The present study investigates the effectiveness of a deep learning neural network for non-invasively localizing the seizure onset zone (SOZ) using multi-modal MRI data that are clinically acquired from children with drug-resistant epilepsy. A cortical parcellation was applied to localize the SOZ in cortical nodes of the epileptogenic hemisphere. At each node, the laminar surface analysis was followed to sample 1) the relative intensity of gray matter and white matter in multi-modal MRI and 2) the neighboring white matter connectivity using diffusion tractography edge strengths. A cross-validation was employed to train and test all layers of a multi-scale residual neural network (msResNet) that can classify SOZ node in an end-to-end fashion. A prediction probability of a given node belonging to the SOZ class was proposed as a non-invasive MRI marker of seizure onset likelihood. In an independent validation cohort, the proposed MRI marker provided a very large effect size of Cohen's d = 1.21 between SOZ and non-SOZ, and classified SOZ with a balanced accuracy of 0.75 in lesional and 0.67 in non-lesional MRI groups. The subsequent multi-variate logistic regression found the incorporation of the proposed MRI marker into interictal intracranial EEG (iEEG) markers further improves the differentiation between the epileptogenic focus (defined as SOZ resected during surgery) and non-epileptogenic sites (i.e., non-SOZ sites preserved during surgery) up to 15 % in non-lesional MRI group, suggesting that the proposed MRI marker could improve the localization of epileptogenic foci for successful pediatric epilepsy surgery.