3D Reconstruction from CT Images Using Free Software Tools

Abstract

Computed Tomography (CT) is a commonly used imaging modality across a wide variety of diagnostic procedures (World Health Organisation 2017). By generating contiguous cross-sectional images of a body region, CT has the ability to represent valuable 3D data that enables professionals to easily identify, locate, and accurately describe anatomical landmarks. Based on 3D modeling techniques developed by the field of Computer Graphics, the Region of Interest (ROI) can be extracted from the 2D anatomical slices and used to reconstruct subject-specific 3D models. This chapter describes a 3D reconstruction pipeline that can be used to generate 3D models from CT images and also volume renderings for medical visualization purposes (Ribeiro et al. 2009). We will provide several examples on how to segment 3D anatomical structures with high-contrast detail, namely skull, mandible, trachea, and colon, relying solely on the following set of free and open-source tools: ITK-SNAP (Yushkevich et al. 2006) and ParaView (Ahrens et al. 2005).