Spinocerebellar ataxias type 2 (SCA2) is a rare genetic disorder characterised by the degeneration of the Cerebellum, its connections and many Brainstem areas. A voxel-based morphometry (VBM) analysis was performed on 12 genetically determined SCA2 patients and 31 controls, normalising the brains with two different atlases: one was created in-house with DARTEL (a diffeomorphic registration method) and the other was SUIT (an exclusive Cerebellum atlas). We administered two versions of a popular executive/planning functions test: the Tower of London, in the traditional and in a computerised version that does not require the use of hands, to correlate the regional atrophy with the tests' performances and to discover the different associations of Cerebellum's areas to cognitive dysfunctions. SCA2 showed a diffuse infratentorial atrophy with the whole Cerebellum and Brainstem affected, the overall patterns were highly overlapping between atlases with some minor differences. The DARTEL VBM also allowed detecting two sovratentorial clusters of atrophy, one in the left Inferior Parietal Lobule and the other in the Corticospinal Tracts. Additional analyses revealed a partial involvement of many White Matter tracts and of the Thalamus in the pathology. The classical Tower of London version correlated maximally with the right Lobule IV-V, when the computerised version correlated with the right Crus 1. The correlations of different versions of the test suggested a dissociation between the dysfunctions in SCA2: the Posterior Cerebellum was linked to the executive dysfunction while the Anterior Cerebellum was linked to the coordinative dysfunction.