Before revision:  We make the code and trained networks freely available  .
After revision:  We make the code and trained networks freely available . Conclusions: Biomedical images follow imaging protocols that can be leveraged as prior information into deep convolutional neural networks to improve performance. The network segmentations match human manual corrections performed in 3D, and are comparable in performance to human segmentations obtained from scratch in 2D for abnormal brain anatomies .