Alfonso,

Thanks again for the thoughtful reply.  

For the initial seed-voxel bivariate correlations (step 1) and follow-up seed-voxel bivariate correlations (step 3/4), I generated the SPM.mat file using an F-test [1 0; 0 1] but then used t-contrasts to find the significant correlations (1, -1 and -1,1).  

In step 6, results (i.e., single subject regression coefficients) were used only to perform a within-group dependent samples t-test to determine whether there were statistically significant differences in magnitude of regression coefficient for each path (e.g., roi1 --> roi2 vs. roi2 --> roi1).  Denoised time-series were only used for visualization.   I understand why the Cohen's D will be biased for the follow-up seed-voxel bivariate correlations and the ROI-ROI bivariate regressions, but is there any issue of bias with the Cohen's D values calculated from the initial seed-voxel analyses (e.g., roi1a --> roi2a and roi1b --> roi2b)?  

We are basically seeing two separate paths, one of which seems to be strengthened in Tx group (roi1a path), and another that seems to be weakened in Tx group (roi1b path). Would it be valid to determine power/sample size for future studies based on these Cohen's D values?

Thanks again for sticking with me through this and being so generous with your replies.

All the best,
Patrick