3dTcat and stim_time Files

Hi all,

I searched for an answer to this here, but couldn’t find one… I’m having problems wrapping my head around the stimuli times I get from Eprime after 3dTcat’ing off 2 TRs.

We get 3 TRs at the beginning: 1 magnet ramp-up that does not get recorded, and then 2 additional dummy scans that do get recorded. Eprime starts at the beginning of the 2 dummy scans which are just blank slides. Our TR=2, and there are 175 TRs recorded (0…174). We use 3dTcat…[2…$] to get rid of the first 2 TRs from the data. I understand that those are gone and as if they never existed… all we have is (0…172). In the Eprime file, for example, let’s say we calculate that the first dummy scan starts at time = 0, the second dummy is time = 2, then our first stimulus is at time = 4, then at 6, etc…

If we do not tcat off the 2 dummy scans, we would say the first event time = 4. But if we get rid of the 2 dummies, do we shift the times so the first event is at time = 0, or does the BRIK still see the first even as time = 4 even though it is now BRIK 0?

This hurts my head…


Hi Wade,

From the perspective of 3dDeconvolve, it knows nothing of
the two deleted time points. So you are correct to think
that from its perspective time=0 corresponds with time=4s
at the scanner.

That is to say, subtract 4 seconds from all of the stimulus
times, so that the first event might happen at (the new)
time=0 (from the perspective of 3dDeconvolve).

Consider Example 2 from “timing_tool.py -help”, and apply
something like:

timing_tool.py -add_offset -4 -timing scanner.txt -write_timing regress.txt
  • rick