FSL for Basic and Clinical Investigators

FSL 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 FSL 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 FSL programs for these purposes, there will also be extensive discussion of a variety of software tools that extend the power of FSL. 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, BioImage Suite, and FreeSurfer.

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

The presentations will include both lectures and interactive laboratory exercises. During the week there will be a number of homework assignments designed to reinforce the topics covered in class.

Register for the course here.

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

Questions about course arrangements or content should be directed to admin@neurometrika.org

 

 

Educational Objectives 

  • Understand the basic organization of the FSL GUI
  • Understand the organization of the FSL utilities
  • Understand the basic fMRI data preprocessing steps
  • Be able to construct a preprocessing sequence including geometric distortion 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 FSL atlases for region labeling
  • Be able to utilize FreeSurfer for region labeling
  • Be able to export FSL 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 BioIMage Suite for visualization and Talairach<->MNI coordinate conversion

 

Tentative Schedule (times approximate)

Day 1

9:00AM-12:00PM      FSL introduction

  • FSL architecture and overview
  • FSL utilities
  • Preprocessing

12:00PM-1:00PM LUNCH

1:00PM-5:00PM      Single subject analysis

  • Model specification
  • Model estimation
  • Inference
  • Structure/function visualization
  • Region of interest processing     
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     Preprocessing

  • Optimizing fMRI acquisition
  • Introduction to detection and repair of EPI artifacts
  • first ART demonstration

4:00PM-5:00PM     Statistics review: descriptive statistics, t-tests, correlation, regression

Day 3

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

  • Experimental task design in fMRI
  • Statistical modeling: summary statistics
  • First-level design theory
  • First-level design demonstrations
  • Covariates in first-level designs
  • First-level contrast specification

12:00PM-1:00PM LUNCH

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

  • Sources of artifacts in EPI
  • Detection and repair of EPI artifacts
  • second ART demonstration

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


Day 4

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

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

12:00PM-1:00PM LUNCH 

1:00PM-5:00PM      Multiple group second-level design and modeling

  • Multiple group second-level design theory
  • Multiple group second-level design demonstration
  • Covariates in second-level design    
Day 5

9:00AM-10:30PM      Visualization, anatomical labeling and structural analysis

  • Visualization with FSL, FreeSurfer, and MRIcron
  • Visualization demonstration
  • Anatomical labeling using the FSL atlases
  • Anatomical labeling demonstration

10:45AM-12:00PM Structural processing

  • Voxel based morphometry in FSL

12:00PM-1:00PM LUNCH 

1:00PM-3:00PM    Diffusion tensor imaging

  • Principles of diffusion tensor imaging
  • DTI processing in FSL
  • Tractography using FSL

3:30-5:00PM    The Nipype batch processing environment

  • Batch processing using FSL
Topics
  • FSL installation and setup
  • Introduction to FSL
  • FSL Interface overview
  • File format conversion
  • Preprocessing
  • Optimizing fMRI acquisition
  • Artifact identification and mitigation
  • The general linear model
  • First level model specification
  • Second level model specification
  • Conjunction analysis
  • Anatomical labeling
  • Batch processing
  • Visualization
  • Morphometry
  • Extensions
  • Further reading