A 3D medical image segmentation system for MRI modelling of the nasal passages

Eddie Edwards

MRI of nasal airway showing segmentation Rendering of the nasal sinus
MRI of the nasal passage A rendering of the 3D sinus after segmentation

Goal

To build a user friendly system for identifying anatomical features in medical images. The user should be able to take advantage of a number of semi-automated algorithms and manual techniques to segment general 3D structures, but also to tackle the specific problem of extracting the nasal sinus from MRI.

The extracted model of the nasal passage can be used to model air flow in a number of potential clinical applications, including decongestant effectiveness, sleep apnoea and general understanding of the breathing process. Throughout the project, an ENT clinician and/or engineer from the aeronautics lab will be treated as "the users" and they will provide non-technical specifications of what they require and assess prototypes of the system. The overall aim will be to make a system that is useful to the team. There will be at least 3 meetings with the users throughout the project development. A supplementary goal will be greater automation of the segmentation process.

Description

The Insight Toolkit (ITK) is a software system for segmentation and registration of medical images. It provides a library of C++ classes that implement several state-of-the-art segmentation algorithms. Though there are a number of example applications that are available with ITK, most of these either work on 2D images or are completely automated and do not allow user interaction. An exception is ITKSnap, which should be seen as a model for the package that will be developed from this project. Segmentation of anatomical structures from 3D medical images generally requires manual delineation or other interaction in regions where the object boundary is not clear.

The principal aim of this project is to produce a user interface for ITK that combines the power of some of the automated techniques with the flexibility of manual intervention in the segmentation process. There will be a number of aspects to this project. Some thought will need to go into the GUI design. The ability to visualise and navigate through a 3D dataset will be an early requirement, followed by manual delineation of points, lines and/or regions on this view. These features will then be input via the GUI to selected automated algorithms, whose parameters can also be adjusted.

Platform

Part of the process of the group project will involve deciding on a platform the system. ITK (and VTK) are implemented in C++, so this is an obvious choice. However, there are also bindings for TCL, Java and Python, so any of these could be used instead. There are installations of VTK and ITK available in DoC for linux, but both libraries can be installed under Windows. There are a number of widget sets (such as Qt or FLTK ) that can be used, but if implemented under Windows it may also be possible to use MFC. An early task for the group will be to decide upon a platform yourselves.

Possible division of work

There are a number of ways that the work can be divided. As a rough guide the following may be appropriate:

Supplementary goals

It is hoped that the project will progress quickly in the early stages, especially as there are a number of example applications that can be built upon. Some sugested further developments that would make the system more useful might include:
Eddie Edwards
Last modified: Wed Nov 28 00:55:26 GMT 2012