ADisc pipeline [download] is a matlab based pipeline to automatically segment a 3D brain MRI into left and right cerebrum, left and right cerebellum, and brain stem without any image registration (L Zhao et al, Medical Image Analysis, 14(3): 360-372, 2010).
Interhemispheric Fissure Shape Analysis package [download] contains the matlab functions for quantifying the bending of cerebral interehemispheric fissure caused by Yakovlevian torgue in segmented brain hemispheric MRI volume (L Zhao et al, LNSC, vol. 5762, pp. 216 - 223, 2009).
Scale Space Cortical Morphometry Toolbox [download] is a Matlab toolbox for local cortical surface morphometric feature (thickness, volume and surface area) extraction and scale space search based statistical analysis of the features using linear mixed effects models. Document of introduction and demo of usage is included in the package.
To use this toolbox you will also need SurfStat tools which can be downloaded here.