[Freesurfer] roi-to-roi functional connectivity analysis

Hi Surfers,

Has anyone done ROI-to-ROI functional connectivity analysis using Freesurfer?

Current FC pipeline computes the seed-to-voxel correlation for each voxel and thus generates a whole brain correlation map. Is there an easy way to compute the 0-lag correlation between the average time course of two ROIs?

One way I presume can work is to take the average time courses generated from the fcseed-sess and do it by hand. For example, just compute the correlation coefficient between "lh.hippo.dat" and "rh.hippo.dat". But does that regress out the white matter and ventricles?

Is there a way to do this properly? What should go to the mkanalysis-sess in this case?

Thank you for your help.

Lingqiang