Robust and automated tools such as FreeSurfer or ANTs for brain segmentation and quantification have been of utmost importance in the recent advancements in the Neuroimaging field. However, the reproducibility and variability of their results are often uncertain. In this study, we analyzed their reproducibility and compared their outputs for different brain structures. We observe that both tools give high reproducibility for volumetric studies and give similar results in most of the examined cases. However, in some structures (pallidum, rostral-anterior cingulate) there are more pronounced and significant differences. Our results also indicate slightly better reproducibility of ANTs over FreeSurfer.