Pop up the help text for the permutation test plug-in; it's quite comprehensive and should answer all your usage questions. The help text will also point you to the following algorithmic description, which you should cite in any publication based on data processed by this permutation test algorithm:

Belmonte MK, Yurgelun-Todd DA. Permutation testing made practical for functional magnetic resonance image analysis. IEEE Transactions on Medical Imaging 20(3):243-248 (March 2001).

For your event-related design you will want to generate an ideal waveform using "waver" or using "balloon." The latter is my implementation of the balloon haemodynamic model designed by Buxton, Wong, and Frank (Buxton RB, Wong EC, Frank LR. Dynamics of blood flow and oxygenation changes during brain activation: the balloon model. Magnetic Resonance in Medicine 39(6):855-864 (1998).)

NOTE TO AFNI MAINTAINERS: I have been asking for the past three years to have balloon.c included in the standard AFNI distribution, but have received no response to my multiple requests. If there is some aspect of the program that is preventing it from passing your source code review, I would very much like to know what it is. I still think, as I did three years ago when I first asked, that this program could be useful for other AFNI users. WILL YOU PLEASE REPLY? (See my previous requests at "[afni.nimh.nih.gov];, second paragraph, and at "[afni.nimh.nih.gov];.)