Automated Ventricular System Segmentation in Paediatric Patients Treated for Hydrocephalus Using Deep Learning Methods

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Abstract

Hydrocephalus is a common neurological condition that can have traumatic ramifications and can be lethal without treatment. Nowadays, during therapy radiologists have to spend a vast amount of time assessing the volume of cerebrospinal fluid (CSF) by manual segmentation on Computed Tomography (CT) images. Further, some of the segmentations are prone to radiologist bias and high intraobserver variability. To improve this, researchers are exploring methods to automate the process, which would enable faster and more unbiased results. In this study, we propose the application of U-Net convolutional neural network in order to automatically segment CT brain scans for location of CSF. U-Net is a neural network that has proven to be successful for various interdisciplinary segmentation tasks. We optimised training using state of the art methods, including "1cycle" learning rate policy, transfer learning, generalized dice loss function, mixed float precision, self-attention, and data augmentation. Even though the study was performed using a limited amount of data (80 CT images), our experiment has shown near human-level performance. We managed to achieve a 0.917 mean dice score with 0.0352 standard deviation on cross validation across the training data and a 0.9506 mean dice score on a separate test set. To our knowledge, these results are better than any known method for CSF segmentation in hydrocephalic patients, and thus, it is promising for potential practical applications.

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Klimont, M., Flieger, M., Rzeszutek, J., Stachera, J., Zakrzewska, A., & Jończyk-Potoczna, K. (2019). Automated Ventricular System Segmentation in Paediatric Patients Treated for Hydrocephalus Using Deep Learning Methods. BioMed Research International, 2019. https://doi.org/10.1155/2019/3059170

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