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!
Note
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.
Install
Unix for Neuroimagers
- What is Unix?
- Unix Tutorial #1: Navigating the directory tree
- Unix Tutorial #2: Copying and Removing Files
- Unix Tutorial #3: Reading Text Files
- Unix Tutorial #4: Shells and Path Variables
- Unix Tutorial #5: For-Loops
- Unix Tutorial #6: Conditional Statements
- Unix Tutorial #7: Scripting
- Unix Tutorial #8: The Sed Command
- Unix Tutorial #9: Automating The Analysis
fMRI Short Course with FSL
- Introduction
- fMRI Tutorial #1: Downloading the Data
- fMRI Tutorial #2: Overview of The Flanker Task
- fMRI Tutorial #3: Looking at the Data
- fMRI Tutorial #4: Preprocessing
- fMRI Tutorial #5: Statistics and Modeling
- fMRI Tutorial #6: Scripting
- fMRI Tutorial #7: 2nd-Level Analysis
- fMRI Tutorial #8: 3rd-Level Analysis
- fMRI Tutorial #9: ROI Analysis
- fMRI Tutorial #10: Summary
- fMRI Short Course: Appendices
FreeSurfer
E-Prime
AFNI
SPM
Functional Connectivity with the CONN Toolbox
Parametric Modulation
Note
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
ASL Analysis
Frequently Asked Questions
Open Science
Advanced Normalization Tools (ANTs)
Tract-Based Spatial Statistics (TBSS)
Statistics for Neuroimagers
Machine Learning for Neuroimagers
Slicer
Using the Supercomputer
Matlab for Neuroimagers
ITK-Snap
Python for Neuroimagers
Meta-Analysis for fMRI
Introduction to Neurodesk
Note
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).”