I am working on resting-state functional connectivity using freesurfer by following the instructions from: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough

I made sure that the seed region (for ever subject) I am using is at the correct place on raw structural image. After running the analysis and looking at the RSFC maps, very few subjects showed very high FC at or close to seed region but for most of the subjects I am not getting high FC at/close to seed region.

I would really appreciate any suggestion or tips on this e.g. what could be wrong during the analysis?

Thanks.

MJ