Syllabus, Fall 2022
Boston University
Meeting time: Tuesday & Thursday 9:30–10:45am
Location: PSY 210 (64 Cummington Mall)
Joseph T. McGuire, Ph.D.
Assistant Professor, Department of Psychological & Brain
Sciences
Email: jtmcg@bu.edu
Office hours:
- In-person drop-in hours on Tuesdays, 1:30–2:30pm, at 677 Beacon St,
Room 212
- Individual Zoom meeting slots available through the signup link on
Blackboard
- Other times by appointment (email to schedule)
We will use the following textbook:
Principles of fMRI, by Martin A. Lindquist and Tor D. Wager,
published by Leanpub. You
can buy the book in PDF format at this URL.
Other readings will be drawn from the primary literature and distributed via Blackboard.
The following textbook is OPTIONAL supplemental reading:
Functional Magnetic Resonance Imaging, 3rd Edition, by Scott A.
Huettel, Allen W. Song, & Gregory McCarthy, published by Sinauer
Associates.
For in-class exercises and demonstrations we will use the Connectome Workbench software package. We will talk about this in more detail in the first few class meetings. Information about installing Connectome Workbench is at this URL.
We will also use R and RStudio. You can download RStudio at this URL.
It will be helpful if you can bring a laptop or similar device to class, especially for Thursday classes when we will typically have data exercises and Blackboard-based quizzes. If it’s difficult for you to bring a laptop to class, let me know and we can make other arrangements.
This course is about cognitive neuroscience: how the human brain implements the information-processing functions of the human mind. We will approach cognitive neuroscience with an emphasis on research methods. How do we know what we know? What markers of brain function can we measure noninvasively? What pitfalls and controversies do we encounter when making inferences from complex human neuroscience data sets?
The goals of the course are for you (1) to become familiar with important findings and big unknowns in cognitive neuroscience, (2) to gain an understanding of the tools available for addressing those unknowns, and (3) to hone your skills at reading scientific papers and drawing conclusions from quantitative data.
Tuesday classes will generally begin with small-group discussions of the week’s readings. You are expected to complete the reading several days in advance and participate in an online discussion forum before class (see details below). On Thursdays, we will usually spend time on a data-oriented, hands-on exercise, followed by a lecture-style introduction to topics for the upcoming week’s readings.
For the first half of the semester or so, we will talk about different cognitive neuroscience methods from week to week. For the second half of the semester, we will focus on functional magnetic resonance imaging and go into detail about research approaches and inferential issues in functional neuroimaging.
As of the beginning of the semester, BU is not requiring face masks in classrooms. You are welcome to wear a mask, and we will adapt our norms around masking in class in response to the needs of members of the class and evolving conditions.
There may be times when people need to miss class for health-related reasons or because of quarantine/isolation requirements. Please let me know by email if there will be time periods when you are unable to come to class. We’ll work out a way for you to keep up with class activities.
Most weeks will have three assigned readings. Usually at least one will be an overview/review paper and at least one will be an empirical research article. Sometimes one of the readings will be a textbook section. Readings will be posted on Blackboard, together with a set of discussion prompts.
Each student will be part of a Blackboard discussion forum with a subgroup of the class. Your assignment each week is to read the readings, post comments in response to the discussion prompts, and then post replies to some of your classmates’ comments. Your initial post should be completed sometime between Tuesday and Sunday of the preceding week. At 8am Monday (beginning Monday Sep. 12 for the Week 2 readings), I will open the forum so you can see each other’s posts. Between then and the start of class on Tuesday, please post replies to at least two of your classmates’ comments.
The length of your initial post should be approximately one paragraph per reading (three paragraphs total in a typical week). Response posts don’t have to be longer than a sentence or two. Forum posts will be graded based on the degree to which they are thoughtful, creative, and responsive to the discussion prompts. The lowest two grades will be dropped (so, if you like, you can skip the online discussion for two weeks). Late posts can receive partial credit as long as they are submitted before class.
At the beginning of Tuesday’s class, you will have some time to talk with your group. One member of each group will be designated the discussion leader each week. The discussion leader’s job is to guide the small-group discussion and report out highlights of the discussion to the whole class afterward.
For the first half of the semester, we will often have a short Blackboard-based quiz at the beginning of Thursday classes. I will give you a lot of information beforehand about what to expect on each quiz.
In many of our Thursday classes we’ll then do an in-class exercise that involves interacting with data. I will ask you to complete a worksheet as you work through the exercise. You are not graded directly on the results you obtain, but you are expected to engage with the exercise and do your best. Working together with members of your group is encouraged.
Many academic journals publish commentaries on new scientific papers, written by researchers who were not involved in the work. The commentaries are typically a few pages long and accomplish three things: (1) summarize the paper, (2) explain the importance of its main findings in the context of the field, and (3) gently point out some of its potential limitations.
Your assignment is to write an approximately 1000-word “News & Views” style commentary on a published research article in human cognitive neuroscience from 2021 or later. You are responsible for choosing a target article that we have not read in class and that did not have an associated commentary when it was published.
Your topic (your choice of a target paper) is due via Blackboard by the end of the day on Friday Oct. 7, an outline is due on Friday Oct. 14, and your commentary is due via Blackboard by the end of the day on Friday Oct. 21.
Your assignment by the end of the semester is to develop a proposal for a new research project in some area of human cognitive neuroscience, and describe the proposed project in a concise paper. You should describe the background and motivation for your proposal, your hypothesis, the methods you would use, and the possible outcomes. I encourage you to start thinking about this early in the semester, and I am more than happy to discuss it with you!
The format for the paper is modeled after the Research Plan for an NSF fellowship application (2 pages long, single-spaced). More details about the format will be provided later in the semester.
Your topic is due via Blackboard by the end of the day on Friday Nov. 11. An outline is due on Friday Dec. 2. You will lead a 10-minute small-group discussion about your research proposal during class on Tuesday Dec. 6. The paper is due via Blackboard by the end of the day on Friday Dec. 16.
You are responsible for adhering to the applicable Academic Conduct Code:
For undergraduate students, the Boston University Academic Conduct Code.
For graduate students, the GRS Academic and Professional Conduct Code.
Please make sure you are familiar with those documents, as they describe how academic misconduct is defined and how any instances of possible misconduct would be handled.
Participants in this course have a wide range of personal and academic backgrounds, and it’s important to me to create a learning space where everyone feels they belong. If you have feedback as we go along about ways of improving the inclusivity of the course, I would like to hear it. If there is feedback you prefer to send me anonymously during the semester, a web submission form is available (see Blackboard for the link).
Specific topics and readings are subject to change. Refer to Blackboard for the latest information.
Course introduction, neuroanatomy, and localization of function.
Studies of brain structure and focal brain injury.
Electroencephalography, electrocorticography, and local field potential.
Brain stimulation.
MR signal generation, image formation, and BOLD contrast.
Processing and analyzing functional MRI data.
Experimental design and inference.
Mapping early visual responses.
Brain networks and functional connectivity.
Meta-analysis and data aggregation.
Pattern analysis and decoding.
No new readings due. Plans for class TBA.
Individual differences and prediction of future behavior.
Course wrap-up and ten-minute small-group presentations of research proposals.