SurfSeg

Volumetric segmentation using explicit surfaces.

This is a small C++14 library to perform segmentation in volumetric images with explicit (hyper)surfaces defined via meshes. A C++ API is provided as well as a set of mex files for MATLAB.

Some MATLAB scripts have been created to show how to use the library.

How to build

The project can be built using CMake. To build, navigate to the project directory and run:

mkdir build
cd build
cmake ..

and then run the resulting generator (most likely a makefile or Visual Studio project).

In order to build this project you will need the GEL library. If you use Windows and compile GEL with provided Visual Studio files, you can set the environment variable GEL_LIB_ROOT_DIR before calling CMake to specify where GEL is stored. However, you may have to tweak this manually.

You will also need the MESH tool to compile the mex function which computed the Hausdorff distance between two meshes. Again, you can set the MESH_LIB_ROOT_DIR environment variable before calling CMake to specify where the tool is stored -- but you will likely need to adjust the CMakeLists.txt manually to get linking to work. If you want to skip this and don't care about this mex function, then set the CMake variable SKIP_MEX_HAUSDORFF to true.