Anna, 

Thanks for responding!

I don't want to split the timeseries, I want to use all the timepoints (volumes) available. 
But, this creates the issue of having many more timepoints for a group vs the other and so the correlations will be calculated with different number of timepoints.  

Just to be sure I'm cler, the correlation between ROI for the controls would be based on 480 timepoints while the correlation for the patients would be based on 240 timepoints. Then I'd compare between groups those correlations.

Is this a problem that these correlations are based on different timeseries length?

best

patrick