Great, I'm glad that worked.

RE your question, if you have a ROI template in MNI space, the easiest thing is to calculate the func to MNI warp for each participant, invert the warps, then apply that to the ROI template to get an ROI image for each participant in func space - all outside of GTG.  Then, use GTG to extract timeseries for the ROIs by selecting the warped template as the ROI mask and telling GTG that this image is in functional space.  I think this is your second option....