The current implementation of the MAGeT-Brain pipeline allows for subject-based segmentation of the hippocampal subfields, hippocampal white matter, cerebellar lobules, and the striatum, globus pallidus, and thalamus. For hippocampal and cerebellar segmentation, five atlases, created from manual segmentation on five high-resolution MRI templates, are used to derive subject-based segmentation (Winterburn et al., 2013; Amaral et al., 2016; Park et al., 2014). However, segmentation of the striatum, globus pallidus, and thalamus are derived from a single input atlas, which was derived from reconstructed histological data warped onto the Colin27 MRI template. As this subcortical atlas was created long before our more recent atlases, the resulting difference in input atlas source requires two separate executions of MAGeT-Brain.