Summary Epilepsy is a severe neurological disorder involving debilitating seizures that affects over 1% (65 million) of the world?s population. The cascade of alterations in brain structure and physiology leading to epilepsy continues to remain poorly understood. Since epilepsy is not detected in patients until after the onset of seizures, insights into pathologic changes triggered in the brain during epileptogenesis, which include neurodegeneration, gliosis, calcification, and dendritic damage, are almost exclusively gained from established rodent models. A major limitation in early diagnosis and development of targeted intervention is the lack of reliable markers of the epileptogenic process, with end-point histology providing severely limited insight into the progression of epileptogenic changes across brain areas. This R21 proposal aims to investigate in vivo quantitative MR contrast mechanisms using, 1) oscillating gradient diffusion MRI (OG-dMRI); and 2) quantitative magnetic susceptibility mapping (QSM), to achieve non-invasive, sensitive, and targeted detection of specific microstructural epileptogenic sequelae across the brain in the pilocarpine rat model of status epilepticus. Further, in combination with 3D scanning electron microscopy, we will elucidate the microstructural basis of OG-dMRI and QSM findings to validate the MR contrast mechanisms as markers of specific epileptogenesis- induced pathologic sequelae. We will target these goals in three specific aims: 1) to investigate oscillating- and pulsed-gradient dMRI for detection of hippocampal neuronal and dendritic degeneration, which is one of the main hallmarks of epileptogenesis; 2) to investigate in vivo detection of progressive calcification and iron deposits in the epileptogenic thalamus using QSM; and, 3) to elucidate the microstructural basis and origins of OG-dMRI and QSM findings using 3D serial block-face scanning electron microscopy and histopathological analyses. The key innovative techniques developed in this R21 project will establish highly-specific, quantitative, and endogenous MRI-based markers for targeted detection of microstructural processes in the brain, which will allow non-invasive imaging of progressive pathological changes occurring during epileptogenesis. This project will produce techniques and data crucial to afford insights into the development and progression of epilepsy in the brain, and further, to elucidate the underlying pathological correlates of both dMRI and QSM findings in the epileptogenic brain.