Welcome to AFNI’s documentation!

• 1. Installation and Background
  • 1.1. Install AFNI on Your Own Computer
  • 1.2. Install AFNI on Administered Systems
  • 1.3. Work with Docker/Containerized AFNI
  • 1.4. Download other/specific AFNI/SUMA software
  • Unix Tutorial
  • 1.5. Prep for Bootcamp
  • 1.6. Miniconda: Python(s) in a convenient setup
• 2. Educational resources
  • 2.1. AFNI Bootcamp Recordings
  • 2.2. AFNI Bootcamp handouts
  • 2.3. (Useful) Outside lectures
  • 2.4. List of all AFNI GUI tips and keyboard shortcuts
  • 2.5. List of all AFNI environment variables
  • 2.6. List of all startup tips
  • 2.7. List of all AFNI colorbars
  • 2.8. Classified program list
  • 2.9. Shell script and command line tips
• 3. All program helps
  • 3.1. Links to program help files
  • 3.2. Links to program manuals
• 4. AFNI Codex: Code Examples from publications
  • 4.1. Overview
  • 4.2. FMRI Codex
• 5. SUMA
  • 5.1. Intro
  • 5.2. SUMA Viewer
  • 5.3. SUMA Controllers
  • 5.4. SUMA Clipping Planes
  • 5.5. Standard Meshes For Group-Level Analysis
  • 5.6. SUMA Programming Notes
• 6. FATCAT
  • 6.1. FATCAT Commands
  • 6.2. 1dDW_Grad_o_Mat++: dealing with DW gradients
  • 6.3. @GradFlipTest: checking on gradient flips
  • 6.4. 3dROIMaker: making (networks of) ROIs
  • 6.5. 3dTrackID: making tracts
• 7. Statistics
  • 7.1. When and how to center a variable?
  • 7.2. Deconvolution Analysis of FMRI Time Series Data
  • 7.3. Nonlinear Regression Analysis of FMRI Time Series Data (NLfim)
  • 7.4. Notes on 3dREMLfit
  • 7.5. Analysis of Variance (ANOVA)
  • 7.6. Multivariate modeling (MVM) approach for group analysis
  • 7.7. Linear Mixed-Effects (LME) Modeling
  • 7.8. Mixed-Effects Meta Analysis (MEMA)
  • 7.9. False Discovery Rate (FDR)
  • 7.10. Nonparametric Statistical Analysis of FMRI Data
• 8. Templates & Atlases
  • 8.1. AFNI Atlases
  • 8.2. How to make an atlas for yourself
  • 8.3. @SSwarper base volumes
  • 8.4. India Brain Template (IBT)
  • 8.5. Other templates and atlases
• 9. Non-human processing
  • 9.1. Macaque Templates and Atlases
  • 9.2. Macaque Demos
  • 9.3. Other templates and atlases
• 10. Tutorials, Examples
  • 10.1. Self Guided Demo Scripts
  • 10.2. AFNI GUI features
  • 10.3. AFNI general behavior
  • 10.4. APQC: afni_proc.py quality control
  • 10.5. FATCAT: DWI {Pre-pre-, Pre-, Post-pre}processing
  • 10.6. FATCAT Visualization
  • 10.7. Walnut Brain
  • 10.8. Drawing ROIs
  • 10.9. Cluster Explorer
  • 10.10. FATCAT Matrix Plot
  • 10.11. 3dMVM Validator
  • 10.12. Automatic Images
  • 10.13. Sound features in AFNI
  • 10.14. Working with ROIs
  • 10.15. Using FreeSurfer
  • 10.16. Reface and Deface datasets
  • 10.17. SurfLayers Demo
  • 10.18. Meta analysis examples
• 11. Demo Material
  • 11.1. Bootcamp Material
  • 11.2. FATCAT Demo Install
  • 11.3. Demo Data
  • 11.4. Template Surfaces
• 12. Developer Documentation
  • 12.1. Make a pull request to the afni repository
  • 12.2. Elementary OpenMP in AFNI
  • 12.3. Running tests
  • 12.4. Cmake for AFNI - making AFNI is a piece of C(m)ake
  • 12.5. Sphinx Documentation
  • 12.6. Contribute Your Own Docs
  • 12.7. How to Format Help Strings
• 13. References, papers and citations
  • 13.1. Citations and references
• 14. Contributors
  • 14.1. Thanks
• 15. Glossary
• 16. Main AFNI pages

Indices and tables

• Index

• Module Index

• Search Page