Bios 642 / BME 499.098 / Psych 808:
Introduction to Functional MRI

Schedule & Basic Info

Class Meeting Time:	9AM to Noon, Monday-Friday, Aug 9 through Aug 20
Class Meeting place:	East Hall 1084
Lab Meeting Time:	1PM-3PM
Lab Meeting place:	East Hall B250, 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 8/9	Tue 8/10	Wed 8/11	Thu 8/12	Fri 8/13
Lecture 9am- Noon	Course Motivation (JJ) Intro to Neuroanatomy (JJ) Intro to BOLD & Task Design (DN)	Physics I: Fields, gradients, spins (DN)	Physics II: Image formation, hardware, SNR (DN)	Physics III: Physiology of BOLD Non-BOLD methods, ASL (LH/DN)	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 8/16	Tue 8/17	Wed 8/18	Thu 8/19	Fri 8/20
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: Advanced Designs (TN) Optimizing Designs(TN) Design Case Studies	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

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• 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

• 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 9 Lab: Task Design w/ E'
Instructor: Derek Nee

Tue Aug 10 Lecture: Physics I
Instructor: Doug Noll

Goals:

• 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

• Movie of magnetization being excited in standard frame (laboratory frame - left) and rotating frame of reference (right)
  (RF is is in light blue and magnetizatio is in red)
  
• Movie of magnetization being excited in standard frame (laboratory frame) with line tracing motion of magnetization
• Movie of off-resonance RF pulse
  

Tue Aug 10 Lab: Task Design II
Instructor: Derek Nee

Wed Aug 11 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

Wed Aug 11 Lab: fMRI Lab Tour (Group A)
Instructor: Luis Hernandez & Doug Noll

Thu Aug 12 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

part2 - 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 12 Lab: fMRI Lab Tour (Group B)
Instructor: Luis Hernandez & Doug Noll

Fri Aug 13 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
• 
  

Fri Aug 13 Lab: Matlab & Data Exploration
Instructor: Luis Hernandez

Week 2

---

• Basic Stats: LN_BasicStats_6.pdf
  
• SPM Introduction: LN_SPMintro_6.pdf
  Includes material on voxel-world space differences, and Left-Right, Radiological/Neurological SPM99/SPM2 conventions.
• SPM pipeline slide: SPM_ProcPath.pdf

Mon Aug 16 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 17 Lecture: Stats II
Instructor: Tom Nichols

• Temporal modeling: TempMod.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.pdf
  Illustration of use of 'World spaces', for functional-anatomical coregistration, and spatial normalization for group analyses

Tue Aug 17 Lab: SPM II
Instructor: Tom Nichols & Luis Hernandez

• SPM Lab 2: PDF | TXT
  
• Download the event-related timings: ERtiming.tgz
• Cropped T1 Atlas: scalpedT1.img scalpedT1_GM.hdr
• Atlas Gray Matter mask: avg152T1_GM.img avg152T1_GM.hdr

Wed Aug 18 Lecture: Stats III
Instructor: Tom Nichols

• Spatial modeling (or lack there of) & thresholding SpatialMod.pdf
  Includes material on FWE and FDR methods.

Wed Aug 18 Lab: SPM III
Instructor: Tom Nichols & Luis Hernandez

• SPM Lab 3: PDF | TXT
  
• Please choose a final project from the list.

Thu Aug 19 Lecture: Task Design II
Instructor: Tom Nichols & guests

• Group analyses in fMRI: RFX.pdf
• fMRI design optimization: SPMdesopt.pdf
• Nonparametric group analysis with SnPM: Nonparametric.pdf

Thu Aug 19 Lab: Project work
Instructor: Tom Nichols & Luis Hernandez
You will use this time to work on your project

Fri Aug 20 Lecture: Project presentations
Instructor: you!

Fri Aug 20 Lab: none