Commonly, in lesion-behaviour studies structural changes in brain matter are depicted and analysed. However, in addition to these structural changes, brain areas might be structurally intact but non-functional due to malperfusion. These changes may be detected using perfusion- weighted MRI (PWI). Perfusion parameters most commonly used [e.g. time-to-peak (TTP)] are semi-quantitative and perfusion is evaluated in relation to a nonaffected reference area. Traditionally, the mean of a larger region in the non-affected hemisphere or the cerebellum has been used ["mean contra-region of interest (ROI) comparison"]. Our results suggest that this method is prone to biases (in particular in periventricular regions) because perfusion differs between different parts of the brain, for example, between grey and white matter. We reduced such potential biases with voxelwise inter-hemispheric comparisons. Each voxel is compared with its homologous voxel and thus white matter with white matter and grey matter with grey matter. This automated method seems to correspond with results deriving from manual delineation of perfusion deficits. The TTP delay maps with a threshold of 3 s seem to be best comparable to manual delineation. Our method avoids the observer-dependent choice of a reference region and involves the spatial normalisation of perfusion maps. It is well suited for whole-brain analysis of abnormal perfusion in neuroscience studies as well as in clinical contexts.