fc of 2 ROIs

 Dear all,

I am using the fc_gui to calculate the functional connectivity between two ROIs of my patient and control groups. I included all my participants in the same analysis (one directory for patients and one for controls). The ROI_FCMaps that are outputted include the timeseries of all the participants in that directory. Is the zFCMap...txt the correlation coefficient outputted from using all participants' timeseries in one correlation analysis? In other words, are the timecourses of all participants concatenated and correlated as if they came from one participant? The correlations that I get in these text files appear unreasonable and it seems that it is not the two timeseries of each participant that are correlated, ending up with a correlation coefficient for each participant and then taking the mean of all participants' correlation coefficients (which is what is represented by the zFCMap...txt) ?

Would appreciate clarification on how the correlation coefficients are calculated

Thank you!
Helen