I used AAL Atlas, and the size of adjacency matrices for each of the 800 subjects is 116 * 116.
Executing precisely the code you provided took approximately the same time, or maybe a little more. But not hours, for sure.
Yes, I have installed the parallel computing toolbox.
I did not execute the comparison part. I was interested in obtaining the correlation matrices of all the subjects and all the graph metric values for each subject (all those metrics listed on the GUI module for 800 odd subjects). This is what took approximately 65 hours. I just wanted to confirm with you if this is a reasonable time.
I appreciate your quick responses. It makes the toolbox extremely user-friendly.