Accurate cortical thickness measurement is important for the image-based study of many neurodegenerative diseases. Cortical thickness measurement methods can be broadly classified into two categories: surface-based and voxel-based. There is considerable variability in cortical thickness measurements using different methods, even in similar patient populations, and there is no formal agreement on what constitutes the best cortical thickness measurement method. Most researchers have examined longitudinal change in dementia populations, showing significant decline in hippocampal regions. Minimal data in stroke patients have been published. The accuracy of different methods needs to be compared in order to demonstrate the optimal method of estimating cortical thickness changes over time in a stroke population.