Hi, Colm-
The dreaded "-weight_ts .." option now awaits you in 3dNetCorr. All you have to do is "@update.afni.binaries -d", and the power shall be yours.
Note that I think the correlation values will be pretty sensitive to this. In many ways, I don't think it is so much a weight as a scaling-- I don't think it just "emphasizes" more points than others, and I wouldn't use it for censoring. Even if your initial time series were zero-meaned already, this would then alter that.
I'm a bit curious what the application of weighting/scaling time points in the average ROI time series is?
--pt