Medical Imaging

SimpleITK has a fantastic python API for medical image processing, but it has a steep learning curve. In this post I will document how to resample images using the Resample filter via the complicated, but really useful task of extracting oblique slices in a 3D image. If you imagine a 3D image as a cube then an oblique slice is formed by sampling the image on a plane that has an arbitrary normal and does not align with the canonical axial, sagittal, coronal planes (see Fig. 1).