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This page includes the course calendar.
Course Format
The course employs twiceweekly lectures and weekly laboratory and discussion sessions.
Laboratory includes fMRI data acquisition sessions and data analysis workshops. Assignments include reading of both textbook chapters and primary literature as well as fMRI data analysis in the laboratory. For each of the Discussion sections with an assigned article to read, students should post two questions to the class discussion forum at least 24 hours in advance.
Prerequisites
Probability, linear algebra, differential equations, and introductory or collegelevel subjects in neurobiology, physiology, and physics are required.
Required Textbook
Huettel, S. A., A. W. Song, and G. McCarthy. Functional Magnetic Resonance Imaging. 1st edition. Sunderland, MA: Sinauer Associates, Inc., 2004. ISBN: 9780878932887.
Note: The 2nd edition of this book was published after the Fall 2008 term, and Dr. Gollub recommends its use. Huettel, S. A., A. W. Song, and G. McCarthy. Functional Magnetic Resonance Imaging. 2nd ed. Sunderland, MA: Sinauer Associates, Inc., 2009. ISBN: 9780878932863.
This book will be supplemented by readings in the research literature and other books.
Grading Policy
Grading criteria.
ACTIVITIES 
PERCENTAGES 
Problem sets 
20% 
Lab reports 
30% 
Midterm exam 
20% 
Final exam 
30% 
Problem sets are due one week after end of module. Lab reports are due one week after the analysis lab session.
Grades will be reduced by 10% per day until 1 week after due date, after which no assignments will be accepted.
Calendar
Course calendar.
SES # 
LECTURES 
LABS 
DISCUSSIONS 
KEY DATES 
Part 1. Overview 
1 
Introduction to the course (Gollub)
Introduction to fMRI (Rosen)




Part 2. Functional neural systems 
2 
Neural systems I (Dickerson) 
MRI safety training
Lab 1: introduction to fMRI data and analysis (Bolar)


Problem set 1 out 
3 
Neural systems II (Dickerson) 

Human subject safety issues (Gollub) 

4 
Neural systems III (Dickerson) 
Lab 2: fMRI acquisition (WhitfieldGabrieli, Triantafyllou) 

Lab 1 due 
5 
Cerebrovascular anatomy and neural regulation of CNS blood flow (Dickerson) 

The hemoneural hypothesis (Moore) 

Part 3. Physics of image acquisition 
6 
MRI physics I (Wald) 

BottomUp dependent gating of frontal signals in early visual cortex (Vanduffel) 
Problem set 1 due 
7 
MRI physics II (Wald) 
Lab 3: the life cycle of medical imaging data (Pujol) 

Lab 2 due 
8 
MRI physics III (Wald) 

Response monitoring in Autism Spectrum Disorders (ASD) (Manaoch) 
Problem set 2 out 
Part 4. Imaging physiology 
9 
Imaging physiology I: brain at the baseline (Bolar) 
Lab 4a: MRI physics, part I (Trinatafyllou) 

Lab 3 due 
10 
Imaging physiology II: brain activation (Bolar) 

Visual topography of human intraparietal sulcus (Sommers) 

11 
Imaging physiology III: BOLD imaging (Bolar) 

Brain correlates of autonomic modulation (Napadow) 
Problem set 2 due
Problem set 3 out

12 
Imaging physiology IV: BOLD(cont.) and nonBOLD techniques (Bolar) 
Lab 5: diffusion weighted imaging workshop (Pujol) 

Lab 4a due 
13 
Quantitative perfusion and diffusion imaging biomarkers (Sorensen)
Physics of diffusion weighted imaging (Yendiki)


No discussion due to extra lecture content 

Part 5. Experimental design 
14 
General principles of experimental design (Savoy) 
Lab 4b: MRI physics, part II (Triantafyllou) 

Lab 5 due 
15 
Phsychological state variables in imaging (Gabrieli) 

Primer on matrix algebra for fMRI data (Greve) 
Problem set 3 due 
16 
Overview of statistical analysis, preprocessing (Greve) 
Lab 6a: statistical analysis of fMRI data, part I (Yendiki) 

Lab 4b due 

MidTerm exam 



Part 6. Statistical analysis 
17 
Stats 2: level 1 (Greve) 

Eventrelated singleshot volumetric functional magnetic resonance inverse imaging of visual processing (Polimeni) 
Problem set 4 out 
18 
Stats 3: level 1 (cont.) (Greve) 
Lab 6b: statistical analysis of fMRI data, part II (Yendiki) 

Lab 6a due 
19 
Stats 4: level 2 (Greve) 

How humans make inferences about self and others (Mitchell) 

20 
Stats 5: correction for multiple measures (Vangel) 
Lab 6c: statistical analysis of fMRI data, part III (Yendiki) 

Lab 6b due 
21 
Stats 6: exploratory analysis, PCA, ICA, fuzzy clustering (Vangel)
Stats 7: causality (Vangel)


No discussion due to extra lecture content 

Part 7. Structure and functional analysis 
22 
Structuralfunctional integration (Salat) 
Lab 6d: statistical analysis of fMRI data, part IV (Yendiki) 


23 
Quantitative neuroimaging biomarkers (Helmer)
Surfacebased anatomical analysis (Salat)


No discussion due to extra lecture content 
Problem set 4 due 
24 
Spatial normalization for group analysis (Sabuncu) 
Complete work on labs 6c, 6d as needed 

Labs 6c, 6d due 
25 
Granger causality analysis for fMRI (Vangel) 

Neurohumoral hypothesis  redoux (Moore) 


Final exam 


