Methods for Functional Neuroimaging
Course Description
Methods for Functional Neuroimaging provides a graduate level introduction to functional neuroimaging methods. The lectures will focus on the fundamentals of task design, preprocessing, statistical modeling, artifact detection, and visualization of data associated with simple fMRI experimental designs of the type routinely used in clinical neuroimaging research. Lectures will be linked with a series of interactive laboratory exercises that will provide students with experience using SPM8 and MRIcron to combine structural and functional neuroimaging data in the service of detecting differential patterns of task-related activity. Course prerequisites include an introductory statistics course. Some knowledge of imaging physics will also be useful. Students are expected to have access to a PC with MATLAB, SPM8 and MRIcron software.
Lectures will be held Fridays from 4-6PM.
Laboratories will be held Fridays from 6-8PM
Evaluations will be weighted as follows:
120 points: final exam grade
80 points: homework grades (each assignment is worth a maximum of 10 points)
Homework assignments are due one week after their corresponding laboratory and should be turned in to Corinna at cbauer@bu.edu .
Course Web Site: The site includes general information about the course, activities and links to the other sites of interest. Students are encouraged to visit this page regularly and make suggestions for improvements. Resources and readings are listed below. Required materials are marked with an asterix (*).
Tentative Schedule
22JAN
Lecture - Experimental Functional Neuroimaging Introduction
Research questions
Determination of study type
Observational, experimental or quasi-experimental
Hypothesis specification
Participant selection
Sample size / power analysis
Ethical considerations
Reading:
Laboratory - Introduction to SPM, MATLAB, Image Conversion
- SPM8 Manual Chapter 20 DICOM Import*
- MATLAB 7 Getting Started Guide*
- MATLAB Tutorials
29JAN
Lecture - Introduction to First-Level Analysis
Reading:
Laboratory - Preprocessing Steps
05FEB
Lecture - none
Laboratory - First-Level Analysis
- Introduction to Statistical Parametric Mapping*
- SPM8 Manual Chapter 28 Auditory fMRI Data*
- Auditory data
19FEB
Lecture - none
Laboratory - First-Level Analysis
- SPM8 Manual Chapter 29 Face fMRI Data*
- Repetition priming for faces data
26FEB
Lecture - Image Acquisition
Structural imaging
MPRAGE/SPGR acquisition
Functional imaging
EPI acquisition
Field strength
Echo time
Repetition time
Slice acquisition order
Slice angle
Voxel dimensions
Field map
Reading:
Laboratory – Multimodal visualization
Coregistration of structural and functional images
Multiplanar views
Volume rendering
Surface rendering
05MAR
Lecture - Preprocessing
Geometric distortion correction
Slice timing correction
Realignment
Spatial filtering
Temporal filtering
Anatomical space conversion
Direct transformation to a common anatomical space
Indirect transformation to a common anatomical space
Reading:
Laboratory - Preprocessing
- SPM8 Manual Chapter 1 - Slice TimingGeometric distortion correction*
- SPM8 Manual Chapter 2 - Realign*
- SPM8 Manual Chapter 3 - Realign and Unwarp*
- SPM8 Manual Chapter 4 - Coregistration*
- SPM8 Manual Chapter 5 - Segment*
- SPM8 Manual Chapter 6 - Normalize*
- SPM8 Manual Chapter 7 - Smooth*
19MAR
Lecture - Quality Assurance
Instrumental and physiological noise sources
Artifact prevention
Artifact detection
Artifact effect mitigation
Laboratory - Quality Assurance
26MAR
Lecture - Task Design
Design fundamentals
Task timing
Block design
Stochastic design
Mixed design
Self-paced
Parametric modulators
Sparse temporal sampling
Session length
Reading:
Laboratory - Task Design
02APR
Lecture - Statistical Background for Functional Neuroimaging
Matrix algebra for statistics
Correlation and regression
ANOVA
ANCOVA
Classical and Bayesian estimation
Regression diagnostics
Reading:
Laboratory - Statistical Model Specification
- SPM8 Manual Chapter 8 - fMRI Model Specification*
09APR
Lecture - Single-Subject Analysis
Within-session design
Across-session design
Covariates
Reading:
Laboratory - Single-Subject Analysis
- SPM8 Manual Chapter 9 - fMRI Model Estimation*
M16APR
Lecture - Group Analysis
Single group
Multiple group
Longitudinal design
Covariates
Reading:
Laboratory - Group Analysis
- SPM8 Manual Chapter 10 - Factorial Design Specification*
- SPM8 Manual Chapter 30 - Face Group fMRI Data*
- Multi-subject event-related fMRI - Repetition priming data*
23APR
Lecture - Inference
Hypothesis testing
Parameter confidence intervals
Critical threshold
Correction for multiple comparisons
Gaussian random field theory
Reading:
Laboratory - Anatomical labeling
Common anatomical spaces
Probabilistic atlases
Manual labeling
Automated labeling
30APR
Lecture – Structural analysis
Voxel-based morphometry
Acquisition
Preprocessing
Estimation
Inference
Surface-based morphometry
Region of interest morphometry
Reading:
Laboratory – Structural analysis
Final exam distribution
07MAY
Final exam due