> Is it statistically inappropriate to make such a comparison
> (i.e., problem with unequal variances when looking at 1 TR
> vs 4 TR?)
The issue of efficiency (power) for each condition aside, the comparison itself should not be a problem during individual subject analysis.
> My strategy thus far has been to extract the percent
> signal change at each of 11 time points, then use
> 3dANOVA3 with subjects, time, and condition as factors.
> Would alternate methods offered by AFNI be more
> appropriate? Any suggestions?
What are those 11 time points? Time lags from deconvolution?
If you decide to run group analysis with 3dANOVA3, make sure you have the most recent version of it. And it does not have the capability of running 2nd-order contrasts yet.
Gang