Bios 642 / BME 499.098 / Psych 808:
Introduction to Functional MRI
August 2005
Schedule & Basic Info
| Class Meeting Time: |
9AM to Noon, Monday-Friday, Aug 8 through Aug 19 |
| Class Meeting place: |
East Hall 4448 |
| |
| Lab Meeting Time: |
1PM-3PM |
| Lab Meeting place: |
East Hall B250, B254, PC lab in the basement of East Hall |
| |
Downlad Files (notes, data):
|
Here
|
Final Project:
|
FinalProj.html
|
| Instructors: |
Luis Hernandez, John Jonides, Tom Nichols, & Doug Noll |
Course Calendar
| |
Week 1
|
| |
Mon 8/8 |
Tue 8/9 |
Wed 8/10 |
Thu 8/11 |
Fri 8/12 |
| |
Lecture
9am-
Noon |
Course Motivation (JJ)
Intro to Neuroanatomy (JJ)
Intro to BOLD & Task Design (DN) |
More Motivation
Physics I: Fields, gradients, spins (DN) |
Physics II: Image formation, hardware, SNR
(DN) |
Physics III: Physiology of BOLD |
Noise & Artifacts
Physiological noise, movement artifacts, susceptibility(LH/DN) |
| |
Lab
1pm-
3pm |
Task Design with E' (Derek Nee) |
Task Design with E' (Derek Nee) |
fMRI Lab: Safety, tour, scanning.
(A-groups; B-groups off) |
fMRI Lab: Safety, tour, scanning.
(B-groups; A-groups off) |
Matlab intro, Data exploration |
| |
| |
Week 2
|
| |
Mon 8/15 |
Tue 8/16 |
Wed 8/17 |
Thu 8/18 |
Fri 8/19 |
Lecture
9am-
Noon |
Stats I: Stats refresher
General Linear Model (TN) |
Stats II: fMRI Modeling (TN) |
Stats III: Multiple comparisons, Group
analyses (TN) |
Task Design II: Optimizing Designs (TN)
Intor to FSL (JM)
Non-BOLD methods, ASL (LH) |
Presentations, Q & A |
| |
Lab
1pm-
3pm |
SPM I: Intro, preprocessing (TN/LH) |
SPM II: Single-subject analyses (TN/LH) |
SPM III: Group analyses, project work |
Project work |
(none) |
| |
Course Syllabus & Class Goals
Week 1
Mon Aug 8 Lecture: Motivation and Fundamentals
Instructors: John Jonides & Doug Noll
After this class, you will:
- Understand the major research value of
neuroimaging data
- Learn some elementary basics of human brain anatomy:
- Learn the directions and planes of section in the brain
- Learn the major structures of the brain
- Learn about the ventricular and vascular system in the brain
- Learn to identify some major structures in the brain on MRI
images
- Understand the basic underlying princples of BOLD fMRI and the
fMRI response
- Know the two main kinds of task designs in fMRI
- Block designs
- Event-related designs
Materials for class
- Jonides Lecture
- Noll Lecture: Intro to fMRI (grayscale version)
- Reading: Primer on MRI and fMRI
- Reading: "Experimental design for brain fMRI," Aguirre and
D'Esposito, pp.
369-370, in Functional MRI, Moonen and Bandettini, Eds., Springer, 1999.
- Reading: "Event-related functional MRI," Buckner and Braver,
Ibid., pp. 441-450.
- Reading:
"Searching for a baseline: Functional imaging and the resting brain."
Gusnard and Raichle, Naure Reviews: Neuroscience, 2:685-694, 2001.
Mon Aug 8 Lab: Task Design w/ E'
Instructor: Derek Nee
Tue Aug 9 Lecture: More Motivation & Physics I
Instructor: Doug Noll
Goals:
- Understand the types of designs used to answer different
psychological questions.
- Develop the classical description of the motion of a nuclear spin
in a magnetic field, including the Larmor relationship.
- Describe the quantum mechanical basis of the magnetic resonance
signal and its implications to signal strength and relaxation.
- Use the rotating frame concept to describe excitation.
- Describe signal strength for a pulse-echo experiment in terms of
T1, T2, TE and TR.
Topics:
- Magnetic
fields in MRI
- The Nuclear
spin
- Larmor
relationship
- Motion of a
top in a gravitational field
- Motion of a
spin in a magnetic field
- Energy
states/quantum mechanics model
- Rotating
frame of reference
- Excitation
- T1-relaxation
- T2-relaxation
- Signal strength vs. TE, TR
Readings:
Lecture Notes
Some movies:
Tue Aug 9 Lab: Task Design II
Instructor: Derek Nee
Wed Aug 10 Lecture: Physics
Instructor: Doug Noll
Goals:
- Introduce the concept of a magnetic
field gradient and the space-frequency relationship.
- Introduce the Fourier transform and
demonstrate how 1D localization can be done.
- Describe phase encoding and 2D imaging
methods.
- Describe slice selection and pulse
sequence basics.
- Describe basic hardware components of
an MRI system
Readings:
Course notes on the web.
Topics:
- Magnetic field gradients
- Coils for gradients
- Distributions of magnetization
- The Fourier transform (time vs. spectrum)
- Frequency encoding - 1D imaging
- Phase encoding methods
- 2D imaging - 2D Fourier transform
- Other 2D methods
- Slice selection
- Pulse sequences
- Hardware components
Readings: Lecture Notes
Homework Set #1
Homework #1 Solutions
Wed Aug 10 Lab: fMRI Lab Tour (Group A)
Instructor: Luis Hernandez & Doug Noll
Thu Aug 11 Lecture: Physics III
Instructor: Doug Noll, Luis Hernandez
part 1a - Noise
- Describe the most common sources of
additive noise in MRI.
- Introduce the basic relationships
between imaging parameters and noise.
Readings: Noise Notes
part 1b - BOLD
Goals:
- Describe magnetic susceptibility and
how changes in the magnetic susceptibility of hemoglobin it can affect
T2* relaxation.
- Describe the metabolic and vascular
physiology changes associated the neuronal activation.
- Describe temporal dynamics of changes
in physiology and BOLD signal.
- Introduce some basic models of the
BOLD effect and describe responses to long and short stimuli.
Readings:
Course notes on the web.
Topics:
- Magnetic properties of hemoglobin
- T2* relaxation and effect of hemoglobin
- Metabolic changes with neural activation
- Vascular physiology changes
- MRI signal changes
- Signal change vs. pulse sequence parameters
- Temporal behavior of BOLD response
- Long and short stimuli
- Models of BOLD effect
Readings: BOLD Notes
Homework Set #2
Thu Aug 11 Lab: fMRI Lab Tour (Group B)
Instructor: Luis Hernandez & Doug Noll
Fri Aug 12 Lecture: Noise & Artifacts
Instructor: Luis Hernandez
- Understand the following confounds in fMRI and what corrections
exist
- Slice Timing effects (temporal shifting)
- Movement (rigid body realignment)
- Physiological Artifacts: respiration and heart beat
(regression filters)
- Electronic Noise (filters and autoregressive models)
- Morphology (non-linear warping)
- Image distortions ( susceptibility, ghosting, off-resonance)
- As a side effect, you will be introduced to signal processing
concepts:
- linear transformations
- sampling, re-sampling, interpolation
- optimization, cost functions
Reading: Class Notes
Fri Aug 12 Lab: Matlab & Data Exploration
Instructor: Luis Hernandez
- Ways of checking Preprocessing steps
Time series, movies, normalization
- Examples of badly normalized, well-normalized, etc
Mon Aug 15 Lecture: Stats I
Instructor: Tom Nichols
Mon Aug 15 Lab: SPM I
Instructor: Tom Nichols & Luis Hernandez
- SPM Lab 1: PDF | TXT
- Download complete updated SPM2 and SPM99 with local
modifications: SPM-99-2-loc.tgz
Extract this by running WinZip; extract to the directory c:\temp\fmri
(please create the fmri directory
if not already present).
Tue Aug 16 Lecture: Stats II
Instructor: Tom Nichols
- Temporal modeling: TempMod_6.pdf
(includes extra slides on smoothing and slice-timing)
- SPM intro, part 2: LN_SPMintro2_6.pdf
Specifying fMRI designs & understanding the results page
- SPM Spaces: SPM_Spaces_6.pdf
Illustration of use of 'World spaces', for functional-anatomical
coregistration, and spatial normalization for group analyses
Tue Aug 16 Lab: SPM II
Instructor: Tom Nichols & Luis Hernandez
Wed Aug 17 Lecture: Stats III
Instructor: Tom Nichols
- Spatial modeling (or lack there of) & thresholding SpatialMod_6.pdf
Includes material on FWE and FDR methods.
- Conjunctions
- Group analyses in fMRI: RFX_6.pdf
Includes coverage of FSL's method
- Nonparametric group analysis with SnPM: Nonparametric_6.pdf
Wed Aug 17 Lab: SPM III
Instructor: Tom Nichols & Luis Hernandez
Thu Aug 18 Lecture: Task Design II
Instructor: Tom Nichols, Jeanette Mumford & Luis Hernandez
- Advanced designs: DesOpt_6.pdf
- Introduction to FSL's fMRI anlaysis tools FSLintro2005_6.pdf
- ASL:
- Understand Basic Principles in Spin labeling : spin
inversion, flow vs. perfusion,
- Overview of available techniques : pulsed vs. continuous
- Compare of BOLD with ASL : sensitivity, specificity, noise
properties
- Other non-BOLD techniques (T2 weighted, Mn contrast agents.)
Thu Aug 18 Lab: Project work
Instructor: Tom Nichols & Luis Hernandez
You will use this time to work on your project
Fri Aug 19 Lecture: Project presentations
Instructor: you!
- Project presentations
- Preview of topics in fall seminar series
Fri Aug 19 Lab: none
Last modified: Wed
Jun 22 17:07:40 EDT 2005
Tom Nichols
nichols@umich.edu
UM Biostatistics