Getting Started

This page explains how to install SuperElastix.

SuperBuild On Linux

The SuperElastix SuperBuld is a script that automatically downloads and installs dependencies before compiling the main project. SuperElastix depends on ITK and elastix. The following steps assume that CMake, git and a compiler toolchain is installed. To build SuperElastix, clone the repository and invoke the SuperBuild.

$ git clone https://github.com/SuperElastix/SuperElastix
$ mkdir build
$ cd build
$ cmake ../SuperElastix/SuperBuild
$ make -j4

To check that SuperElastix was build successfully, go into the SuperElastix-build directory and run the test suite with the following command

ctest -j4

Warning

Be careful not to run out of memory during the build. A rule of thumb is that we need 4GB of memory per core. For example, if we compile SuperElastix with 4 cores (e.g. make -j4) we need a machine with at least 16GB of RAM.

SuperBuild On Mac OS X

The Mac OS X installation procedure is identical to that of Linux, so simply follow the Linux installation steps above to install SuperElastix. It is assumed that a CMake, git and a compiler toolchain has already been installed. We can check for a working compiler by opening the OS X terminal and run make. OS X will know if the Xcode Command Line Tools is missing and prompt you to install them if this is the case.

SuperBuild On Windows

In this guide we will use CMake to generate build files and the Visual Studio compiler to compile the project.

  1. Setup directories.
    • Download and install CMake GUI.
    • git clone https://github.com/SuperElastix/SuperElastix into a source folder of your choice.
    • Point the CMake source directory to the SuperElastix/SuperBuild folder inside the source directory.
    • Point the CMake build directory to a clean directory. Note that Visual Studio may complain during the build if the path is longer than 50 characters. Make a build directory with a short name at the root of your harddrive to avoid any issues.
  2. Select compiler.
    • Press configure to bring up the compiler selection window.
    • Preferably, choose Visual Studio 12 2013 Win64 as the generator for the project. SuperElastix can only be compiled with Visual Studio 12 or later, and if the OS is 64-bit that is also the prefered for the compiler.
  3. Open Visual Studio, select File -> Open Project/Solution -> Open and choose SuperElastixSuperBuild solution.
  4. Make sure “Release” build type is selected and build the ALL_BUILD project.
  5. Right-click on ALL_BUILD and click Build.
    • When building in Visual Studio 2015 you will get a number of error messages during compilation of ITK. Just press the ‘Ignore’ button for all of them.
  6. The SuperBuildSuperElastix solution only shows each library as a project. To have a more detailed view of SuperElastix open the SuperElastix solution file <build-path>\SuperElastix-build\SuperElastix.sln in a new Visual Studio environment.
  7. Optionally, Unit Tests and example code can be run by right-clicking on RUN_TESTS and clicking Project Only -> Build Only RUN_TESTS. Alternatively, individual tests can be run by right-clicking on a specific selx<...>Test project and choosing Set as StartUp Project.
  8. The SuperElastix commandline executable can be found in <build-path>\SuperElastixApplications-build\CommandlineProgram\Release.

Manually Building the Required Libraries

Instead of letting the SuperBuild download and build the required libraries manually build libraries can be used as well. The following approach allows us to use a system version of ITK or our own version of elastix.

  1. Build ITK.
    • Clone ITK from github.com/InsightSoftwareConsortium/ITK.
    • Configure CMake. Set the following CMake variables: BUILD_SHARED_LIBS=OFF, ITK_USE_REVIEW=ON, ITK_WRAP_*=OFF.
    • Compile ITK. Make sure to note the build settings, e.g. Release x64.
  2. Build Boost
  3. Build elastix.
    • Clone elastix from github.com/kaspermarstal/elastix.
    • Set ITK_DIR to the location of the ITK build directory
    • Configure CMake. Set the following CMake variables: BUILD_EXECUTABLE=OFF, USE_KNNGraphAlphaMutualInformationMetric=OFF
    • Set appropriate ELASTIX_IMAGE_2/3/4D_PIXELTYPES and any components that you might require.
    • If you are developing your own elastix components, make sure they are properly registered by the elastix build system.
    • Compile elastix. Make sure to configure the build settings exactly the same as ITK e.g. Release x64.
  4. Build SuperElastix.
    • Clone SuperElastix from github.com/SuperElastix/SuperElastix.
    • Configure CMake. Point ITK_DIR to the location of the ITK build directory and ELASTIX_DIR to the location of the elastix build directory.
    • Build SuperElastix. Make sure to configure the build settings exactly the same as ITK e.g. Release x64.