SPM8 Basics is an intermediate-level, 5-day workshop is designed for investigators having familiarity with the fundamental principles of fMRI data acquisition and analysis.

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 schemes, including MRIcron, xjView, and FreeSurfer.

The presentations will include demonstrations and tutorials utilizing SPM8. Participants are expected to bring a laptop with MATLAB, SPM8 and MRIcron already installed.

The schedule for upcoming courses can be found here.

Educational Objectives 

• Understand the basic organization of the SPM GUI
• Understand the organization of the SPM "toolbox"
• Be able to construct batch processing scripts for preprocessing and statistical modeling
• Understand the basic fMRI data preprocessing steps
• Be able to construct a preprocessing sequence including slice time correction, realignment, and spatial filtering
• Understand the origins of the artifacts most commonly encountered in fMRI datasets
• Be able to utilize explore an fMRI dataset for artifacts and effect repairs as needed
• Understand the basic fMRI single subject experimental design types
• Be able to implement statistical analysis procedures for the basic single subject fMRI designs
• Understand the basic fMRI single group experimental design types
• Be able to implement statistical analysis procedures for the basic single group fMRI designs
• Understand the basic fMRI multiple group experimental design types
• Be able to implement statistical analysis procedures for the basic multiple group fMRI designs
• Understand the process of incorporation of covariates in fMRI experimental designs
• Be able to construct and estimate statistical models involving covariates
• Be able to utilize the RIC Talairach Daemon for region labeling
• Be able to utilize the SPM Anatomy toolbox for region labeling
• Be able to utilize the FreeSurfer for region labeling
• Be able to use FreeSurfer to visualize statistical maps on the cortical surface
• Be able to use MRIcron for data visualization, including volume rendering

Topics

Introduction to SPM8
      * Workshop overview
      * New features in SPM8
      * The SPM8 interface
      * Introduction to batch processing
      * Structural processing

Preprocessing

      * Preprocessing overview and background
      * Slice time correction
      * Realignment
      * Unwarping
      * Spatial filtering
      * Spatial normalization

Artifact prevention, detection and mitigation
      * Sources of artifacts in EPI
      * Detection and repair of EPI artifacts
      * ART demonstration
      * Visualization with SPM8, FreeSurfer, MRIcron and xjview

First-level experimental design and analysis

      * Experimental design in fMRI
      * Statistical modeling: summary statistics
      * First-level fMRI designs overview
      * First-level fMRI designs demonstration

Second-level design and analysis
      * Second-level fMRI designs overview
      * Second-level fMRI designs demonstration
      * Anatomical localization and labeling
      * Anatomical localization demonstration

Group analysis and batch processing

      * Single group second-level designs
      * Multi-group second-level designs
      * Covariates in second-level designs
      * Batch processing revisited
      * Batch processing demonstration