Lesion Quantification Toolkit: A MATLAB software tool for estimating grey matter damage and white matter disconnections in patients with focal brain lesions

•Freely available MATLAB toolkit for creating anatomically informed lesion measures.•Estimates region-level grey matter damage and white matter disconnections.•Estimates tract-level disconnections and produces disconnection maps.•Estimates increases in region-level shortest path lengths associated with the lesion.•Can produce region-level measures for user-selected brain parcellations.