Thanks, RIck.
Just to provide more information, I'm using local_times in the command, since that is the way my .1Dx files are organize.
OK, so, let's say each run has 100 TRs. If I want to analyze only the first run I could do -CENSORTR 100-299.
If I want to look at the third one I could do -CENSORTR 0-199.
Does this make sense? I tried running these and they seem to work, but I need to compare the results with running 3dDeconvolve on each run separately.
AW