Title: Development of methods to create three-dimensional subject-specific physical and computer models of the upper airways for the diagnosis and treatment of velopharyngeal insufficiency
Funder: Health Education England

Abstract: Background About 1 in 1000 babies born in the United Kingdom develop speech problems as a result of velopharyngeal insufficiency (VPI), which is when the soft palate is unable to block the opening between the oral and nasal cavities. These problems can cause communication difficulties which detrimentally affect educational and social development. Treatment of VPI is usually surgical. However, VPI often persists and further surgery is required to treat it. Imaging is used in the diagnosis of VPI and the planning of surgery as it enables visualisation of the upper airways during speech. Currently the imaging techniques only provide 2D information about the upper airways and limited information about the muscles that move the soft palate. My hypothesis is that providing clinical teams with 3D information, including information about the muscles, will reduce the rates of further surgery by helping the teams to make better diagnoses and better plan surgical treatments. Aim To develop methods to create 3D subject-specific physical and computer models of the upper airways Methods Data collection 2D videos and 3D images of the upper airways of 50 adult volunteers will be acquired using existing MRI protocols. Data analysis Computer models will be created by: Using slice-to-volume registration methods to combine the 2D videos and 3D images into 3D videos. Using segmentation methods based on convolutional neural networks (CNNs) to outline anatomical structures in the 3D videos. Creating interactive 3D videos of the outlines of the structures. Users will be able to select which structures are shown and hidden in the videos.Physical models will be created by: Using CNN-based segmentation methods to outline different anatomical features in the 3D images. Transferring the outlines into software for 3D printing.Timelines for delivery 2019 April: start PhD. September: start recruitment.2020 January: start investigating different slice-to-volume registration methods. July: start investigating different CNN-based registration methods.2021 March: finish recruitment. June: determine the most appropriate registration and segmentation methods and determine how to transfer outlines of anatomical structures into software for 3D printing. December: start writing thesis.2022 March: finish PhD.Anticipated impact I anticipate that the models will improve the treatment outcomes of VPI patients by providing clinical teams with additional information that will help the teams to better identify the causes of VPI and better plan surgery to treat VPI. Improved treatment outcomes will reduce the rate of further surgery and will therefore avoid additional: Inconveniences for patients and their families; Workloads for clinical teams; Additional costs for health and care services.I intend to start translating the models into clinical practice as soon as possible after my Fellowship so that patients, clinical teams, and health and care services start benefiting from them within five years of the end of the Fellowship. Dissemination I will disseminate the findings of my research to researchers, clinicians, patients and the public by: Publishing articles in scientific journals; Presenting at: International conferences; The meetings of regional cleft services; Events organised by charities for people with speech problems; Blogging in plain English.

Lay abstract: Background to the research About 1 in 1000 babies born in the United Kingdom develop speech problems as a result of a medical condition called velopharyngeal insufficiency (VPI). These speech problems can have a negative effect on a patient's learning and ability to socialise. VPI is usually treated using surgery. However, patients often continue to have VPI after treatment. These patients can need extra surgery, which can be inconvenient for them and their families, creates more work for clinicians, and increases costs for health and care services. Clinicians use X-rays and small cameras to take videos that show the inside of a VPI patient's mouth when (s)he talks. These videos help them: Find the cause of VPI; Decide on the best type of treatment for a patient; Monitor a patient's progress after treatment.At the moment, the videos are two-dimensional (2D) so only provide 2D information about the inside of the mouth. Providing clinicians with three-dimensional (3D) information about the inside of the mouth should help them to better diagnose and treat VPI, and could therefore reduce the number of patients who need extra surgery. Aim(s) of the research My research aims to develop methods to create 3D models that show the inside of a person's mouth when (s)he talks. These models will be interactive 3D videos: users will be able to choose which part(s) of the inside of the mouth are shown in the videos. The models will provide clinicians with 3D information about the inside of a person's mouth. Design and methods used I will develop methods to create 3D videos of the inside of a person's mouth by combining 2D videos and 3D pictures. I will use magnetic resonance imaging (MRI) to take 2D videos and 3D pictures of the inside of the mouth and will use advanced computer-based methods to combine these into 3D videos. I will use MRI to take the videos and pictures because, unlike the X-rays and small cameras that clinicians currently use, it can take 3D pictures as well as 2D videos. MRI is often used in hospitals but at the moment is not often used by clinicians who diagnose and treat VPI. The 50 participants in my research will be adult volunteers. I will only include adult volunteers at this stage because I would first like to develop methods to create 3D videos before testing them on younger volunteers. Only including adult volunteers should not affect the development of the methods because the ways of taking videos and pictures are the same for people of all ages. I will include 50 participants in my research because the advanced computer-based methods perform better when they are adjusted using videos and pictures from a larger number of participants. Patient and public involvement I will involve VPI patients and their families in this research to ensure that the methods I develop are acceptable to them. Since many VPI patients are children or young persons, I will ask a Young Person's Advisory Group as well as a VPI patient group to: Review my research plan; Give me advice on how I could: Explain my research to people of different ages; Make my experiments more acceptable to young patients and VPI patients; Raise awareness of my research in the VPI community (patients, families, clinicians and researchers). Dissemination I will communicate the findings of my research to researchers, clinicians, patients and the public by: Publishing papers in scientific journals; Presenting at international conferences and departmental meetings; Participating in public events about research; Participating in events organised by charities for people with speech problems; Blogging in plain English.

Research activity codes: 4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: RESPIRATORY