Migraine is a special type of primary headaches that cause suffering in millions of people from all over the world. The exact pathophysiology and causes are unknown, the choice of treatment varies according to headache frequency, headache severity and the patient’s condition. In order to gain a better understanding of factors that induce migraine, functional magnetic resonance imaging (fMRI) can be used to compare brain functional connectivity of people with and without migraine. During thesis work, I analysed preprocessed fMRI scans within the framework of a project of SE-NAP 2 Genetic Brain Imaging Migraine Research Group, Semmelweis University, Department of Pharmacodynamics, which group investigates the connection between migraine and stress. In the whole sample, amygdala showed an increased response to fearful facial expressions. Since I didn’t find any brain area showing greater neuronal activity in synchrony with the amygdala in controls, I carried out a whole-brain correlation analysis as well as a Region of Interest (ROI) correlation analysis in order to make sure of the significant activation of amygdala. Only the ROI analysis showed some amygdala activation both in controls and in migraineurs. I used these coordinates to do a psychophysiological interaction (PPI) analysis. Only controls’ amygdala had significant functional connectivities. Finally, a PPI analyis carried out with the original amygdala coordinates resulted negatively correlated brain areas both in controls and in migraineurs. Negative correlation is not a popular field of research, however it would deserve to get more attention, since brain regions can have not only excitatory, but also inhibitory effects on each other.