Course Syllabus

Psych 50: Introduction to Cognitive Neuroscience

Course Description: How does our brain give rise to our abilities to perceive, act and think? Survey of the basic facts, empirical evidence, theories and methods of study in cognitive neuroscience exploring how cognition is instantiated in neural activity. Representative topics include perceptual and motor processes, decision making, learning and memory, attention, reward processing, reinforcement learning, sensory inference and cognitive control


Instructor:  Justin Gardner, PhD

Office: Room 300, Jordan Hall (Department of Psychology)

Office Hours: Upon request by email



Meeting time: Winter quarter, TTh 10:30AM - 11:50AM

Sections: Required (Fridays at the times listed below)

Location: Building 420 (Jordan Hall), Room 40

Pre-requisite: None

Undergraduate Requirements: Disciplinary Breadth: Natural Sciences, Ways: Scientific Method and Analysis, Ways: Social Inquiry


Teaching Assistants and Sections:

Name email Office hours Office hours location

Dan Birman (Head TA)

Use Piazza during finals

Jordan, 326

Guillaume Riesen -- Jordan, 308
Jon Walters -- Jordan, 330
Akshay Jagadeesh

Jordan, 330

Minyoung Lee


Jordan, 326

Emma Master

-- Psych Lounge, 1st floor Jordan Hall
Storm Foley -- Psych Lounge, 1st floor Jordan Hall
Stephanie Zhang


Lathrop Tech Lounge

Henry Ingram -- Huang Cafeteria, near Coupa
Kawena Hirayama


Psych Lounge, 1st floor Jordan Hall

Office hour and email policies: Questions you have are generally questions that others will have, so please share them in sections or on Piazza. It is not necessary to make an appointment for office hours. 

Morning sections

Time Room # TAs
9:30a 420-419 2 Dan, Stephanie
10:30a 420-419 12 Dan, Stephanie
9:30a 420-050 3 Minyoung, Emma
10:30a 420-050 4 Minyoung, Emma
11:30a 420-050 13 Stephanie, Emma

Afternoon sections

Time Room # TAs
11:30a 200-217 10 Storm
12:30p 200-217 11 Jon
12:30p 420-050 5 Akshay, Henry
1:30p 420-050 6 Akshay, Henry
12:30p 460-334 7 Guillaume, Kawena
1:30p 460-334 9 Guillaume, Kawena
2:30p 160-325 8 Storm, Henry, Kawena


Learning goals

We are our brains. The overall goal of this class is to introduce you to the scientific study of how our brains work to make us who we are. This class should prepare you to take more specialized upper level classes in specific areas of cognitive neuroscience. 

After taking this course you should be able to...

...demonstrate familiarity with basic anatomy and physiology of the brain. You should gain familiarity with fundamental terminology and basic knowledge about brain systems and functions. You should be able to recognize and understand these terms when you encounter them in reading literature (both popular press and primary) or listening to lectures about cognitive neuroscience. Chapter reading and quizzes will be used to build this knowledge. Examples of basic factual knowledge:

What are neurons and glial cells? What functions do they preform?
What is an action potential? Why is it important for cognitive function? How do ionic currents make it possible?
Where is prefrontal cortex? What might happen to someone if they had damage to it?
What is dopamine? What it is thought to signal in the brain?

...explain how the brain allows us to do everyday behaviors. Cognitive neuroscience aims to provide explanations for how the brain gives rise to behavior. You should be able to take any behavior that you engage in like walking, talking or deciding whether to drink a cup of coffee or eat cheese and be able to discuss what might be going on inside the brain to allow you to preform that behavior. This is not just knowing what parts of the brain are involved in different functions, but being able to apply conceptual models derived from cognitive neuroscience to new situations. We will practice this through weekly thought questions discussed in section. For example: 

I decide to swing at a pitch while playing whiffle ball. How would a diffusion model explain my reaction time and choice?
I recognize someone I just met, but I can't remember their name. What are the processes in the brain that have and have not worked properly?
I slowly learn to balance on my new RipStik casterboard. Would reinforcement learning provide a good theory for how I have learned to do this? If so, what would my dopamine neurons be doing when I fall off the board?


We will not cover everything there is to know about cognitive neuroscience in one quarter. Cognitive neuroscience is a rich field that draws on many disciplines from biology, chemistry, psychology, computer science, engineering, mathematics, philosophy and beyond. The objective is not to be exhaustive (and exhausting!) in what we cover. Instead the goal is to give you basic background and conceptual knowledge as outlined above by going in to depth in a few areas to illustrate the concepts and knowledge that structure the scientific study of cognitive neuroscience. 

  1. Input Our brains have many sensors and systems that allow us to get information about the outside world. For example, touch, smell, balance, etc. We will use the visual system as a canonical system for understanding how information about the world gets into the brain. This will allow us to understand what is meant by bottom-up processing from sensory transduction to cortical streams of processing supporting high-level categorization and sensory inference. 
  2. Output We will next flip our thinking about the brain from something that passively takes in information and processes it to something that generates movement. 
  3. Feedback If the brain can act to contract muscles and make movements it can also act on itself to change things like sensory processing. We will discuss in depth a canonical system that does just that: attention.
  4. Broadcast We will next turn from cognitive processes like attention that offer very specific control of information processing to ones that can distribute information widely and modulate activity across lots of the brain; neuromodulatory systems. We will discuss in-depth the one we know the most about - the dopamine system and its role in reinforcement learning.
  5. Memory Memory will give us a chance to see many of the above concepts put together to explain a cognitive function. It will also show us how neuroscience can inform our understanding of cognition as we see different systems and process underlie different forms of memory.

Along the way, various topics will come up - emotion, language, decision-making, consciousness, free-will, psychoactive drugs, disease, mental illness, brain metabolism, brain-machine interfaces, mind-control - we will try to fit these into the above frameworks for thinking about the brain. Undoubtedly, there will be a part of cognitive functioning that we do not cover (hey, why haven’t we talked about why I sneeze when I see a bright light? - you are wired funny. Yes, that’s true. It really happens). You will have opportunities in sections to take the framework that are discussed in lectures and apply them to understanding other things that were not covered. So, for example, in section we might talk about the auditory system and how it is the same or different from the visual system. 

Ethics and morality

Some aspects of the material covered in a cognitive neuroscience course may bring up ethical and moral considerations for you that you feel strongly about. For instance, it might challenge your religious beliefs. It might challenge notions of when someone should be culpable for behavior that is abhorrent but for which they might not have control. They may challenge your notions of self, of memory, of personality. All these are extremely important issues since they bear on how we act as a society, how we educate, how we deal with crime and punishment, how we think about who we are and how we act with others. Much foundational work in cognitive science has been done using animal experiments which raise important questions of how we weight humane treatment of animals against the quest for knowledge and betterment of human society and health. 

We encourage you all to think about these issues openly and frankly as they should be in an academic environment like Stanford. Having said that, we hope that you will come in with as open a mind as possible and not pre-judge what you are learning about. We will have opportunities in sections at the beginning and end of the quarter to discuss issues related to ethical and moral considerations that come out of the study of cognitive neuroscience.


Chapter readings will be from the following textbook, but will be supplemented by occasional readings posted on Canvas. The textbook is available in the Stanford bookstore and on a 2-hour course reserve at Green Library.

Brain and Behavior: a Cognitive Neuroscience Perspective, 1st Edition (2015) David Eagleman and Jonathan Downar. Oxford University Press.



Date Assignments Topic
Tu 1/9 Introduction
Th 1/11 Reading due before class Hierarchical processing
Section: Fri 1/12 Thought question due by 8AM Sensory processing lab
Su 1/14 Quiz due by midnight
Tu 1/16 Reading due before class Sensory processing
Th 1/18 Reading due before class Sensory decision making: evidence accumulation
Section: Fri 1/19 Thought question due by 8AM Evidence accumulation lab
Su 1/21 Quiz due by midnight
Tu 1/23 Reading due before class Motor systems
Th 1/25 Reading due before class Action potential
Section: Fri 1/26 Thought question due by 8AM Action potential
Su 1/28 Quiz due by midnight
Tu 1/30 Reading due before class Energy consumption in the brain
Th 2/1 Reading due before class Executive Control
Section: Fri 2/2 Thought question due by 8AM Methods jigsaw
Su 2/4 Quiz due by midnight
Tu 2/6 Reading due before class Attention
Th 2/8 Reading due before class Attention
Section: Fri 2/9 Thought question due by 8AM Attention
Fri 2/9 (Optional) review session: 380-380W 5pm-7pm
Su 2/11 Quiz due by midnight Midterm released noon
Mo 2/12 Take-home midterm (~2-3 hrs) due by midnight
Tu 2/13 Sensory substitution and learning (David Eagleman)
Th 2/15 Consciousness
Section: Fri 2/16 Thought question due by 8AM Sheep's brain dissection
Su 2/18 Quiz due by midnight
Tu 2/20 Reading due before class Prediction error and dopamine
Th 2/22 Reading due before class Value based decisions
Section: Fri 2/23 Thought question due by 8AM Reinforcement learning lab
Su 2/25 Quiz due by midnight
Tu 2/27 Reading due before class Memory: Different systems
Th 3/1 Reading due before class Memory: Pattern completion and separation
Section: Fri 3/2 Thought question due by 8AM Memory
Su 3/4 Quiz due by midnight
Tu 3/6 Reading due before class Memory: LTP and synapses
Th 3/8 Reading due before class Spatial cognition
Section: Fri 3/9 Thought question due by 8AM LTP and synapses
Su 3/11 Quiz due by midnight
Tu 3/13 Reading due before class Emotion
Th 3/15 Reading due before class Social cognition
Section: Fri 3/16 Thought question due by 8AM Final project posters
Su 3/18 Quiz due by midnight
We 3/21, 12:15P Final (Hewlett 200, Wednesday 3/21: 12:15p-3:15p)

Weekly study guide

We will provide a weekly study guide available in Files. This is a central document that summarizes learning goals each week. In it you will find an overview of the week and a set of learning goals for each of the lectures and study sections. There will be a reading guide which will provide you some detail about what we hope you should be taking away from the readings. In particular, lists of key terminology that we expect you to learn. We will also provide some of the key slides from lectures with brief explanations as a reference for some of the main take-aways. Note that full slides and section materials will be posted to Files. 

Assignments and exams

Quizzes: Education research shows that quizzing is an effective way to improve learning, so we will provide quizzes that are based on the material covered each week. They should be done closed-book at home. After taking the quiz once, you may go back and take the quiz a second time, open book. Your grade will be based on the second taking of the quiz. Both quiz attempts are to be completed on Canvas by midnight each Sunday.

Thought questions: Each week we will also provide a thought question to aid in the development of conceptual thinking. These thought questions are to be completed on Canvas by 8AM each Friday. Your section grade each week will be based in part on turning in a complete answer to the thought question, as well as participation in section. Thought questions should be done open-book.

Final section poster: In the last section you will work with a small group to present about an application of cognitive neuroscience in society. This is an opportunity to use the general principles covered in the course to focus in depth on a specific topic. Each individual group member will be responsible for an independent part of the poster.

Readings: To help you keep track of readings each reading has a corresponding assignment in Canvas. Please mark these assignments as complete as you finish them.

Midterm and Final: The midterm and final will be composed of quiz and thought questions similar to ones provided each week. The midterm exam will be a take home (open-book) and the final in-class (no books or internet, but you may bring one page of hand-written notes). To study for the exams, we recommend that you review the study guides, quizzes and thought questions. Take some time in particular to read the sample answers for thought questions. These are posted each week as examples of the best answers that the teaching team found among the class. Previous midterm and finals will be available on Canvas.

Your final grade will be based on the following:

15% Quizzes (2 lowest grades will be dropped)

25% Sections (15% - participation and weekly thought questions. 2 lowest grades will be dropped; 10% - final section poster)

25% Midterm 

35% Final 

Policy on missed classes and work

Attendance at all lectures and sections is expected. If you are sick, have a commitment like an athletic tournament or assignment from another class which makes you unable to complete a quiz or thought question, then you may drop at most 2 quizzes and 2 thought questions without affecting your grade as noted above. You do not need to inform the instructor or your TA. No further accommodations for missed assignments can be provided on an individual basis without an official Accommodation Letter (see below). Note that late assignments will not be graded and will be counted against the 2 allowable drops.

Sections are an important part of the course in which we dive deeper into subjects covered in lecture and reading. We also have numerous demonstrations and labs which we hope will more deeply develop your conceptual understanding of cognitive neuroscience. Whether these sections achieve their learning goals depends in large part on you - being engaged, asking questions, helping each other understand what you find difficult and teaching each other.

However, if for unavoidable reasons such as away games beyond the normal 2 absences you cannot attend a section or exam please have your coach or responsible official email your TA (please cc the Head TA) to confirm that you were absent for an official Stanford event. These excused absences will be graded solely on the written portion of the thought question -- make sure you turn it in on time even if you are not on campus! In your assignment, please leave a comment as a reminder to your TA that you have an official reason to be absent so that your TA will remember to ignore attendance for that week.

Use of laptops and phones in class

We ask that you refrain from using laptops, tablets and phones in class as their use can be very disruptive to others. While note taking on a computer is permitted, we recommend taking notes with pen and paper (you can take pictures of them and digitize later if you wish) because research has shown that the act of writing helps retention of concepts.

Students with Documented Disabilities

Students who may need an academic accommodation based on the impact of a disability must initiate the request with the Office of Accessible Education (OAE).  Professional staff will evaluate the request with required documentation, recommend reasonable accommodations, and prepare an Accommodation Letter for faculty dated in the current quarter in which the request is being made. Students should contact the OAE as soon as possible since timely notice is needed to coordinate accommodations.  The OAE is located at 563 Salvatierra Walk (phone: 723-1066, URL: Please send your letter to your TA (cc the Head TA) at the start of the quarter to give us time to plan accommodations.

Honor code

We will abide by the Stanford University Honor code. Please familiarize yourself with it.

Course Summary:

Date Details