msx00/cor-fem

Cor-FEM is a research tool for medical image registration, which means lining up two 3D scans of the same body part so they match up even when the shape has changed between scans. It uses a technique called the finite element method, a way of modeling how soft, flexible material bends and deforms, to handle non-rigid registration, where the organ is not just moved or rotated but also stretched or squeezed. The authors say this is one of the first non-linear versions of this approach built for a specific technical setting called zero boundary condition. Right now the released version is built specifically for prostate scans, though the authors plan to add settings for the kidney, liver, and other abdominal organs later. The overall pipeline takes a 3D medical volume file, such as a nii, nii.gz, or nrrd scan, and turns it into a surface mesh, smooths that mesh, and then runs the registration step to line it up against another scan. Three main scripts handle this: volume2mesh.py builds the mesh from the volume, mesh_smooth.py cleans it up, and cor-fem-prostate.sh runs the actual registration. The README reports that on a public prostate dataset called mu-RegPro, this method ran faster on average than three other named FEM-based registration methods it was compared against. The code is mainly built and tested on Ubuntu, though Windows is allowed if you turn off the Blender-related parts of the code first. The project is written in Python, has 15 stars, and is explicitly aimed at research use rather than production or clinical use. The authors note that file paths in the shell script need to be checked and edited before running, and that registration settings may need adjusting for different organs, scan types, and image resolutions. The README states that citation information and license details will be added later, so neither is available yet.