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:

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.

Start the AFNI GUI Advanced

  • Read datasets from multiple directories:

    afni dir1 dir2 ...
  • Read specific datasets:

    afni file1 file2 dir1/file3 ...
  • Read datasets recursively, from the current directory and recursively from all directories below it:

    afni -R
  • 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 ...


    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:



... 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.


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


Main controller

Image window

Graph window

Overlay panel

Datamode panel

Chooser menu