This contains data related to our recent study that investigated the use of convolutional neural networks (CNNs) to label the hippocampus and amygdala on whole brain 7T MP2RAGE MRI scans in healthy subjects and individuals with epilepsy. The resource contains MRI scans, manual labels of the hippocampus and amygdala, code used to train the CNN, CNN-based predicted hippocampus and amygdala labels, and code/scripts used to analyze the output of the CNN.