Welcome to Andy’s Brain Book!


This resource is sponsored by the University of Michigan.

Hello! This book, Andy’s Brain Book, is the ReadTheDocs companion to Andy’s Brain Blog. It is intended for fMRI beginners, with more advanced imaging techniques being added later on. If this is your first time here, watch this video for a quick overview of the website.

This book, Andy’s Brain Book, is intended for fMRI beginners, with more advanced imaging techniques being added later on.

If you are completely new to fMRI analysis, I recommend starting with the installation page. Good luck!


Reading this book is easier with a slightly larger font size; I recommend using a zoom of 125%. You can do this on a Macintosh by holding down the Command key and pressing +, or from the browser menu you can click on View -> Zoom In.


Functional Connectivity with the CONN Toolbox


The following modules are under construction. Check back soon for more updates!

Image Visualization with MRIcroGL

Introduction to the Human Connectome Project (HCP)

Finite Impulse Response (FIR) Models

fMRI Concepts

Diffusion Analysis with MRtrix

Frequently Asked Questions

Open Science

Advanced Normalization Tools (ANTs)

Tract-Based Spatial Statistics (TBSS)

Statistics for Neuroimagers

Machine Learning for Neuroimagers

Using the Supercomputer

Matlab for Neuroimagers

Python for Neuroimagers

Meta-Analysis for fMRI


This book is under construction. More chapters will be added in the coming weeks; my goal is to have a complete draft of the fMRI Short Course by the first week of June.

4.24.2019: Finished the sections Unix Tutorial #4, fMRI Short Course chapters on smoothing and quality checking FEAT output, and added a playlist covering all of the sections done in the Preprocessing module.

5.06.2019: Added sections to FAQ about resampling, biased analyses, and flipped orientations. Wrote the chapters for the Statistics part of the short course; videos coming soon.

5.25.2019: Finished the Unix Module, and added videos for 2nd and 3rd level analysis in the fMRI short course.

5.31.2019: First draft of the Unix and fMRI courses are complete.

10.14.2019: E-Prime module is complete.

10.16.2019: FreeSurfer module complete.

1.13.2020: SPM written module complete (videos not up yet)

4.13.2020: SPM videos uploaded

5.21.2020: CONN Tutorials complete

12.08.2020: First part of MVPA tutorial complete, from preprocessing to group-level analysis. Later on, will add other statistical analyses, such as prevalence analysis.

01.20.2022: There is now a DOI for Andy’s Brain Book! If you would like to cite it, use the following template: “We followed the AFNI preprocessing pipeline as outlined in Andy’s Brain Book (Jahn, 2022. doi:10.5281/zenodo.5879293).”