5.1.1. AFNI GUI: Startup

Start the AFNI GUI

  • The basic way to start the AFNI GUI at the command line is by typing:

    afni
How does the AFNI GUI load datasets into memory when started?

The afni GUI reads datasets from the current directory. If there are no datasets in current directory, it tries to read sub-directories 1 level deeper.
 ../../_images/afni_controller_window.png

Start the AFNI GUI Advanced

This describes how to read datasets from multiple directory locations or specific subsets of files in a directory. See also the next section below about specifying a special directory to always load, such as one with reference volumes.

  • Read datasets from multiple directories (the -all_dsets means that all dsets in the directories will be loaded, with directory path shown in the selection menu):

    afni -all_dsets dir1 dir2 ...

  • Read specific datasets (e.g., if the directory has very many datasets and browsing a subset is easier; or opening specific datasets across multiple directories):

    afni file1 file2 dir1/file3 ...

  • Read datasets recursively, starting from the current directory and then into all directories below it (loading all at the same time; otherwise, exclude -all_dsets):

    afni -R -all_dsets

  • Create ‘sessions’ of files from multiple sub-directories, gathering datasets with a single subject identified, like in the BIDS file hierarchy (more details in help):

    afni -bysub sub-xyz ...

    or

    afni -BIDS sub-xyz ...

  • See afni -help or afni -hview for more details about these options or click here.

Set special directories: datasets always loaded

There are also special directories that can be specified to always also be loaded when you run the AFNI GUI. These often contain reference templates and atlases, and this “always load” functionality means that copies of these datasets don’t have to be in every working directory.

These are specified with AFNI environment variables, such as:

  • AFNI_GLOBAL_SESSION

  • AFNI_ATLAS_PATH

... and more

For example, having AFNI_GLOBAL_SESSION = /home/nbohr/REF_TEMPLATES in your AFNI settings file (~/.afnirc) would load datasets in the “REF_TEMPLATES/” directory so they are always available for viewing in the AFNI GUI.

Note

AFNI reads the settings file named ~/.afnirc from your home directory, if it is present. This file is used to change many of the defaults (cf the list of all AFNI environment variables to set there).

Jump within GUI Guide

Starting

Main controller

Image window

Graph window

Overlay panel

Datamode panel

Chooser menu

Maps