[Freesurfer] connectivity between two ROIs

Dear all,

I would like to use the fsfast functional connectivity pipeline to compute connectivity between two binarized ROIs. One of the ROIs is a surface ROI, the other is a hippocampal subfield. Based on the tutorial on http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr..., I created the time courses for the two ROIs. However, in order to regress out the signal from the ventricles, CSF, and white matter as well as the motion parameters, it seems that I need to run a whole-brain analysis (or at least one hemisphere). Is that correct? Would it be possible to compute connectivity just between two given ROIs without needing to run the analysis on the hemisphere?

Thanks a lot!

Best,

Hamdi