In this work we aim to improve the detection of Focal Cortical Dysplasia on MRI images using a multimodal approach. We propose to estimate the thickness of the cortex jointly using partial volume maps of T1-weighted MPRAGE and T2- weighted FLAIR images by fitting spheres into the gray matter of the brain such that the amount of probability-weighted gray matter contained in each sphere is maximized. Results on nine patients show that the FCD lesions for all patients could be detected using the multimodal approach compared to T1 alone (FCD detected in only 7 patients) and Freesurfer (4 patients).