Dear Alfonso,
 
Thank you very much for your help.I listed below what I have done. 

1- Subject-effects: 'Patients', 'Controls', 'PatientsMotion', and 'ControlsMotion'; Between-subjects:[0 0 1 0],[ 0 0 0 1]. I didn't get any connectivity for selected regions. It means motion doesn't effect the connectivity.

2-Subject-effects:  'Controls' and 'ControlsMotion'; Between-subjects:[1 0] and I did the same thing for patients. What the results are present? 

3-Subject-effects: 'Controls' ; Between-subjects:[1]. This is simply connectivity of control group. The results are different from #2. If #1 is true, motion doesn't effect the connectivity, why I had different results?

Could you please help me to clear my mind?

Thanks,
Elveda 






Many thanks,
Elveda