I am trying to calculate functional connectivity maps using FreeSurfer pipeline: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough.

After defining a seed region on raw anatomical image, I co-registered functional data with anatomical data (as reference) and made sure that the seed is at correct place on both anatomical (top left in attached image) and functional (top right) data. Using SPM, I confirmed co-registration was fine.

But after running all the steps of FC, looks like the FC maps are not correct: sig.nii.gz at -fthresh 2 3 (shown at bottom left) because I am not getting significant FC at seed location. Here, bottom right shows the seed location on surface after I convert the seed to fsaverage space (for visualization purpose).

Any thoughts, ideas or tips on what went wrong here, would be really appreciated.

Thanks.