SPM Essentials

SPM8 Essentials is an introductory, 3-day workshop designed for investigators having some familiarity with the fundamental principles of fMRI data acquisition and analysis. Requiring no previous experience using SPM, 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 basic fMRI experimental designs. While the primary emphasis will involve using the core SPM8 programs for these purposes, there will also be discussion of a few 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 and xjView).

As the presentations will include demonstrations and tutorials utilizing SPM8, participants are expected to bring a laptop with MATLAB, SPM8 and MRIcron already installed. Detailed setup instructions can be found here.

This course is not offered on a regular basis. Inquiries about future scheduling should be directed to admin@neurometrika.org.

 

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
  • Be able to use MRIcron for data visualization, including volume rendering

Tentative Schedule

Day 1

9AM-10:30AM  Introduction to SPM8

Workshop overview
SPM8 interface
SPM8 architecture
MATLAB basics
Batch processing introduction

10:45AM-12:00PM  Preprocessing 1
Preprocessing overview and background
Realignment

12:00PM-1:00PM LUNCH

1:00PM-4:00PM  Preprocessing 2

Unwarping
Slice time correction
Spatial filtering
Spatial normalization
Global normalization

4:15-5:00PM  Statistics review: t-tests, regression, ANOVA, ANCOVA and the general linear model 

Day 2

9AM-10:45AM      Artifact prevention, detection and mitigation
Sources of artifacts in EPI
Detection and repair of EPI artifacts
ART demonstration

11AM-12:00PM      Visualization
Visualization with SPM8, FreeSurfer, MRIcron and xjview

12:00PM-1:00PM LUNCH

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

4:15-5:00PM Anatomical labeling
Anatomical localization and labeling
Anatomical localization demonstration

Day 3

9AM-12PM  Second-level design and analysis
Second-level fMRI designs overview
Second-level fMRI designs demonstration

12PM-1:00PM LUNCH

1:00PM-3:00PM  Group analysis and batch processing
Single group second-level designs
Multi-group second-level designs
Covariates in second-level designs

 

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