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An automated framework for localization, segmentation and super-resolution reconstruction of fetal brain MRI

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Michael Ebner, Guotai Wang, Wenqi Li, Michael Aertsen, Premal A Patel, Rosalind Aughwane, Andrew Melbourne, Tom Doel, Steven Dymarkowski, Paolo De Coppi, Anna L David, Jan Deprest, Sébastien Ourselin, Tom Vercauteren

Original languageEnglish
Article number116324
JournalNeuroImage
Volume206
Early online date5 Nov 2019
DOIs
Accepted/In press29 Oct 2019
E-pub ahead of print5 Nov 2019
Published1 Feb 2020

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Abstract

High-resolution volume reconstruction from multiple motion-corrupted stacks of 2D slices plays an increasing role for fetal brain Magnetic Resonance Imaging (MRI) studies. Currently existing reconstruction methods are time-consuming and often require user interactions to localize and extract the brain from several stacks of 2D slices. We propose a fully automatic framework for fetal brain reconstruction that consists of four stages: 1) fetal brain localization based on a coarse segmentation by a Convolutional Neural Network (CNN), 2) fine segmentation by another CNN trained with a multi-scale loss function, 3) novel, single-parameter outlier-robust super-resolution reconstruction, and 4) fast and automatic high-resolution visualization in standard anatomical space suitable for pathological brains. We validated our framework with images from fetuses with normal brains and with variable degrees of ventriculomegaly associated with open spina bifida, a congenital malformation affecting also the brain. Experiments show that each step of our proposed pipeline outperforms state-of-the-art methods in both segmentation and reconstruction comparisons including expert-reader quality assessments. The reconstruction results of our proposed method compare favorably with those obtained by manual, labor-intensive brain segmentation, which unlocks the potential use of automatic fetal brain reconstruction studies in clinical practice.

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