Evaluation of a deep learning approach for the segmentation of brain tissues and white matter hyperintensities of presumed vascular origin in MRI

Neuroimage Clin. 2017 Oct 12:17:251-262. doi: 10.1016/j.nicl.2017.10.007. eCollection 2018.


Automatic segmentation of brain tissues and white matter hyperintensities of presumed vascular origin (WMH) in MRI of older patients is widely described in the literature. Although brain abnormalities and motion artefacts are common in this age group, most segmentation methods are not evaluated in a setting that includes these items. In the present study, our tissue segmentation method for brain MRI was extended and evaluated for additional WMH segmentation. Furthermore, our method was evaluated in two large cohorts with a realistic variation in brain abnormalities and motion artefacts. The method uses a multi-scale convolutional neural network with a T1-weighted image, a T2-weighted fluid attenuated inversion recovery (FLAIR) image and a T1-weighted inversion recovery (IR) image as input. The method automatically segments white matter (WM), cortical grey matter (cGM), basal ganglia and thalami (BGT), cerebellum (CB), brain stem (BS), lateral ventricular cerebrospinal fluid (lvCSF), peripheral cerebrospinal fluid (pCSF), and WMH. Our method was evaluated quantitatively with images publicly available from the MRBrainS13 challenge (n = 20), quantitatively and qualitatively in relatively healthy older subjects (n = 96), and qualitatively in patients from a memory clinic (n = 110). The method can accurately segment WMH (Overall Dice coefficient in the MRBrainS13 data of 0.67) without compromising performance for tissue segmentations (Overall Dice coefficients in the MRBrainS13 data of 0.87 for WM, 0.85 for cGM, 0.82 for BGT, 0.93 for CB, 0.92 for BS, 0.93 for lvCSF, 0.76 for pCSF). Furthermore, the automatic WMH volumes showed a high correlation with manual WMH volumes (Spearman's ρ = 0.83 for relatively healthy older subjects). In both cohorts, our method produced reliable segmentations (as determined by a human observer) in most images (relatively healthy/memory clinic: tissues 88%/77% reliable, WMH 85%/84% reliable) despite various degrees of brain abnormalities and motion artefacts. In conclusion, this study shows that a convolutional neural network-based segmentation method can accurately segment brain tissues and WMH in MR images of older patients with varying degrees of brain abnormalities and motion artefacts.

Keywords: Brain MRI; Brain atrophy; Convolutional neural networks; Deep learning; Motion artefacts; Segmentation; White matter hyperintensities.

Publication types

  • Evaluation Study

MeSH terms

  • Aged
  • Artifacts
  • Brain / blood supply
  • Brain / diagnostic imaging*
  • Brain / pathology*
  • Female
  • Humans
  • Image Processing, Computer-Assisted
  • Magnetic Resonance Imaging / methods*
  • Male
  • Neural Networks, Computer*
  • Pattern Recognition, Automated
  • Reproducibility of Results
  • White Matter / blood supply
  • White Matter / diagnostic imaging*
  • White Matter / pathology*