Check our last publication Hippocampus segmentation on epilepsy and Alzheimer’s disease studies with multiple convolutional neural networks at Heliyon. In this work we propose an automatic hippocampus segmentation method studied over Alzheimer’s disease and epilepsy patients, with hippocampus resection, reaching state-of-the-art performance. This work also showcases the difficulty of automated methods to properly segment the hippocampi in cases of resection.