Testing a deep convolutional neural network for automated hippocampus segmentation in a longitudinal sample of healthy participants

Neuroimage. 2019 Aug 15;197:589-597. doi: 10.1016/j.neuroimage.2019.05.017. Epub 2019 May 7.


Subtle changes in hippocampal volumes may occur during both physiological and pathophysiological processes in the human brain. Assessing hippocampal volumes manually is a time-consuming procedure, however, creating a need for automated segmentation methods that are both fast and reliable over time. Segmentation algorithms that employ deep convolutional neural networks (CNN) have emerged as a promising solution for large longitudinal neuroimaging studies. However, for these novel algorithms to be useful in clinical studies, the accuracy and reproducibility should be established on independent datasets. Here, we evaluate the performance of a CNN-based hippocampal segmentation algorithm that was developed by Thyreau and colleagues - Hippodeep. We compared its segmentation outputs to manual segmentation and FreeSurfer 6.0 in a sample of 200 healthy participants scanned repeatedly at seven sites across Canada, as part of the Canadian Biomarker Integration Network in Depression consortium. The algorithm demonstrated high levels of stability and reproducibility of volumetric measures across all time points compared to the other two techniques. Although more rigorous testing in clinical populations is necessary, this approach holds promise as a viable option for tracking volumetric changes in longitudinal neuroimaging studies.

Keywords: Convolutional neural networks; FreeSurfer; Hippocampus; Longitudinal; Magnetic resonance imaging; Manual tracing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Algorithms*
  • Child
  • Deep Learning*
  • Female
  • Healthy Volunteers
  • Hippocampus / anatomy & histology*
  • Humans
  • Image Processing, Computer-Assisted / methods*
  • Magnetic Resonance Imaging
  • Male
  • Middle Aged
  • Neuroimaging / methods*
  • Young Adult

Grant support