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Background  Brain pathology is relatively unexplored in chronic obstructive pulmonary disease (COPD). This study is a comprehensive investigation of grey matter (GM) and white matter (WM) changes and how these relate to disease severity and cognitive function.    Methods  T1-weighted and fluid-attenuated inversion recovery images were acquired for 31 stable COPD patients (FEV 1  52.1% pred., PaO 2  10.1 kPa) and 24 age, gender-matched controls. T1-weighted images were segmented into GM, WM and cerebrospinal fluid (CSF) tissue classes using a semi-automated procedure optimised for use with this cohort. This procedure allows, cohort-specific anatomical features to be captured, white matter lesions (WMLs) to be identified and includes a tissue repair step to correct for misclassification caused by WMLs. Tissue volumes and cortical thickness were calculated from the resulting segmentations. Additionally, a fully-automated pipeline was used to calculate localised cortical surface and gyrification. WM and GM tissue volumes, the tissue volume ratio (indicator of atrophy), average cortical thickness, and the number, size, and volume of white matter lesions (WMLs) were analysed across the whole-brain and regionally – for each anatomical lobe and the deep-GM. The hippocampus was investigated as a region-of-interest. Localised (voxel-wise and vertex-wise) variations in cortical gyrification, GM density and cortical thickness, were also investigated. Statistical models controlling for age and gender were used to test for between-group differences and within-group correlations. Robust statistical approaches ensured the family-wise error rate was controlled in regional and local analyses.    Results  There were no significant differences in global, regional, or local measures of GM between patients and controls, however, patients had an increased volume ( p  = 0.02) and size ( p  = 0.04) of WMLs. In patients, greater normalised hippocampal volume positively correlated with exacerbation frequency ( p  = 0.04), and greater WML volume was associated with worse episodic memory ( p  = 0.05). A negative relationship between WML and FEV 1  % pred. approached significance ( p  = 0.06).    Conclusions  There was no evidence of cerebral atrophy within this cohort of stable COPD patients, with moderate airflow obstruction. However, there were indications of WM damage consistent with an ischaemic pathology. It cannot be concluded whether this represents a specific COPD, or smoking-related, effect.    Electronic supplementary material  The online version of this article (doi:10.1186/s12890-017-0435-1) contains supplementary material, which is available to authorized users.

White matter lesions characterise brain involvement in moderate to severe chronic obstructive pulmonary disease, but cerebral atrophy does not