There are 2 different ways to code stimulus timing. If it is synchronized with your TR, you can simply list it as a vector of 0's and 1's with 1 indicating an "on" period during that TR. If it is not TR-locked (your situation), you can code it with the global time in seconds (relative to the 1st volume). In case a stimulus lasts more than one TR, there are some convenient shortcuts as well. More information can be found by typing
waver -help (pay attention to option -tstim)
and at the following site (option -stim_times)
http://afni.nimh.nih.gov/afni/doc/misc/3dDeconvolveSummer2004/index_html/view?searchterm=summer%202004
Gang