Course Syllabus
An introduction to human neuroimaging using magnetic resonance Magnetic resonance imaging (MRI) has become an important scientific tool for measuring living human brain structure and function. This course is for students who would like to learn the physical basis of MRI and how the method is used to make anatomical images of brain structures (sMRI and dMRI), measure quantitative tissue properties (qMRI), and assess brain activity (fMRI). The course is designed to be helpful to people beginning to use MRI in their research and also to people who would like to understand the strengths and limits of the methods when reading journal articles or listening to talks. We specifically aim to accommodate students from various backgrounds (e.g. engineering, neuroscience, psychology). The format is primarily lecture but often accompanied by lively class discussions! The course work comprises homework (small programming examples and tutorials), and two take-home exams. This course leads naturally to Psych 204b. Classroom Sapp Center for Science Teaching and Learning, room 118 Course assistant: Finzi, D. Link to lecture videos Github sites for Matlab tutorials
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Lecture Schedule
Week/Day | Date |
Topic |
Reading | Homework |
1.1 | 1/08 |
Introduction: The Instrument |
Chapters 1 |
Link to homework tutorials (github) |
1.2 | 1/10 |
MR signals I |
Chapters 2 | |
2.1 | 1/15 |
MR signals II |
Chapters 3 (Conceptual) |
HW1 released mrTut01_MR |
2.2 | 1/17 |
Contrast mechanisms |
Chapter 4 (Conceptual) |
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3.1 | 1/22 |
Image formation I |
Chapter 5 |
HW1 due at 11:59 HW2 released mrTut02_Imaging |
3.2 | 1/24 | Gross anatomy and vasculature |
Chapter 5
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mrTut03_LinearSystems |
4.1 | 1/29 |
BOLD physiological mechanisms |
Chapter 6, 7 |
HW2 due at 11:59 HW3 released |
4.2 | 1/31 |
BOLD mechanisms cont'd |
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5.1 | 2/5 |
Image formation II |
Adam |
HW3 due at 11:59 MIDTERM released BW away |
5.2 | 2/7 |
The human face perception system |
Dawn |
BW away |
6.1 | 2/12 |
BOLD contrast and time series |
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MIDTERM must be completed by 11:59 HW4 released |
6.2 | 2/14 | Quantitative modeling: Population Receptive Fields Signal detection, ROC |
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mrTut04_Diffusion |
7.1 | 2/19 |
Diffusion Imaging: Principles and applications |
Chapter 5 Le Bihan review |
HW4 due at 11:59 HW5 released |
7.2 | 2/21 |
Modeling diffusion data I – |
Wandell review | |
8.1 | 2/26 |
Fiber tractography principles |
HW5 due at 11:59 mrTut05_Visualization |
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8.2 | 2/28 |
Ensemble tractography |
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9.1 | 3/5 |
Quantitative MRI measures. |
HW6 released | |
9.2 | 3/7 |
Encoding models and inverted encoding models |
Justin Gardner |
BW away |
10.1 | 3/12 |
Quantitative modeling |
Wandell, Chial, Backus; |
HW6 due at 11:59
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10.2 | 3/14 | Data and computational management tools |
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Homework can be done over the course of a week.
Discuss with others, but complete the homework (and exams) on your own.
The midterm and final exams must be completed during a 24 hour time period (of your choosing) within the week. The final exam period this year is March 18-22.
Note: Grades are due 3/27
Course Summary:
Date | Details | Due |
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