The cholinergic system arising from the substantia innominata (SI) of the basal forebrain has an important role in the cognitive functions of Parkinson's disease (PD). We performed magnetic resonance imaging based volumetric analysis to evaluate the SI volume in patients with PD-intact cognition (PD-IC), PD-mild cognitive impairment (PD-MCI), and PD dementia (PDD). The mean normalized SI volume was significantly decreased in patients with PD-IC (1.54 ± 0.12, p < 0.001), PD-MCI (1.49 ± 0.12, p < 0.001), and PDD (1.39 ± 0.12, p < 0.001) compared with that of control subjects (1.68 ± 0.11). The normalized SI volume did not differ between patients with PD-IC and PD-MCI; however, the normalized SI volume was significantly decreased in patients with PDD compared with that in those with PD-IC (p < 0.001) or PD-MCI (p = 0.016). The normalized SI volume was significantly correlated with general cognitive status (r = 0.51, p < 0.001) as well as with performance in each cognitive subdomain, with a particularly significant independent association with attention (β = 0.33, p = 0.003) and object naming (β = 0.26, p = 0.017). The present study demonstrated that the SI volume in PD differs depending on cognitive status and is significantly correlated with cognitive performance.

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