Course Syllabus

W18-PSYCH-204A-01

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
Schedule    Tuesday, Thursday from 1:30-2:50pm (01/07/2019 - 03/15/2019)
Textbook:     Huettel et al., FMRI (Third Edition, Oxford).  

Course assistant:  Finzi, D.  
Office hours:          Thursdays, 4-5pm, Jordan Hall, building 420, room 452
By appointment:    Ask

Link to lecture videos
https://talks.stanford.edu/psychology/psych-204a-introduction-to-human-neuroimaging-using-mri/ 
(Sign in with SUNET ID and password)

Github sites for Matlab tutorials

 

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)
3.1 1/22

Image formation I
Linear Systems

Chapter 5

HW1 due at 11:59

HW2 released

mrTut02_Imaging 

3.2 1/24 Gross anatomy and vasculature

Chapter 5
(p. 147 et seq.)

 

mrTut03_LinearSystems
4.1 1/29

BOLD physiological mechanisms
Electrophysiological thinking
History of MRI

Chapter 6, 7
Logothetis & Wandell; Boynton et al. 

HW2 due at 11:59

HW3 released

4.2   1/31

BOLD mechanisms cont'd

 

5.1 2/5

Image formation II
Parallel imaging
Multiband acquisitions

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

 

MIDTERM must be completed by 11:59

HW4 released

6.2 2/14 Quantitative modeling: Population Receptive Fields 
Signal detection, ROC

 

Dumoulin and Wandell;

Wandell and Winawer

mrTut04_Diffusion
7.1 2/19

Diffusion Imaging: Principles and applications

Chapter 5
(p. 138 et seq.) 

Le Bihan review

HW4 due at 11:59

HW5 released

7.2 2/21

Modeling diffusion data I –
Ball and stick, multiple tensors, multishell, NODDI

Wandell review
8.1 2/26

Fiber tractography principles
Fascicle labeling (Tracula, AFQ)
Tractography evaluation (LiFE)

HW5 due at 11:59

mrTut05_Visualization

8.2 2/28

Ensemble tractography
Diffusion Kurtosis Imaging

9.1 3/5

Quantitative MRI measures.
Proton density, Molecular Tissue Volume, T1, T2

HW6 released
9.2 3/7

Encoding models and inverted encoding models

Justin Gardner

BW away

10.1  3/12

Quantitative modeling
NODDI
G-Ratio imaging

Wandell, Chial, Backus;
Pestilli self-potraits of the brain
Dale, Fischl & Sereno

HW6 due at 11:59 

 

10.2 3/14 Data and computational management tools

Tentative - LMP
Markus;
Calhoun;

 

 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