Automatic extraction of the intracranial volume in fetal and neonatal MR scans using convolutional neural networks

Neuroimage Clin. 2019:24:102061. doi: 10.1016/j.nicl.2019.102061. Epub 2019 Nov 9.


MR images of infants and fetuses allow non-invasive analysis of the brain. Quantitative analysis of brain development requires automatic brain tissue segmentation that is typically preceded by segmentation of the intracranial volume (ICV). Fast changes in the size and morphology of the developing brain, motion artifacts, and large variation in the field of view make ICV segmentation a challenging task. We propose an automatic method for segmentation of the ICV in fetal and neonatal MRI scans. The method was developed and tested with a diverse set of scans regarding image acquisition parameters (i.e. field strength, image acquisition plane, image resolution), infant age (23-45 weeks post menstrual age), and pathology (posthaemorrhagic ventricular dilatation, stroke, asphyxia, and Down syndrome). The results demonstrate that the method achieves accurate segmentation with a Dice coefficient (DC) ranging from 0.98 to 0.99 in neonatal and fetal scans regardless of image acquisition parameters or patient characteristics. Hence, the algorithm provides a generic tool for segmentation of the ICV that may be used as a preprocessing step for brain tissue segmentation in fetal and neonatal brain MR scans.

Keywords: Brain extraction; Brain segmentation; Deep learning; Fetal MRI; Intracranial volume segmentation; Neonatal MRI; Skull stripping.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Brain / diagnostic imaging*
  • Deep Learning
  • Fetus / diagnostic imaging*
  • Head / diagnostic imaging*
  • Humans
  • Image Processing, Computer-Assisted
  • Magnetic Resonance Imaging
  • Neural Networks, Computer
  • Organ Size