Introduction to MRI for Cognitive Neuroscience

• General
  • Introduction
    • Popular software for MRI analysis
    • Why SPM?
    • Other resources
    • Mailing list etiquette
    • Feedback
  • Preliminaries
    • Some basic terminology
    • File types
    • Navigating your way around the brain
  • Structural MRI Overview
    • Types of structural MRI sequences
    • Types of structural MRI analyses for T1-weighted images
    • Basic steps in a VBM analysis
  • Functional MRI Overview
    • Types of functional MRI sequences
    • Basic steps in an fMRI analysis
• Image processing
  • DICOM importing
    • DICOM importing in SPM
    • Options
  • MRI Quality Assessment
    • Structural MRI quality assessment
  • Tissue class segmentation
    • A very, very brief introduction to Bayesian probability
    • Voxel intensities vary across tissue types
    • Distributions of voxel intensities
    • Bias and correcting for it
    • Tissue probability maps
    • “Unified segmentation”
    • Optimizing starting estimates for normalization
    • Tissue class segmentation in SPM
    • What to do when tissue class segmentation fails in SPM
  • Registration (aka spatial normalization)
    • MNI space vs. “Talairach” space
    • Correspondence between macroanatomical and cytoarchitectural characteristics
    • Modulation
    • Cases in which whole-brain registration may not be necessary
  • Smoothing
    • Gaussian smoothing
    • Why smooth MRI images?
    • How much to smooth
    • When not to smooth MRI images
• Statistics
  • Multiple comparisons and how to deal with them
    • Why performing multiple comparisons present a challenge
    • Principled control over false positives
    • Spatial correlation
    • Ways of dealing with multiple comparisons
    • Limiting the number of comparisons using anatomical hypotheses
• Miscellaneous
  • Selecting files in SPM
    • Using regular expressions to filter files
    • Recursive file selection
    • Selecting volumes from 4d files in SPM
  • Using SPM’s Display tool
    • Selecting and displaying an image
    • Using Display to reorient an image
    • Reorienting multiple images
    • Other display tools
  • Using SPM’s CheckReg Tool
    • Using CheckReg to check coregistration of mean functional and structural
    • Image information available from CheckReg
    • Using CheckReg to check normalization to MNI space
    • Displaying volumes from 4d files
  • Creating an explicit mask
  • Spatially restricting analyses
    • Using a an explicit mask to constrain voxelwise analysis
    • Conducting a region of interest (ROI) analysis
    • Supplementing restricted analyses with whole-brain analyses
    • Avoiding nonindependence and circularity
  • Viewing or changing SPM Defaults
    • Editing spm_defaults.m
    • Creating a custom version of spm_defaults.m
    • Changing default values from the Matlab command line
  • Building ROIs in MarsBaR
    • Downloading and installing MarsBaR
    • Defining a (spherical) ROI
    • Creating an image ROI
    • Viewing a MarsBaR (.mat) ROI
    • Viewing an image ROI
    • Using a script to create ROIs
  • Frequently Asked Questions
    • Why won’t my structural image segment properly?
    • Why is voxelwise FDR correction not available in SPM8, like it was in SPM5?
    • How do I unsubscribe from the SPM or FSL email list?
• References