SPM8 for Basic and Network Analysis Chicago is an advanced-level, 5-day workshop designed for investigators having familiarity with the fundamental principles of fMRI, at least one year of experience in functional neuroimaging data analysis, and experience using SPM.

The workshop will focus on using SPM8 and its extensions for preprocessing, statistical modeling and visualization of data associated with a range of fMRI experimental designs. While the primary emphasis will involve using the core SPM8 programs for these purposes, there will also be extensive discussion of a variety of software tools that extend the power of SPM8. Some of these tools facilitate fMRI quality assurance through artifact detection and mitigation at various analysis stages. Other tools support a variety of data visualization methods, including MRIcron, xjView, BioImage Suite, and FreeSurfer.

Later in the week, the presentations will provide an introduction to network analysis using SPM8 along with practical demonstrations tied to the key conceptual issues. The focus will be on techniques other than the usual massively univariate analyses commonly used for modeling fMRI data. Topics covered will include functional connectivity examined using bivariate correlation or regression, psychophysiological interaction analysis, and dynamic causal modeling.

Preparation: The workshop will involve demonstrations and interactive exercises involving SPM8, its extensions and associated programs. These demonstrations will be integrated with the didactic portions of the lectures. The interactive software exercises will demonstrate the details of the various data modeling techniques and participants will gain practical experience through the worked examples. Therefore, to gain the full benefit from the program, we ask that participants bring laptops with MATLAB and SPM8 installed. Detailed setup instructions can be found here.

The workshop will be held September 26-30, 2011 in Room 107 of the Kellog Conference Center in Wieboldt Hall at 340 East Superior Street at Northwestern University, Chicago, IL. Kellogg Conference Center building.

Directions from the Red LIne are here.

Nearby places to eat can be found here.

Register for the course here.

Hotels:

Questions about course arrangements or content should be directed to admin@neurometrika.org

The course instructors are Thomas Zeffiro, Darren Gitelman, Robert Savoy and Susan Whitfield-Gabrieli.

Tentative Schedule

Day 1

SPM architecture and Preprocessing

9:00AM-12:00PM      SPM introduction

• SPM8 architecture and overview
• MATLAB basics
• SPM toolboxes
• Introduction to batch processing
• Preprocessing overview and background
• Realignment
• Unwarping

12:00PM-1:00PM LUNCH

1:00PM-5:00PM      Preprocessing and artifact mitigation

• Slice time correction
• Spatial normalization
• Spatial filtering
• Optimal EPI acquisition
• Sources of artifacts in EPI
  

Day 2 

Univarate modeling

9:00AM-12:00PM      First-level models

• Statistical modeling: summary statistics
• Experimental task design in fMRI
• First-level design theory
  
• First-level design demonstrations
• First-level contrast specification
• Covariates in first-level designs

12:00PM-1:00PM LUNCH

1:00PM-2:30PM     Quality Assurance

• Detection and repair of EPI artifacts using ART

2:30-5:00PM Second-level models

• Single group second-level design theory
• Single group second-level design demonstration
• Multiple group second-level design theory
• Multiple group second-level design demonstration
• Second-level contrast specification
• Covariates in second-level design
  

Day 3

Functional connectivity

9:00AM-12:00PM

• The uses of network analysis
• Principles of correlation and regression
• Functional connectivity overview

• The functional connectivity toolbox can be found here.

12:00PM-1:00PM LUNCH

1:00PM-5:00PM

• Functional connectivity toolbox demonstrations
  • Resting state experiment
  • Task experiment

Here are some example connectivity toolbox batch files:

complete batch file - setup - preprocessing - analyses - results

• Functional connectivity example studies

Day 4

Factorial designs and PPI

9:00AM-12:00PM

• General linear model review - ANOVA, regression and ANCOVA
• PPI overview
• Psychophysiological interaction analysis
• Physiophysiological interaction analysis

12:00PM-1:00PM LUNCH

1:00PM-5:00PM

• PPI software demonstrations
  • Psychophysioloigcal interactions
  • Physiophysiological interactions
• PPI example studies

Day 5

Dynamic causal modeling

9:00AM-12:00PM

• Dynamic causal modeling overview
• Anatomical model selection
• First-level models
• Second-level models

12:00PM-1:00PM LUNCH

1:00PM-5:00PM

• Dynamic causal modeling demonstration
• Dynamic causal modeling exercises

The DCM exercise instructions can be found here.

• Dynamic causal modeling example studies