When you run the command "afni", it prints some information to the terminal window. The version of the program is listed there. For example, if I run afni on my machine right now, I get the following (I've put the version information in boldface):
GPL AFNI: Analysis of Functional NeuroImages, by RW Cox (rwcox@nih.gov)
This is Version 2.52f of 24 Apr 2003
** This software was designed to be used only for research purposes. **
** Clinical uses are not recommended, and have never been evaluated. **
** This software comes with no warranties of any kind whatsoever, **
** and may not be useful for anything. Use it at your own risk! **
** If these terms are not acceptable, you aren't allowed to use AFNI.**
** See 'Define Datamode->Misc->License Info' for more details. **
Thanks go to A Jesmanowicz for inspiration
Initializing: X11.. Widgets...... Input files:
*** No datasets or sessions input -- Dummy dataset created.
Time series = 0 files read
NLfit & NLerr= Found 16 models
Plugins = 45 libraries read
-orient = RAI