Quantitative assessment of water fraction, relaxation time, and frequency shift using a multi-compartment model can be useful in understanding diseases and disorders affecting the human brain. We aimed to explore tissue microstructure information contained in voxel signals by analysing voxel compartment water fraction, $$$T_2^*$$$ and frequency shift derived from 7T multi-echo gradient recalled echo MRI data. We recruited four patients with focal cortical dysplasia and compartmentalised normal and dysplastic cortical regions. Parameterisation of tissue characteristics in focal cortical dysplasia can potentially delineate cortical areas which have undergone microstructural changes. This provides a promising framework for studying neurodegenerative processes.