Magneto/Electro-encephalography (M/EEG) source connectivity is an emergent tool to identify brain networks with high time/space resolution. Here, we aim to identify the brain core network (s-core decomposition) using dense-EEG. We also evaluate the effect of the functional connectivity methods used and more precisely the effect of the correction for the so-called source leakage problem. Two connectivity measures were evaluated: the phase locking value (PLV) and phase lag index (PLI) that supposed to deal with the leakage problem by removing the zero-lag connections. Both methods were evaluated on resting state dense-EEG signals recorded from 19 healthy participants. Core networks obtained by each method was compared to those computed using fMRI from 487 healthy participants at rest (from the Human Connectome Project - HCP). The correlation between networks obtained by EEG and fMRI was used as performance criterion. Results show that PLV networks are closer to fMRI networks with significantly higher correlation values with fMRI networks, than PLI networks. Results suggest caution when selecting the functional connectivity methods and mainly methods that remove the zero-lag connections as it can severely affect the network characteristics. The choice of functional connectivity measure is indeed crucial not only in cognitive neuroscience but also in clinical neuroscience.