> 1. 3dSynthesize -cbucket CbucketFileFrom3dDeconvolve+orig -matrix
> x1DFrom3dDeconvolve -select ... prefix EffectsOfNoInterest
>
> How do I go about selecting the correct options for -select...? In a search I
> noticed most people used -select polort.

If you only had drifting effect (modeled with -polort) in the baseline, '-select polort' should be good enough. If you added other stuff in your baseline with -stim_base (such as head motion parameters), you can use -select baseline

> 2. 3dcalc -a Corr_subj01+tlrc'[SubbrickForR2]' -b
> Corr_subj01+tlrc'[SubbrickForBeta]'-expr
> "'ispositive(b)*sqrt(a)-isnegative(b)*sqrt(a)'-prefix Corr_subj01R
>
> Which R^2 value do I want to use from 3dDeconvolve? I have the Full R^2
> (assuming this is the one I want to use), the Global R^2, and the Seed R^2.
> The same question again, but this time for Coefficent?

Seed R^2 since it shows the correlation between the seed and the rest of the brain. Same for Coefficient.

HTH,
Gang