1.1. Install AFNI on Your Own Computer

• 1.1.1. Overview
  • Preamble Ramble
  • Setting up systems
  • Optional reading: technical notes around installing
• 1.1.2. Linux, Ubuntu 15.10 and earlier
  • Things to note before starting
  • Install prerequisite packages
  • Install AFNI binaries
  • Install R
  • Setup Python (opt)
  • Prepare for Bootcamp
  • Evaluate setup/system (important!)
  • Niceify terminal (optional, but goood)
  • Install extras (optional, but recommended for Bootcamp prep)
  • Keep up-to-date (remember!)
• 1.1.3. Linux, Ubuntu 16.04 - 17.10
  • Things to note before starting
  • Install prerequisite packages
  • Install AFNI binaries
  • Install R
  • Setup Python (opt)
  • Prepare for Bootcamp
  • Evaluate setup/system (important!)
  • Niceify terminal (optional, but goood)
  • Install extras (optional, but recommended for Bootcamp prep)
  • Keep up-to-date (remember!)
• 1.1.4. Linux, Ubuntu 18.04
  • Things to note before starting
  • Install prerequisite packages
  • Install AFNI binaries
  • Install R
  • Setup Python (opt)
  • Prepare for Bootcamp
  • Evaluate setup/system (important!)
  • Niceify terminal (optional, but goood)
  • Install extras (optional, but recommended for Bootcamp prep)
  • Keep up-to-date (remember!)
• 1.1.5. Linux, Ubuntu 20.04
  • Things to note before starting
  • Quick setup
  • (slow setup) Install prerequisite packages
  • (slow setup) Install AFNI binaries
  • (slow setup) Install R
  • (slow setup) Prepare for Bootcamp
  • (slow setup) Evaluate setup/system (important!)
  • (slow setup) Niceify terminal (optional, but goood)
  • (slow setup) Install extras (optional, but recommended for Bootcamp prep)
  • (slow setup) Keep up-to-date (remember!)
  • A note on setting up Python/using Conda (opt)
• 1.1.6. Linux, Ubuntu 22.04
  • Things to note before starting
  • Quick setup
  • (slow setup) Install prerequisite packages
  • (slow setup) Install AFNI binaries
  • (slow setup) Install R
  • (slow setup) Prepare for Bootcamp
  • (slow setup) Evaluate setup/system (important!)
  • (slow setup) Niceify terminal (optional, but goood)
  • (slow setup) Install extras (optional, but recommended for Bootcamp prep)
  • (slow setup) Keep up-to-date (remember!)
  • A note on setting up Python/using Conda (opt)
• 1.1.7. Linux, Fedora
  • Things to note before starting
  • Quick setup
  • (slow setup) Install prerequisite packages
  • (slow setup) Install AFNI binaries
  • (slow setup) Install R
  • (slow setup) Prepare for Bootcamp
  • (slow setup) Evaluate setup/system (important!)
  • (slow setup) Niceify terminal (optional, but goood)
  • (slow setup) Install extras (optional, but recommended for Bootcamp prep)
  • (slow setup) Keep up-to-date (remember!)
  • A note on setting up Python/using Conda (opt)
• 1.1.8. Linux, Red Hat
  • Things to note before starting
  • Install prerequisite packages
  • Install AFNI binaries
  • Install R
  • Setup Python (opt)
  • Prepare for Bootcamp
  • Evaluate setup/system (important!)
  • Niceify terminal (optional, but goood)
  • Install extras (optional, but recommended for Bootcamp prep)
  • Keep up-to-date (remember!)
• 1.1.9. Mac OS, 10.9-15 (via command line)
  • What to do?
  • Setup terminal
  • Install Xcode and XQuartz
  • Setup Mac env variables
  • Install AFNI binaries
  • Reboot
  • Install R
  • Install Netpbm
  • Setup Python (opt)
  • Prepare for Bootcamp
  • Evaluate setup/system (important!)
  • Niceify terminal (optional, but goood)
  • Install extras (optional, but recommended for Bootcamp prep)
  • Keep up-to-date (remember!)
  • Enable more SUMA keypresses (recommended)
• 1.1.10. Mac OS, 10.13-15 (via App)
  • Welcome to the Jungle
  • Take the File and Run
  • Start Your Engines
  • Use your M-O-U-S-E!
  • Don’t let the fear install
    • Command Line Tools for Xcode
    • XQuartz
    • Homebrew 🍺
    • R ☠️
    • AFNI
    • afni_system_check
    • Class / Bootcamp data download
    • Shiny packages
  • All Done
  • Setup Python (opt)
  • Keep up-to-date (remember!)
  • Older Version BETA V1
• 1.1.11. macOS, 12+ (Apple Silicon: M1, M2, …)
  • What to do?
  • Install Rosetta 2 (admin)
  • Install Homebrew and packages (admin)
  • Install R (admin)
  • Update Path
  • Install R Libraries
  • Install AFNI
  • Evaluate setup/system (important!)
  • Optional Extras
    • Setup Python (a method)
  • Prepare for Bootcamp (install demo data)
    • Setup terminal (opt)
    • Niceify terminal (add convenience!)
    • Install extras (recommended for Bootcamp prep)
    • Keep up-to-date (remember!)
    • Enable more SUMA keypresses (recommended)
• 1.1.12. macOS, 12+ (Intel chip)
  • What to do?
  • Install Homebrew and packages (admin)
  • Install R (admin)
  • Update Path
  • R Libraries
  • Install AFNI
  • Evaluate setup/system (important!)
  • Optional Extras
    • Setup Python (a method)
  • Prepare for Bootcamp (install demo data)
    • Setup terminal (opt)
    • Niceify terminal (add convenience!)
    • Install extras (recommended for Bootcamp prep)
    • Keep up-to-date (remember!)
    • Enable more SUMA keypresses (recommended)
• 1.1.13. Windows 10: Windows Subsystem for Linux (WSL)
  • Things to note before starting
  • Install Linux
  • Install VcXsrv Windows X Server
  • More setup tips for Ubuntu+Windows
  • Install prerequisite: AFNI and package dependencies
  • A note on transferring data between Ubuntu and Windows
• 1.1.14. old Windows 10: Bash on Ubuntu (beta)
  • What to do?
  • Notes
  • Install prerequisite: “Bash on Windows”
  • Install prerequisite: Xming X Server for Windows
  • Install prerequisite: AFNI and package dependencies
  • Useful setup tips (optional, but recommended)
  • Prepare for Bootcamp
  • Evaluate setup/system (important!)
  • Niceify terminal (optional, but goood)
  • Keep up-to-date (remember!)