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
  • 1.5. Prep for Bootcamp
  • 1.6. Miniconda: Python(s) in a convenient setup
• 2. Starting with AFNI
  • 2.1. Overview
  • 2.2. Where to begin
  • 2.3. Asking questions and following updates
• 3. Educational resources
  • 3.1. AFNI Bootcamp Recordings
  • 3.2. AFNI Bootcamp handouts
  • 3.3. (Useful) Outside lectures
  • Unix Tutorial
  • 3.4. Shell script and command line tips
• 4. All program helps
  • 4.1. Alphabetical list of program helps
  • 4.2. Classified program list
• 5. AFNI GUI (afni)
  • 5.1. GUI Guide
  • 5.2. List of all AFNI GUI tips and keyboard shortcuts
  • 5.3. List of all AFNI environment variables
  • 5.4. List of all startup tips
  • 5.5. List of all AFNI colorbars
• 6. SUMA GUI (suma)
  • 6.1. Intro
  • 6.2. SUMA Viewer
  • 6.3. SUMA Controllers
  • 6.4. SUMA Clipping Planes
  • 6.5. Standard Meshes For Group-Level Analysis
  • 6.6. SUMA Programming Notes
• 7. FATCAT
  • 7.1. FATCAT Commands
  • 7.2. 1dDW_Grad_o_Mat++: dealing with DW gradients
  • 7.3. @GradFlipTest: checking on gradient flips
  • 7.4. 3dROIMaker: making (networks of) ROIs
  • 7.5. 3dTrackID: making tracts
• 8. NIFTI
  • 8.1. The NIFTI format
  • 8.2. NIFTI and BRIK/HEAD: Similarities, differences and mappings
  • 8.3. Space names, qform_code and sform_code
  • 8.4. Using NIFTI data in AFNI
• 9. Statistics
  • 9.1. Gang’s Stats Blog
  • 9.2. When and how to center a variable?
  • 9.3. How to get the degrees of freedom (DF) in an AFNI file?
  • 9.4. Deconvolution Analysis of FMRI Time Series Data
  • 9.5. Duration modulation (DM) blocks (3dDeconvolve)
  • 9.6. Nonlinear Regression Analysis of FMRI Time Series Data (NLfim)
  • 9.7. Notes on 3dREMLfit
  • 9.8. Analysis of Variance (ANOVA)
  • 9.9. Multivariate modeling (MVM) approach for group analysis
  • 9.10. Linear Mixed-Effects (LME) Modeling
  • 9.11. Mixed-Effects Meta Analysis (MEMA)
  • 9.12. False Discovery Rate (FDR)
  • 9.13. Nonparametric Statistical Analysis of FMRI Data
• 10. Templates & Atlases
  • 10.1. AFNI Atlases
  • 10.2. How to make an atlas for yourself
  • 10.3. @SSwarper base volumes
  • 10.4. India Brain Template (IBT)
  • 10.5. Other templates and atlases
  • 10.6. List of atlases (and more) in afni_atlases_dist
• 11. Non-human processing
  • 11.1. Macaque Templates and Atlases
  • 11.2. Macaque Demos
  • 11.3. Other templates and atlases
• 12. Tutorials, Examples
  • 12.1. Self Guided Demo Scripts
  • 12.2. AFNI GUI features
  • 12.3. AFNI general behavior
  • 12.4. APQC: afni_proc.py quality control
  • 12.5. FATCAT: DWI {Pre-pre-, Pre-, Post-pre}processing
  • 12.6. FATCAT Visualization
  • 12.7. Walnut Brain
  • 12.8. Drawing ROIs
  • 12.9. Cluster Explorer
  • 12.10. FATCAT Matrix Plot
  • 12.11. 3dMVM Validator
  • 12.12. Automatic Images
  • 12.13. Sound features in AFNI
  • 12.14. Working with ROIs
  • 12.15. Using FreeSurfer
  • 12.16. Reface and Deface datasets
  • 12.17. SurfLayers Demo
  • 12.18. Meta analysis examples
• 13. Demo Material
  • 13.1. Bootcamp Material
  • 13.2. FATCAT Demo Install
  • 13.3. Demo Data
  • 13.4. Template Surfaces
• 14. Codex: AFNI Code Examples from publications
  • 14.1. Overview
  • 14.2. FMRI Codex
• 15. Citations and Reference Works
  • 15.1. Citations and references
• 16. Developer Documentation
  • 16.1. Make a pull request to the afni repository
  • 16.2. Elementary OpenMP in AFNI
  • 16.3. Running tests
  • 16.4. Cmake for AFNI - making AFNI is a piece of C(m)ake
  • 16.5. Sphinx Documentation
  • 16.6. Contribute Your Own Docs
  • 16.7. How to Format Help Strings
• 17. Contributors
  • 17.1. Thanks
• 18. Glossary
• 19. Main AFNI pages

Indices and tables

• Index

• Module Index

• Search Page