Comparison of task with baseline in afni

In a 2x2 block design, I’m getting some anomalous main-effects that I wouldn’t expect.

As a sanity check, I want to look at a comparison of activation during task vs during baseline (i.e. activation during task as compared to activation during rest/fixation), irrespective of condition, or for a specific condition. I know this is a common option on SPM, but I can’t find any source on what it means statistically.

The output of 3dDeconvolve only gives me the option to see the effect of a given condition within the model, which is not the same thing.

I could, of course, run an entirely new 3dDeconvolve with new stimtime files as if all blocks were a single condition, but a) I would have to re-run 3dDeconvolve on all subjects, and b) would not allow me to see how much activation is seen for just one single condition.

I’d be grateful for any help!

3dDeconvolve’s output of an effect beta means exactly
that: the contrast of the effect vs (implicit) baseline.

The baseline model is essentially supplied via -polor
and motion, probably, but contrasts do not reference
the baseline.

  • rick