Hi, Robin-
I am not sure about 1 vs 3 subj in 3dGroupInCorr-- but if a "group" is expected, it wouldn't surprise me that somethign might fail. For example, what is the standard deviation of 1 value? (Sounds like a koan---what is the sound of one hand clapping?)
Re. Instacorr: the fact that errts is different (and weird) doesn't surprise me---it is a residual dset, so that dset has mean of zero by default, and probably small fluctuations in the brain vs outside. I *might* expect scale to be a bit similar, but it has a nonzero mean, so that might make the difference. Anyways, for residuals, I would either *not* mask (which is perfectly acceptable) or use an externally generated mask (probably done by afni_proc.py already, too, yes?).
For the other question---that seems totally separate, and pretty long. Can we make that a separate thread?
--pt
