Hi Dan,

I've looked into this when I started using conn and it does not use global signal regression. A paper emphasizing this is Chai, Xiaoqian J., et al., 2012, "Anticorrelations in resting state networks without global signal regression.".  Conn uses eroded white matter and csf masks and regresses out the principal component of the signal from those. This method in theory does not suffer from systematic introduction of negative correlation as pointed out by Murphy 2009 (which is the main concern with global signal regression) but it also retains some of the advantages of global signal regression by removing noise from white matter and csf. Maybe Alfonso can enlighten us more on this topic?

Kind regards,
Vincent.