Automatic segmentation of the cortical surface in neonatal brain MRI

Abstract : Clinical studies for preterm infants (less than 32 weeks of gestation) emphasize the fact that an important part of the very or extreme preterm infants will present cognitive, motor or behavioral disorders. The clinical aim is to improve brain development studies and be able to detect and predict abnormalities in neonatal subjects. Among the medical imaging, MRI can provide non-invasive non-ionizing morphological 3D images with a spatial resolution of the order of a millimeter, properties that are well adapted to this issue. In addition, the segmentation of these images provides quantitative anatomical information, such as volume or shape. There are many existing methods for adult MRI that successfully segment brain subparts. However, these methods cannot be directly applied to the newborn, where the maturation of brain tissue modifies the contrasts in the image (for example, the non-myelination of the white matter). Moreover, factors related to the resolution together with structural fineness, especially in the cortex, induce partial volume effects in tissue boundaries. This thesis focuses on the segmentation of the cortical surface in neonatal infants using MR images, with satisfactory accuracy for further applications (such as the generation of surface meshes). In this thesis, we first focused on the so-called atlas or multi-atlas approaches. This family of methods is known for its effectiveness in brain segmentation, thanks to spatial priors that can be embedded in the model for guiding the segmentation. However, since the neonatal cortex is very thin, there are often discontinuities or wrong connections. In order to tackle this issue, a topological correction step is proposed to fill gaps and separate erroneous connections. The results emphasize the potential of these two types of approaches for this purpose.
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Submitted on : Tuesday, December 3, 2019 - 4:20:10 PM
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Carlos Tor Díez. Automatic segmentation of the cortical surface in neonatal brain MRI. Medical Imaging. Ecole nationale supérieure Mines-Télécom Atlantique, 2019. English. ⟨NNT : 2019IMTA0152⟩. ⟨tel-02391662⟩

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