Surgical therapy has become an important therapeutic alternative for patients with medically intractable epilepsy. Correct and anatomically precise localization of the epileptic focus, preferably with non-invasive methods, is the main goal of the pre-surgical epilepsy diagnosis to decide if resection of brain tissue is possible. For evaluating the performance of the source localization algorithms in an actual clinical situation, realistic patient-specific human head models that incorporate the heterogeneity nature of brain tissues is required. In this paper, performance of two of the most widely used software packages for brain segmentation, namely FSL and FreeSurfer has been analyzed. Then a segmented head model from a package with better performance is used to investigate the effects of brain tissue segmentation in EEG source localization.