Hi Lingqiang, sorry, I thought I had responded to this earlier. There is no way to do this in FS. As you suggest, you can get the raw time courses for each ROI. There are also time courses for CSF and WM which you can regressout of each of the ROI time courses. But you'll have to do this all yourself, we don't have tools for it. doug

On 04/03/2012 11:01 AM, Lingqiang Kong wrote:

Hi Surfers,

Sorry this is the same question again, but has anyone tried ROI-to-ROI functional connectivity analysis in Freesurfer?

Instead of computing seed-to-voxel correlation map for the whole brain, is there a way to compute the 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 of each ROI and do it manually for each ROI pair. 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