fMRI Wiki

MontiLab fMRI wiki & tools

This page has a collection of useful information for fMRI analysis. It is divided into three parts:

  1. fMRI Theory & discussions
    1. Important papers you should read about fMRI (including 1st level analysis, group level analysis). For example:
    2. Presentations and advanced discussion about fMRI methods (including graph theory preprocessing pipelines, and the use of non-parametric group statistics). For example:
  2. Scripts, utilities and tutorials
    Scripts & utilities

    • optiBET: Our in-house software which uses freely available routines (from FSL and AFNI) and does much better brain extractions, particularly in patient brains.
    • DesignDiagnostics (matlab): Want to compare how good different designs (e.g., event-related, block, different versions of the same type of design) are? Just download this little tool which, given an X matrix (e.g., onset/offsets of each condition) will tell you how good it is and will run simulations for you.
    • FDR thresholding script: Simple script to perform FDR thresholding
    • Make spherical ROIs: Simple script to create spherical ROIs
    • Split masks into Left and Right hemisphere

    Tutorials: Rendering functional results on structural images

  3. Practical information
  4. Evan’s Helpful Unix Tips & Tricks