The Methods for Functional Neuroimaging lecture series given in the Functional MRI Visiting Fellowship at MGH provides an introduction to the design and analysis of functional neuroimaging experiments. The presentations focus on the fundamentals of fMRI data acquisition, task design, preprocessing, statistical modeling, and inference. Examples used in the lectures are drawn from a range of studies spanning both basic and clinical research applications.

Thomas Zeffiro M.D. Ph.D

SEP2010

Lecture 1 - Optimizing fMRI Data Acquisition

EPI acquisition
Head coil
Field strength
Echo time
Repetition time
Slice acquisition order
Slice angle
Voxel dimensions
Field maps
Session length

Reading:

• Maintaining acquisition and analysis data quality

SEP2010

Lecture 2 - 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:

• Slice Timing
• Rigid Body Registration
• Spatial Normalization
• Image Segmentation

Additional material:

• 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

Lecture 3 - First-Level Design and Analysis

Linear modeling
Effects of interest
Nuisance variables
Modeling hemodynamic effects
Block design
Stochastic design
Mixed design
Self-paced design
Parametric modulators
Sparse temporal sampling

Reading:

• Overview of fMRI Analysis
• Introduction to Statistical Parametric Mapping
• Design efficiency
• The General Linear Model
• Variance Components
• Contrasts and Classical Inference
• Analysis of fMRI Time Series

Additional material:

• SPM8 Manual Chapter 8 - fMRI Model Specification
• fMRI Simulator
• optseq

SEP2010

Lecture 4 - Second-Level Design and Analysis

Single group
Multiple group
Longitudinal design
Covariates

Reading:

• ANOVA and SPM
• Random Effects Analysis
• Hierarchical Models

Additional material:

• SPM8 Manual Chapter 10 - Factorial Design Specification
• SPM8 Manual Chapter 30 - Face Group fMRI Data
• Multi-subject event-related fMRI - Repetition priming data

SEP2010

Lecture 5 - Inference

Hypothesis testing
Parameter confidence intervals
Critical threshold
Correction for multiple comparisons
Gaussian random field theory

Reading:

• Introduction to Random Field Theory

Lecture 6 - Network Analysis

Regional functional specialization and regional integration
Functional and effective connectivity
Bivariate correlation
Independent components analysis
Principal components analysis
Psychophysiologic interactions
Physiophysiologic interactions
Mediation analysis
Path analysis
Dynamic causal modeling

Reading:

doi:10.1016/j.neuroimage.2009.11.015