Alfonso,

I think I understand. I only copied the smoothed data into a folder for loading into CONN. I also need to copy the unsmoothed data to the same location and then set the Setup.rois.roiextract=2.  Is that correct?  Is that all I need to do to setup my batch script correctly for using smoothed and unsmoothed data for the Voxel-To-Voxel analysis and ROI-To-ROI analysis respectively?

Bob