Dear Adeel:
Thank you very much for your kind response to my questions and it is very helpful. After reading your response, I realize it is my fault. I set the maximal node to 36 in my code with the flowing line (I noticed the scheme is different if the number of nodes is greater than 8, but not sure what it is for at that time, so I set the maximal number to 36 to avoid it):
DCM.options.maxnodes = 36;
which basically prevented the use of the functional connectivity constraints! After I removed the above line, now the running time has dramatically reduces to about 5 minutes per iteration. I will also try the idea you suggested (splitting the large network into two DCMs for each hemisphere) and see how it works.
I will let you know if I have more questions. Thank you very much again!
Best regards,
Guoshi Li
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