MITK - Generate Models (MITK-GEM) is a free open-source software pipeline to generate finite element models from image data. It is built on top of the Medical Imaging Interaction Toolkit (MITK) Workbench.

• Interactive image segmentation with 3D graph cuts
• Surface mesh generation
• Tetrahedral mesh generation
• Material mapping

For more information, check our website and our simtk project.

You can find binaries of the MITK-GEM application on our downloads page.

If you'd like to build MITK-GEM from source, follow the instructions below.

• CMake >=3.2 cmake-gui is recommended.
• QT 4.8 (OSX), QT 5 (Windows & Linux)

If you use the latest Ubuntu release (>= 14.04 LTS), you can install all the dependencies with the following command: sudo apt-get install git build-essential cmake-gui qt-sdk libxt-dev libtiff4-dev libwrap0-dev

Ubuntu 12.04 bundles cmake version 2.8.7, but you will need 3.2 in order to build MITK. A manual update is required.

1. Install dependencies: sudo apt-get install git build-essential qt-sdk libxt-dev libtiff4-dev libwrap0-dev
2. Install CMake 3.2+ http://www.cmake.org/download/

• Apple Xcode https://developer.apple.com/xcode/ with activated command line tools. To do so, open Xcode, go to Preferences -> Downloads -> Components -> Command Line Tools.
• QT 4.8 http://download.qt-project.org/archive/qt/
• CMake 3.2+ http://www.cmake.org/download/

• MSVC 2012v4 or MSVC 2013 (e.g. Visual Studio 2013 Community Edition). ** MSVC 2015 IS NOT SUPPORTED**
• Qt 5.0 - 5.4 ** WITH OpenGL ENABLED **. When using the Qt binary installer, pick the msvc2013 64-bit OpenGL build.
• CMake 3.2+ http://www.cmake.org/download/

1. Download the source code git clone https://github.com/araex/mitk-gem src
2. Create a new directory for the build mkdir build
3. Change to the build directory and run CMake cd build; cmake ../src
4. Start the build make -j 8. This will take a long time (up to an hour) and requires internet access.
5. Once compilation is finished, you can find the executable MITK-GEM in the directory build/MITK-GEM-build/bin/

Follow the instructions here http://www.mitk.org/wiki/Developer_Tutorial_(Microsoft_Windows)". Remember to save the source and the build in a ** very short ** top-level directory.

For questions regarding the usage of MITK-GEM, refer to our application FAQ.

This step pulls the most recent version of MITK from our MITK fork. Depending on the server and your internet connection, this might take some time. If you're using a proxy, please confirm that git is configured correctly.

You need to install Nokias QT library. See http://qt-project.org/downloads for instructions.

MITK-GEM is released under the GPLv3 license. However, the plugins are individually licensed and may be used under these conditions separately:

• Material Mapping: BSD 3-Clause License.
• Surface Mesher: BSD 3-Clause License
• Resample Plugin: BSD 3-Clause License
• Padding Plugin: BSD 3-Clause License
• GraphCut3D: GPLv3 because of the used library maxflow.
• Volume Mesher: GPLv3 beaucse of the used library tetgen.