Automated segmentation of the hypothalamus and associated subunits in brain MRI

Neuroimage. 2020 Dec:223:117287. doi: 10.1016/j.neuroimage.2020.117287. Epub 2020 Aug 25.


Despite the crucial role of the hypothalamus in the regulation of the human body, neuroimaging studies of this structure and its nuclei are scarce. Such scarcity partially stems from the lack of automated segmentation tools, since manual delineation suffers from scalability and reproducibility issues. Due to the small size of the hypothalamus and the lack of image contrast in its vicinity, automated segmentation is difficult and has been long neglected by widespread neuroimaging packages like FreeSurfer or FSL. Nonetheless, recent advances in deep machine learning are enabling us to tackle difficult segmentation problems with high accuracy. In this paper we present a fully automated tool based on a deep convolutional neural network, for the segmentation of the whole hypothalamus and its subregions from T1-weighted MRI scans. We use aggressive data augmentation in order to make the model robust to T1-weighted MR scans from a wide array of different sources, without any need for preprocessing. We rigorously assess the performance of the presented tool through extensive analyses, including: inter- and intra-rater variability experiments between human observers; comparison of our tool with manual segmentation; comparison with an automated method based on multi-atlas segmentation; assessment of robustness by quality control analysis of a larger, heterogeneous dataset (ADNI); and indirect evaluation with a volumetric study performed on ADNI. The presented model outperforms multi-atlas segmentation scores as well as inter-rater accuracy level, and approaches intra-rater precision. Our method does not require any preprocessing and runs in less than a second on a GPU, and approximately 10 seconds on a CPU. The source code as well as the trained model are publicly available at, and will also be distributed with FreeSurfer.

Keywords: Convolutional neural network; Hypothalamus; Public software; Segmentation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Aged
  • Alzheimer Disease / diagnostic imaging
  • Alzheimer Disease / pathology
  • Brain Mapping / methods*
  • Deep Learning
  • Female
  • Humans
  • Hypothalamus / anatomy & histology*
  • Hypothalamus / diagnostic imaging*
  • Image Processing, Computer-Assisted / methods*
  • Magnetic Resonance Imaging*
  • Male