Automated quality assessment using appearance-based simulations and hippocampus segmentation on low-field paediatric brain MR images

Abstract

Understanding the structural growth of paediatric brains is a key step in the identification of various neuro-developmental disorders. However, our knowledge is limited by many factors, including the lack of automated image analysis tools, especially in Low and Middle Income Countries from the lack of high field MR images available. Low-field systems are being increasingly explored in these countries, and, therefore, there is a need to develop automated image analysis tools for these images. In this work, as a preliminary step, we consider two tasks: 1) automated quality assurance and 2) hippocampal segmentation, where we compare multiple approaches. For the automated quality assurance task a DenseNet combined with appearance-based transformations for synthesising artefacts produced the best performance, with a weighted accuracy of 82.3%. For the segmentation task, registration of an average atlas performed the best, with a final Dice score of 0.61. Our results show that although the images can provide understanding of large scale pathologies and gross scale anatomical development, there still remain barriers for their use for more granular analyses.