Hi Lingqiang, there is nothing set up to do this. You can use the time courses as you suggest, but this will no remove WM, CSF, etc. Those time courses are there too, so you can remove them yourself if you want. doug

On 03/29/2012 03:44 PM, Lingqiang Kong wrote:

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