clear -- the reader should not have to "fill in" for what you don't say or figure out why you are mentioning something at a particular point. You must cite references appropriately in the text and give the complete reference in the end in a "Works Cited" section.

The literature review paper should likewise be clear and concise. You need not review every paper in an area but should certainly have a reasonable subset to do broad coverage. At the same time you want to be deep in your analysis of the papers in an area. You will need to read a set of papers first (perhaps starting with the latest and using the citations as a guide, but also looking at some of the earliest as well, if the area has a history). Make sure that you describe papers in sufficient detail so the reader can get the question addressed, method, results and conclustion without having to go back to read the paper for themselves. Also, be critical but not nitpicky! You can end with interesting open questions, or controversies or inconsistencies, etc.

Finally, please spell check your paper before turning it in. Ideally, also have a friend proofread it for you, both to catch silly errors and also to see if your ideas make sense, even to someone outside of the class.