For MRI-based studies of cochlea-related diseases, segmenting the cochlea and modiolus is often essential for quantifying disease-related morphological and intensity changes. Methods for automatic 3D segmentation of these structures on MRI scans, however, are not well established. We aimed to develop a semi-automated, multi-atlas based approach to segmenting the cochlea and modiolus, distinguishing between the cochlear basal and mid-apical turns. We found this approach to have good agreement with manual segmentation, demonstrating its potential in quantitative analyses. Moreover, the definition of the three subregions had good validity, as indicated by the high inter-rater agreement in segmentation.