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:
      • Monti M.M. (2011) Statistical analysis of fMRI time-series: A critical evaluation of the GLM approach. Frontiers in Human Neuroscience, 5(28).
      • Mumford JA & Nichols T (2009) Simple group fMRI modeling and inference. Neuroimage 47, 1469–1475.
      • Eklund et al (2015) Can parametric statistical methods be trusted for fMRI based group studies?arXiv:1511.01863.
   2. Presentations and advanced discussion about fMRI methods (including graph theory preprocessing pipelines, and the use of non-parametric group statistics). For example:
      • Denoising data with MultiEcho MRI (Multiecho MRI, Multiecho MRI, MultiEcho MRI…)
      • Are your analyses too parametric? (that’s not normal..!)
      • The problem of motion in connectivity analyses (updated 2019)
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

   • Rendering functional data on surfaces (with Caret)
   • NIFTI to surface: Creating and rendering surfaces with ITK-SNAP and Paraview (external link)
3. Practical information
   • Getting connected to the FUNC
4. Evan’s Helpful Unix Tips & Tricks
   • Useful Unix commands