1.1.1. Overview

Preamble Ramble

AFNI (with SUMA and FATCAT thrown in for free!) can be used most easily on Linux/Unix and Mac systems. Windows users would be advised to make friends with those who have such systems, or to purchase/procure their own– they really aren’t that bad anymore.

AFNI is freely available (see the AFNI README.copyright), and makes use of several other freely available software packages and libraries (such as R, GSL, Python, etc.). This latter feature is great, since there is a lot of well-tested and powerful computational functionality out there, which doesn’t have to be written from scratch. However, it also means that there are several requirements for a computer system to be able to run AFNI in full, many of which might change over time as the other packages develop.

Basically, there’s a lotta ins, a lotta outs, a lotta what-have-yous, a lot of strands to keep in one’s head. Hopefully the present documentation, available scripts, and helpful Message Board polylogues facilitate the installation process. This document is fully intended to be enhanced and improved over time. If you would like to help us by recommending additional sections or details wherever they might be useful, please post a request to the AFNI Message Board.

Setting up systems

Step-by-step instructions for setting up AFNI on a system are provided:

Methods for checking/evaluating each setup are also described on those pages.

A page of Frequently Asked Questions (FAQs) and suggestions for commonly-seen error messages also exists here.

Optional reading: technical notes around installing

This section of purely extra reading defines/describes some of the computer system-ese, which may be of use to interested users. Particularly if one is not used to dealing with these things often, these notes may give a better sense of the terminology and why things are the way there are for in the installation process. In describing where things like default settings and environment variables in AFNI are, it might also help improve your AFNI experience by pointing out the ways in which you can customize your settings (simple example– do you prefer radiological or neurological views in the viewer?). But this is purely optional, and the setup processes can be done independently.

Notes:

  • For most Unix/Linux/Mac systems, package managers are used to facilitate the downloading and installation of most software from standard repositories. Having a central authority performing this task on the computer should help to keep it all in line. Occasionally, the use of multiple package managers may be required on a system, but this is generally avoided. For example:

    • Fedora has yum or dnf

    • Ubuntu has aptitude (so most commands have an apt-get in them)

    • Mac has things like Homebrew (commands have brew in them; mainly what is used for 10.7+) and fink (mainly for 10.5-6)

    Each command basically goes through a list of known packages to install, along with any dependencies. Some of installation involves making sure that these managers are uptodate, and also pointing them to certain repositories for getting very recent versions of programs.

    By default, the package manager will ask the user to verify steps with yes/no questions, and the -y option will automatically answer “yes” to every prompt, to simplify the user’s life.

  • AFNI runs mainly in terminal commands, which means that we are constantly interacting with a shell. The two main types (or flavors) of shell are tcsh and bash (or sh). The choice of shell affects, for instance, the syntax of scripting and some of the system setup. You can see what shell you are using with the command:

    which $SHELL

    By default, most AFNI command line instructions assume that tcsh is the chosen shell for a terminal. Also, many Message Board postings and scripts in demos, which may be useful for reference, are written in tcsh. So, the choice is yours, but choose wisely…

  • The choice of shell also determines how the profile settings are made. These are necessary for things like telling the shell where to look for commands (setting paths), for making aliases (shortcuts for specific commands) and for other things. The profile files are in the home directory, either $HOME/.bashrc (for bash) or $HOME/.cshrc (for tcsh), and we will edit these while setting up AFNI.

  • Many default aspects of how AFNI and SUMA run, what initial viewer settings are, how warning messages are displayed, whether templates are automatically loaded, etc. are determined with settings of environment variables that can be changed by the user. These can be controlled in files that are automatically checked each time AFNI and SUMA run, called ~/.afnirc and ~/.sumarc, respectively. A large list of malleable environment variables (and their default values) are here for AFNI.

  • Many profile and system variables are referenced with a dollar sign $ preceding their name, e.g., $SHELL, $path, $HOME (which is also represented by the symbol ~, and used interchangeably below in many situations), etc. However, note that when defining a variable, it doesn’t have a $ in its name (but it can be defined in terms of variables being referenced with a $).

  • Some installation features require having root or administrator security privileges. These commands are typically prefaced by the word sudo, and when executing (at least the first time), the user will be prompted to enter the appropriate password.