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 105
Schedule:    Tuesday, Thursday from 1:30pm-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

Wandell office hours are by appointment:   Ask.  Glad to meet.  After class is usually a good time.

Link to lecture videos (previous years)
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

• Homework tutorials 
• MRI Simulator         - Under development, and a potential extra credit project for programmers

Topic

Introduction: The Instrument 

Link to homework tutorials (github)

MR signals I
(Instrument, FID)
(01 MR Physics.pdf)

MR signals II
(T1, T2, T2*)
(01 MR Physics.pdf)

HW1 released

mrTut01_MR

MR signals III
(Pulse sequences, BOLD contrast )
(01 MR Physics.pdf)

Image formation I
Linear Systems, Slice selection, K-space sampling
(02 MR Imaging.pdf)

Chapter 5
02 MR Imaging
Start slide 15ish

HW1 due at 11:59

HW2 released

mrTut02_Imaging 

Image formation II
Pulse sequences, Parallel imaging, Image quality, Signal equations; identify sequences
(02 MR Imaging.pdf)

Chapter 5
(p. 147 et seq.)
Slide 60ish

BOLD I 
The human brain parts
What do we want to measure?
History - Mosso, Fulton, Fox-Raichle; 
(03 BOLD.pdf)

Chapter 6, 7
Logothetis & Wandell; Boynton et al. 
Start at end  02 MR Imaging

HW2 due at 11:59

HW3 released

BOLD  II
Vasculature
BOLD (fMRI) and electrophysiological measures
More history and some philosophy

Dumoulin and Wandell;

Wandell and Winawer

(Start at slide 25)

Computational neuroimaging, linearity tests, HRF
(04 Time Series, Statistics)

HW3 due at 11:59

MIDTERM released

BW away

BOLD contrast
Visual field maps
(04 Time Series, Statistics)

PRFs
Statistical reasoning
Hits, FA, ROC/AUC

Brian

MIDTERM must be completed by 11:59

HW4 released

Hongjian He 

Diffusion Imaging: Principles and applications

Chapter 5
(p. 138 et seq.) 

Le Bihan review

HW4 due at 11:59

HW5 released

Modeling diffusion data I –
Ball and stick, multiple tensors, multi-shell

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

HW5 due at 11:59

mrTut05_Visualization

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

Ensemble tractography
Diffusion Kurtosis Imaging

The human face perception system

HW6 released

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

NODDI
G-Ratio imaging
Functional connectivity (resting state)

Data and computational management tools

Markus;
Calhoun;

LMP will present, and we will record.

HW6 due at 11:59 

 Brian