Course Syllabus
An introduction to human neuroimaging using magnetic resonance The course begins with an introduction to the basic MR instrumentation (magnet, gradients, coils) and signals (PD, T1, T2, T2*). Next, we cover how MR images are formed. We then review the acquisition and analysis of some of the most common human neuroimaging measurements, including anatomical, diffusion, and functional signals. Throughout the course we review methods designed to infer the biological basis of MRI signals. The goal of this work is to connect the MRI measurements to brain tissue, structures, and cellular activity. The emphasis on modeling involves the use of some programming and simulation methodology (based on either Python or Matlab). The course includes a series of homework assignments that are short questions or calculations. This course leads naturally to Psych 204b: Computational Neuroimaging (Spr 2017, TuTh 9:00AM-10:20AM, 420-419) taught by Prof. Grill-Spector and Prof. Yamins. Classroom Science Teaching and Learning Center, 105 Course assistant: Mona Rosenke Link to lecture videos Github sites for Matlab tutorials
|
Lecture Schedule
Week/Day | Date |
Topic |
Reading | Homework |
1.1 | 1/09 |
Introduction: The Instrument |
Chapters 1 |
Link to homework tutorials (github) |
1.2 | 1/11 |
MR signals I |
Chapters 2 | |
2.1 | 1/16 |
MR signals II |
Chapters 3 (Conceptual) | HW 1 posted mrTutMR.m (or mlx form) |
2.2 | 1/18 |
Contrast mechanisms |
Chapter 4 (Conceptual) |
|
3.1 | 1/23 |
|
Chapter 5 |
HW 1 due |
3.2 | 1/25 |
Image formation II Multiband acquisitions |
Chapter 5
|
|
4.1 | 1/30 |
|
Chapter 6, 7 |
HW 2 due
|
4.2 | 2/1 |
|
||
5.1 | 2/6 |
|
HW 3 due | |
5.2 | 2/8 |
Quantifying anatomy. Cortical thickness ... (others, such as VBM) |
Gari |
Midterm starts (24 hours to complete, once you start) |
6.1 | 2/13 |
Diffusion Imaging: Principles and applications |
Chapter 5 Le Bihan review |
Midterm due HW 4 posted |
6.2 | 2/15 | Modeling diffusion data I – Ball and stick, multiple tensors, multishell, NODDI |
Wandell review | mrTutDiffusion (or mlx form) |
7.1 | 2/20 |
Fiber tractography principles |
HW 4 due HW 5 posted |
|
7.2 | 2/22 |
Ensemble tractography |
||
8.1 | 2/27 |
Quantitative modeling |
HW 5 due |
|
8.2 | 3/1 |
Advanced Imaging Techniques: |
||
9.1 | 3/6 | The human face perception system | Mona (tentative) | HW 6 due |
9.2 | 3/8 |
Integration with other modalities (ECoG, MEG, EEG) |
Dora | mrTutVisualization (or mlx form) |
10.1 | 3/13 |
Visualization methods |
Wandell, Chial, Backus; |
|
10.2 | 3/15 | Data and computational management tools |
Final available 24 hours to complete once you start. |
March 19-23 Final Exam: 24 hour time period of your choosing Grades Due 3/27
Course Summary:
Date | Details | Due |
---|---|---|