SPM for Basic and Clinical Investigators

SPM8 for Basic and Clinical Investigators is an intermediate-level, 5-day workshop designed for investigators having familiarity with the fundamental principles of fMRI, with at least one year of experience in functional neuroimaging 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 basic and clinical 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.

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

After registering for the course here, please tell us about yourself here.

Information about accomodations for the Boston courses may be found here.

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

 

 

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 export SPM statistical maps to FreeSurfer to visualize results on the cortical surface
  • Be able to use MRIcron for visualization, including volume rendering
  • Be able to use xjView for visualization and labeling
  • Be able to use BioIMage Suite for visualization and Talairach<->MNI coordinate conversion

 

Tentative Schedule (times approximate)

Day 1

9:00AM-12:00PM      SPM introduction

  • SPM8 architecture and overview
  • SPM toolboxes
  • The MATLAB environment
  • Introduction to batch processing
  • Preprocessing

12:00PM-1:00PM LUNCH

1:00PM-3:30PM      Single subject analysis

  • Model specification
  • Model estimation
  • Inference
  • Structure/function visualization

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

Day 2

9:00AM-12:00PM      Preprocessing

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

12:00PM-1:00PM LUNCH

1:00PM-3:30PM     Artifact prevention, detection and mitigation

  • Optimizing fMRI acquisition
  • Sources of artifacts in EPI
  • Detection and repair of EPI artifacts
  • ART demonstration

4:00PM - 5:00PM     Clinical examples: schizophrenia

Day 3

9:00AM-12:00PM   First-level design and estimation

  • Experimental task design in fMRI
  • Statistical modeling: summary statistics
  • First-level design theory

12:00PM-1:00PM LUNCH

1:00PM-3:30PM      First-level design inference

  • First-level designs demonstration
  • Covariates in first-level designs
  • Region of interest processing

4:00PM - 5:00PM    Clinical examples: ADHD 

Day 4

9:00AM-12:00PM      Single group second-level design and modeling

  • Single group second-level design theory
  • Single group second-level designs demonstration

12:00PM-1:00PM LUNCH 

1:00PM-3:30PM      Multiple group second-level design and modeling

  • Multiple group second-level design theory
  • Multiple group second-level designs demonstration
  • Covariates in second-level designs
  • Batch processing revisited

4:00PM - 5:00PM    Clinical examples: autism

Day 5

9:00AM-10:15PM      Visualization, anatomical labeling and structural analysis

  • Visualization with SPM8, FreeSurfer, MRIcron and xjview
  • Visualization demonstration
  • Anatomical labeling with the Talairach Daemon, xjView and the SPM Anatomy Toolbox
  • Anatomical labeling demonstration

10:30AM-12:00PM Structural analysis

  • Voxel based morphometry

12:30PM-2:00PM    Functional neuroimaging in clinical trials

  • Experimental design considerations for clinical trials
  • Covariates in clinical designs
  • Spatial normalization in clinical groups
  • Meta-analysis
  • Power analysis

 

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