An essential aspect of the brain is its complex pattern of connectivity between neurons across different areas. This course will provide a comprehensive overview of the networks of the brain, analyzed from a range of standpoints from the microscopic to the macroscopic, with a particular focus on the organization of the human brain. Specific topics include brain anatomy, connectomics, structural and functional neuroimaging, graph theory and network science, dynamic models, and causal inference. The course will comprise a combination of lectures, paper discussions, and hands-on analysis exercises. The first session each week will be composed of lecture and discussion, and the second session will be focused on discussion and hands-on analyses, with students assigned to lead each discussion.
Prerequisites:
Course Requirements: You will need a laptop computer for use in every class. If you do not have access to a laptop please contact the instructor ASAP and we will help you obtain access to one.
Website: The primary web site for the class is http://BrainNetworksCourse.github.io.
Materials:
Stanford University and its instructors are committed to ensuring that all courses are financially accessible to all students. If you are an undergraduate who needs assistance with the cost of course textbooks, supplies, materials and/or fees, you are welcome to approach me directly. If would prefer not to approach me directly, please note that you can ask the Diversity & First-Gen Office for assistance by completing their questionnaire on course textbooks & supplies or by contacting Joseph Brown, the Associate Director of the Diversity and First-Gen Office (jlbrown@stanford.edu; Old Union Room 207). Dr. Brown is available to connect you with resources and support while ensuring your privacy.
Grades will be determined as follows:
Unless otherwise stated, you can use any published resource you wish to complete the assessments (textbook, Internet, etc). However, you should not discuss the answers with your fellow students in person or electronically unless instructed to do so by the instructors; sharing answers (including computer code) will be viewed as a violation of the Honor Code.
Final project: Each student will complete a final project in which they use an open dataset to test a hypothesis about brain connectivity. The final submission should be a github repository with a computational notebook that includes a writeup of the analyses as well as the code and any data needed to execute the code. Students may work in groups of up to 3 people for the project, but the contribution of each student to the group must be clear and distinct, and group projects are expected to be substantially more involved than individual projects.
Problem sets: Most weeks you will be given one written assignment or problem set to complete. Unless otherwise noted, these will be due at 7 PM on Mondays, submitted via Github Classroom. We will accept late problem sets for up to three days after the PSet is due; after that, no late submissions will be accepted. For unexcused late submissions, one point will be deducted for each day that the PSet is late. Excused late submissions must be accompanied by documentation of an official university function within one day of the due date, or a documented medical excuse.
Excused absences: If you are going to miss an in-class assessment due to an absence for an official University trip, please alert the TAs prior to your absence to schedule a make-up activity.
Grade disputes: Students must wait 24 hours after receiving a grade before they can dispute it, after which disputes must be received within 7 days of receipt of the grade. Grade disputes must be submitted to the instructor by email.
Feedback: We welcome student feedback regarding the course at any point. Please feel free to email us directly, or leave anonymous feedback for the instructional team by placing an anonymous note in Dr. Poldrack’s mailbox at Jordan Hall.
Gender expression/identity: This course affirms people of all gender expressions and gender identities. If you prefer to be called a different name than what is indicated on the class roster, please let me know. Feel free to correct me on your preferred gender pronoun. If you have any questions or concerns, please do not hesitate to contact me.
Code of conduct:
You are expected to treat the instructional team and your fellow students with courtesy and respect.
This class should be a harassment-free learning experience for everyone regardless of gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, race, age or religion. Harassment of any form will not be tolerated.
If someone makes you or anyone else feel unsafe or unwelcome, please report it as soon as possible to one of the instructors. If you are not comfortable approaching the instructional team, you may also contact the Stanford Office of the Ombuds
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: http://studentaffairs.stanford.edu/oae).