fMRI guide

[Image: Chris Rorden]

This guide was written by Bianca de Haan with a bit of input from me. I think it is a nice introduction to functional imaging. This guide closely follows image processing with SPM2, but the concepts can be easily adapted to other tools like FSL, VoxBo, AFNI and other popular packages. The table of contents gives a good impression of the material covered:

  1. The basics of MRI 1

    1.1 The brain in a magnetic field

    1.2 Application of the radiofrequency pulse

    1.3 Relaxation

    1.4 When it all comes together

    1.5 T2* and the spin-echo pulse cycle
  2. From neural activation to the fMRI signal

    2.1 The T2* signal

    2.2 Optimizing the BOLD signal
  3. fMRI task design

    3.1 Block designs

    3.2 Event related designs

    3.3 Summary of fMRI Design
  4. fMRI analysis.

    4.1 Slice timing correction

    4.2 Spatial realignment

    4.3 Spatial normalization

    4.4 Spatial coregistration

    4.5 Spatial smoothing

    4.6 Statistical analysis

    4.7 Choosing a statistical threshold
  5. Literature

To download this guide, choose your preferred format

  1. Acrobat PDF (420kb)

This guide works well with our step-by-step FSL tutorial and SPM2 dataset/scripts:

  1. FSL dataset
  2. SPM2 dataset/scripts