afni.nimh.nih.gov

you can put an asterisk in the place of runs with no events for that condition in a run. so if you had 4 runs, and only 1 and 3 had errors, your file would look like this:

time1 time2...
*
time1 time2...
*

also, probably worth adding -local_times to your 3dDeconvolve command, though AFNI is very smart and usually figures out what you mean anyway.

James