2.2. Registration
Rigid and/or deformable registration was performed either using the Velocity software (Varian Medical Systems) or our SimpleITK registration implemented in Python. Both Velocity and our implementation have options to perform linear registration and deformable registration. Registration can be checked visually with a blend of the two images. Depending on the time between scans and the degree of morphology change, linear registration may be sufficient. In order to proceed with the automatic analysis, every subject’s registration must be approved by the user, after which the second scan is re-sampled with the registration transform applied and saved.The T1 from the mid-RT scan was first registered to the T1w-CE from the pre-RT scan. Once approved, the transformation was applied to all remaining data (contours and metabolite maps) associated with the mid-RT scan. All results were carefully inspected by two authors (A.G.T. and S.K.) and approved by the board-certified medical physicist (E.S.) who is specialized in image registration. The registered images were resampled and then stored in addition to the original images and were used for all remaining analyses.