High-resolution Magnetic resonance imaging (MRI) is helpful in diagnosing diseases such as schizophrenia, alzheimer, dementia etc. Brain segmentation is an important preprocess in medical imaging applications. In this study we compare atlas based segmentation and manual segmentation of hippocampus for volumetric measures. A statistically difference was obtained between automatic and manual measurement. We conclude that contemporary techniques are not adequate to obtain sensitive data in some barin structures such as hippocampus core.