Welcome to AFNI’s documentation!

• 1. Installation and Background
  • 1.1. The Authoritative HowTo for Installing AFNI on Your Own Computer
  • 1.2. Installing AFNI on Administered Systems
  • 1.3. Download other/specific AFNI/SUMA software
  • Unix Tutorial
  • 1.4. Basic Bootcamp Prep
• 2. Educational resources
  • 2.1. AFNI Bootcamp Lecture Recordings
  • 2.2. (Useful) Outside lectures
  • 2.3. List of all startup tips
  • 2.4. List of all AFNI colorbars
  • 2.5. Classified program list
• 3. All program helps
• 4. Code examples from publications
  • 4.1. FMRI examples (brief)
  • 4.2. FMRI examples (detailed)
• 5. SUMA
  • 5.1. Intro
  • 5.2. SUMA Viewer
  • 5.3. SUMA Controllers
  • 5.4. 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?
• 8. Templates & Atlases
  • 8.1. AFNI Atlases
  • 8.2. How to make an atlas for yourself
  • 8.3. @SSwarper base volumes
• 9. Tutorials, Examples
  • 9.1. Self Guided Demo Scripts
  • 9.2. FATCAT: DWI {Pre-pre-, Pre-, Post-pre}processing
  • 9.3. FATCAT Visualization
  • 9.4. Walnut Brain
  • 9.5. Drawing ROIs
  • 9.6. Cluster Explorer
  • 9.7. FATCAT Matrix Plot
  • 9.8. 3dMVM Validator
  • 9.9. Automatic Images
  • 9.10. Sound features in AFNI
  • 9.11. Working with ROIs
• 10. Demo Material
  • 10.1. Bootcamp Material
  • 10.2. FATCAT Demo Install
  • 10.3. Demo Data
  • 10.4. Template Surfaces
  • 10.5. Standard Meshes For Group-Level Analysis
• 11. Boring stuff
  • 11.1. Contribute Your Own Docs
  • 11.2. How to Format Help Strings
• 12. Glossary
• 13. References
• 14. Main AFNI pages

Indices and tables

• Index
• Module Index
• Search Page