Structure segmentation is often the first step in the diagnosis and treatment of various diseases. Because of the variations in the various brain structures and overlapping structures, segmenting brain structures is a very crucial step. Though a lot of research had been done in this area, still it is a challenging field. Using prior knowledge about the spatial relationships among structures, called as atlases, the structures with dissimilarities can be segmented efficiently. Multiple atlases prove a better one when compared to single atlas, especially when there are dissimilarities in the structures. In this paper, we proposed a pipeline for segmenting brain structures using open source tools. We test our pipeline for segmenting brain structures in MRI using the publicly available data provided by MIDAS.