SPM Essentials

SPM8 Essentials is an introductory, 3-day workshop designed for investigators having strong familiarity with the fundamental principles of fMRI data acquisition and analysis. It provides a basic grounding in the conceptual and practical issues associated with using SPM8 for fMRI 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 course instructors are Thomas Zeffiro, Robert Savoy and Susan Whitfield-Gabrieli.

Registration information for this program may be found here.

Information about accomodations may 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

Tentative Schedule

Day 1

9AM-12:00PM      Introduction to SPM8
      * Workshop overview
      * New features in SPM8
      * The SPM8 interface
      * Introduction to batch processing
      * Structural processing

12:00PM-1:30PM LUNCH

1:30PM-4:00PM      Preprocessing
      * Preprocessing overview and background
      * Slice time correction
      * Realignment
      * Unwarping
      * Spatial filtering
      * Spatial normalization

4:30-5:30PM Statistics review: t-tests, regression, ANOVA, ANCOVA and the general linear model 

Day 2

9AM-12:00PM      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

12:00PM-1:30PM LUNCH

1:30PM-4:00PM      First-level experimental design and analysis
      * Experimental design in fMRI
      * First-level fMRI designs overview
      * First-level fMRI designs demonstration

4:30-5:30PM Statistical modeling in SPM8: summary statistics

Day 3

9AM-12PM      Second-level design and analysis
      * Second-level fMRI designs overview
      * Second-level fMRI designs demonstration
      * Anatomical localization and labeling
      * Anatomical localization demonstration

12PM-1:30PM LUNCH

1:30PM-4:00PM      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

4:30-5:30PM Power analysis in neuroimaging

 

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