Resting-state fMRI has been shown its potential for pre-surgical mapping. The potential confounds are commonly removed by regressing out the averaged fluctuation over masks of white matter and cerebrospinal fluid. However, for the patients with brain lesions, these masks may be contaminated by lesions. In current study, we generated masks by segmentation and template approaches. Although these masks were contaminated by lesion in most of our patients, no significant difference in FC was found due to this effect, which might be related to small samples. Comparing to segmentation approach, more variable results were observed when masks obtained by template approach.