While SPM and FreeSurfer are among the most popular programs used for the analysis of functional and structural brain imaging data, their integration in the context of modeling cortical task-related and intrinsic activity can pose significant procedural challenges.  Cortical Functional Neuroimaging With SPM and FreeSurfer is an intermediate-level, 5-day workshop that will provide you with the essential skills required to use SPM and Freesurfer together for modeling fMRI data in native, MNI or cortical surface anatomical spaces  It is designed for investigators having familiarity with the fundamental principles of fMRI measurement and design, with at least six months experience in functional neuroimaging data acquisition and analysis.

This strongly interactive workshop will focus on the use of SPM8, FreeSurfer and their extensions for preprocessing, statistical modeling, visualization and anatomical labeling. Demonstrative examples will be drawn from a wide range of the instructors' experimental work covering a range of basic and clinical fMRI experimental designs.  Extensive coverage will be given to structural and functional MRI quality assurance methods to facilitate artifact detection and mitigation at various analysis stages.

A unique feature of the course will be thorough coverage of methods for automating analysis workflows using the Nipype, a novel and powerful image processing environment of rapidly increasing popularity.

As the presentations will include in-class demonstrations and homework assignments, participants are expected to bring a laptop with MATLAB, SPM8, FreeSurfer and MRIcron already installed. Detailed setup instructions can be found here.

Because of the highly interactive nature of this workshop, enrollment will be limited, so register now to reserve your spot.

Information about accomodations in Boston may be found here.

Register for the course here.

The course will be held from OCT29-NOV02 in the 5th floor conference room at the Constitution Inn in Charlestown, MA..

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

The course instructors are Thomas Zeffiro, Allison Stevens Player, Gary Strangman, Jon Polimeni, Robert Savoy and others.

Educational Objectives 

• Understand how to optimize both structural and functional MRI data acquisition
• Understand the basic fMRI data preprocessing steps
• 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 using the SPM batch editor
• Be able to use SPM to construct a preprocessing sequence to detect task-related or intrinsic brain activity modulations including geometric distortion correction, slice time correction, realignment, and spatial filtering
• Understand the origins of the artifacts most commonly encountered in structural and functional MRI datasets
• Be able to use the SPM ART toolbox to explore an fMRI dataset for artifacts and effect repairs as needed
• Be able to use SPM to transform native space images to MNI space
• Be able to use FreeSurfer to transform native space images to cortical surface space
• Be able to use FreeSurfer to explore a structural MRI dataset for artifacts and effect repairs as needed
• Understand the basic fMRI single subject experimental design types
• Be able to implement statistical analysis procedures in SPM for the basic single subject fMRI designs
• Understand the basic fMRI single group experimental design types
• Be able to implement statistical analysis procedures in SPM and FreeSurfer for the basic single group fMRI designs
• Understand the basic fMRI multiple group experimental design types
• Be able to implement statistical analysis procedures in SPM and FreeSurfer 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 in SPM and FreeSurfer involving covariates
• Be able to utilize the SPM Anatomy toolbox for region labeling
• Be able to utilize the FreeSurfer for region labeling
• Be able to utilize the FreeSurfer for cortical surface visualization of task-related and intrinsic brain activity.
• Be able to export SPM native space statistical maps to FreeSurfer to visualize results on the cortical surface
• Be able to export SPM native space contrast images to FreeSurfer to perform spatial smoothing and statistical modeling on the cortical surface
• Be able to use MRIcron for visualization, including volume rendering in native and MNI anatomical spaces

Schedule

DAY 1

9:00AM-12:00PM

• Workshop Introduction
  
• Analysis Overview (SPM)
  
• SPM Architecture (SPM)
  
• Interface Overview (SPM)
  
• Realignment (SPM)
  
• Slice time correction (SPM)

1:00AM-5:00PM

• Spatial Filtering (SPM)
• Unwarping (SPM)
• Preprocessing Demonstration (SPM)
• Optimal EPI Acquisition
• Sources of Artifacts in EPI
• Homework Assignment (SPM Auditory Tutorial 

DAY 2 

9:00AM-12:00PM

• Review and Questions
• Basic Statistics
• First Level Modeling (SPM)
• Experimental Task Design
• First-level Modeling: Demonstrations (SPM)
• Contrast specification (SPM)
• Covariates (SPM)

1:00PM-5:00PM

• Outlier Detection (SPM)
• First Level Modeling of Outliers (SPM)
• Introduction to FreeSurfer
• Individual Subject Analysis (FS)
• Tkmedit/Tksurfer Demonstration (FS)
• Interaction Subject Analysis Tutorial (FS)

DAY 3

9:00AM-12:00PM

• Review and Questions
• Failure Modes (FS)
• Trouble-shooting Demonstration (FS)
• Trouble-Shooting Tutorial (FS)
• Quality Checking Reconstruction (FS)

1:00PM-5:00PM

• Multimodal Integration (FS)
• Multimodal Integration Tutorial (FS)
• Second-Level models (SPM)
• Second Level Design Theory
• Second Level Design Exercises (SPM)
• Contrast specification (SPM)
  

DAY 4

9:00AM-12:00PM

• Review and Questions
• ROI Analysis (SPM)
• ROI Analysis Tutorial (REX)
• ROI Analysis (FS)
• ROI Analysis Tutorial (FS)

1:00PM-5:00PM

• Group Analysis, GLM, Multiple Comparisons (FS)
• Group Analysis Tutorial (FS)
• Applications of High Resolution fMRI (FS)

DAY 5

9:00AM-12:00PM

• Review and Questions
• Nipype Introduction
• Python Introduction
• Nipype Exercises

1:00PM-5:00PM

• Combining SPM and Freesurfer Using Nipype
• Nipype Exercises (SPM and FS)
• Review and Questions