Hi Megan,
Regarding point 0 (which you did not make, but I am bringing up :), I just noticed that you are using dmBLOCK(1), rather than dmBLOCK, say.
That is something that is only vary rarely done. Generally, we expect the stimulus response to a longer event to convolve into a larger BOLD response, due only to the longer stimulus, while at the same level of basic neuro activity, say.
Given that, we generally recommend using dmBLOCK, dmUBLOCK, or perhaps dmUBLOCK(p), with p < 0 such that |p| is a typical or average response duration (probably across subjects). For example if most subjects responses are around 5s, use dmBLOCK(-5).
1) That is correct. The mean response is in beta #0, and (de-meaned) modulators are in order after that.
2) For this, it might be better to know what Gang has to say.
But yes, that seems correct. Let's say there are 2 subjects that have identical response to the modulation aspects, but one has a modulator mean that is much larger than the other. In such a case, we might expect the mean response to be larger, based on only on the additional modulation aspect. But the difference would then be seen in the main response term, which might not be appropriate.
For such a case, it makes sense to equate the means of the modulators across subjects, and apply AFNI_3dDeconvolve_rawAM2=YES.
3) If there is zero variability in the modulator, either the modulation regressor will de-mean to all zero (or worse, some tiny non-zero values), or if AFNI_3dDeconvolve_rawAM2=YES is used, it will end up being perfectly collinear with the main class regressor. If it ends up being exactly zero, that would be preferable (though it would lead to more GOFORIT warnings, and that subject should be omitted from group tests with the modulator).
If it ends up *almost* zero, they could end up with a large, nonsensical beta.
And if AFNI_3dDeconvolve_rawAM2=YES is applied, it will end up affecting the main response term.
Given all of this, both the main beta and the modulated one might then be questionable for such a subject. So it might indeed be reasonable to drop them from corresponding group tests.
- rick
