You will want to extract the clustering coefficient values for each ROI (for each participant).  These are in the X_propcalc.mat file (or the X_permout.mat file).  You will need to figure out the index # for the ROIs you want.  To do this, look in out.ROI_labels and find the lines corresponding to the two ROIs.  The line numbers will be the index values you need.  Note that this is not necessarily the same as the value of that ROI in the original atlas you used.  For example, if the label for the dlPFC ROI was on line 30 of out.ROI_labels, the values you want can be extracted by running:

dlPFC_CCvals = out.fullmat_graph_meas.clust_coef_pos(:,30,:);

This will give you an n x 1 vector containing the CC values for the dlPFC ROI (if you want the Zen-Horvath CC, use clust_coef_ZH_pos instead of clust_coef_pos).