Hi Alfonso,

Thanks for the reply. We'll try to set the line "if ERODE>0" to "if 1" for our projects. This part of the code only affects the CSF and WM ROIs, right? Is it possible no thresholding is applied to the GM mask either? We checked the ROI time series stored in the CONN files and they appear to have the same issue where almost the entire brain volume was used to compute these mean time series. I'm not sure if it is used anywhere other than the column appended to the ROI-to-ROI matrix, but it may change the interpretation of 'GM' if voxels other than 'GM' are included in calculating the correlations.

Regards,
Jalmar