SPM for Basic and Clinical Investigators - Baltimore

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 six months 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, FSL, 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. Detailed setup instructions can be found here.

This course will be jointly sponsored by the Johns Hopkins Brain Science Institute and the Hopkins Population Center. It will be held March 13-17, 2012 in Baltimore, MD, in Room 202 of the School of Nursing Building (515 N. Wolfe Street, Baltimore, MD 21205), located on the Johns Hopkins East Baltimore campus.

Directions to the classroom in the School of Nursing Building can be found here.

Lodging near the medical campus is available at McElderry House.

Register for the course here.

The fee for the program is $1500. Reduced rates of $1250 for post-doctoral fellows and $1000 for undergraduate, graduate or medical students are available.  A 20% discount is available to all JHU investigators.

This course will be taught by Tom Zeffiro.

Questions about course arrangements or content 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
  • 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 estimate sample size using power analysis

 

Tentative Schedule

Day 1

10:00AM-12:00PM      SPM introduction

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

12:00PM-1:00PM      LUNCH

1:00PM-6:00PM      Single subject analysis

  • Preprocessing
  • Model specification
  • Model estimation
  • Inference
  • Structure/function visualization
  • Homework assignment - Spatial normalization
Day 2

10:00AM-1:00PM      Preprocessing

  • Homework review
  • SPM architecture
  • Preprocessing overview and background
  • Realignment
  • Unwarping
  • Slice time correction
  • Spatial normalization
  • Spatial filtering

1:00PM-2:00PM LUNCH

2:00PM-3:15PM     Outlier detection

  • Introduction to detection and repair of EPI artifacts
  • Outlier detection using ART

3:30PM-5:15PM

  • Introduction to first-level design
  • Statistics review: t-tests, regression, ANOVA, ANCOVA and the general linear model

5:15PM-6:00PM

  • Homework assignment - Single session preprocessing and statistical modeling
Day 3

10:00AM-1:00PM   First-level design and estimation

  • Homework review
  • Statistical modeling: summary statistics
  • First-level design theory
  • First-level design demonstrations
  • Covariates in first-level designs
  • First-level contrast specification

1:00PM-2:00PM LUNCH

2:00PM-3:30PM    Artifact prevention, detection and mitigation 

  • Sources of artifacts in EPI
  • First level model diagnostics using ART

3:45PM-4:30PM    Visualization 

  • Visualization with SPM8, FreeSurfer, FSL, MRIcron and xjview

4:45PM-5:15PM    Batch processing

  • Multi-session batch 

5:15PM-6:00PM

  • Homework assignment - Multi-session single subject preprocessing and statistical modeling
Day 4

 

10:00AM-1:00PM      Single group second-level design and modeling

  • Homework review
  • Second-level designs using the GLM
  • Single group second-level design theory
  • Single group second-level design demonstration

1:00PM-2:00PM LUNCH 

2:00PM-5:15PM      Multiple group second-level design and modeling

  • Multiple group second-level design theory
  • Multiple group second-level design demonstration
  • Covariates in second-level design

5:15PM-6:00PM

  • Homework assignment - Single group analysis

Day 5

10:00AM-11:30PM      Visualization, anatomical labeling and structural analysis

  • Homework review
  • Visualization review
  • Anatomical labeling with the Talairach Daemon, xjView and the SPM Anatomy Toolbox
  • Anatomical labeling demonstration

11:45AM-1:00PM Structural analysis

  • Voxel based morphometry

1:00PM-2:00PM LUNCH 

2:00PM-4:00PM

  • Optimizing fMRI acquisition
  • Meta-analysis
  • Power analysis
  • Reporting an fMRI Study

5:00-6:00PM    Review session

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