It was shown that higher resolution data increases the accuracy of the brain segmentation resulting in a decrease of cortical thickness estimates. However, data is still mostly acquired at a spatial resolution of 1 mm for quantifying cortical thickness. Several software packages allow processing of higher resolution data. However, FreeSurfer constitutes the de facto standard due to its prevalence. Therefore, we investigate the effects of resolution and SNR at two important stages of its standard processing pipeline: the skull stripping and white matter segmentation.