Thank you a lot for using Braph. In order to do your analysis, the following steps are needed:
Import the brain atlas with which your data was extracted into BRAPH through the Brain Atlas interface. After your atlas has been uploaded, go to Subject Cohorts and choose New EEG Cohort. You could find more details about how to use the Brain Atlas interface on http://braph.org/manual/brain-atlas/.
In order to import your groups into Braph, they need to be arranged so that the .mat files of different groups are placed in different folders. The folders are uploaded to BRAPH via the EEG Cohort Editor interface by pressing the Load subject group from mat … button. More information about the capabilities of the EEG Cohort Editor can be found at http://braph.org/manual/fmri/fmri-cohort/ (the EEG flow is analogous to the fMRI’s one).
From the cohort, choose Graph Analysis -> New EEG graph analysis which will bring you to the EEG Graph Analysis interface. Here you could choose the type of graph and correlation you would like to use, as well as a definition for the community structure.