charlestac / mitk-gem

MITK - Generate Models (MITK-GEM) is a free open-source software pipeline to generate finite element models from image data.

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.

Features

• 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.

Download

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.

Dependencies

• CMake >=3.2. cmake-gui is recommended.
• QT 5.5. ** QT 5.6 is not supported! **

Supported compilers

The versions of supported compilers are:

• MSVC 2012 Update 4 ** MSVC 2015 is not supported! **
• GNU 4.7.3
• Clang 3.4
• AppleClang 5.0 Newer versions might work, but have not been tested.

Prerequisites

Ubuntu (>= 14.04 LTS)

• Install dependencies: sudo apt-get install git build-essential cmake-gui libxt-dev libtiff4-dev libwrap0-dev libgmp3-dev libcgal-dev mesa-common-dev freeglut3-dev
• Qt 5.5

Ubuntu 12.04 LTS

Ubuntu 12.04 bundles cmake version 2.8.7, but you will need 3.4 in order to build MITK-GEM. A manual update is required.

• Install CMake 3.2 or later
• Install dependencies: sudo apt-get install git build-essential libxt-dev libtiff4-dev libwrap0-dev libgmp3-dev libcgal-dev mesa-common-dev freeglut3-dev
• Qt 5.5

Mac OSX

• 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.
• Most recent version of the Xcode command line tools xcode-select --install.
• Qt 5.5
• CMake 3.2 or later
• GMP. We recommend using homebrew brew install gmp

Windows

• MSVC 2012v4 or MSVC 2013 (e.g. Visual Studio 2013 Community Edition). ** MSVC 2015 IS NOT SUPPORTED**
• QT 5.5 msvc2013 ** WITH OpenGL ENABLED **. When using the Qt binary installer, pick the msvc2013 64-bit OpenGL build.
• CMake 3.2 or later
• GMP. We recommend getting a prebuilt version using the CGAL installer

Build instructions

Linux & OSX

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/

Windows

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.

Optional features

Using GridCut

GridCut is an alternative min-cut / max-flow solver to use instead of maxflow in the GraphCut3D plugin. We've seen significant performance increase in both speed and memory efficiency. For licensing reasons we cannot redistribute GridCut (neither in the source nor binary release), so you have to download and install it manually:

1. Go to the GridCut website and download the source code.
2. Copy the contents of the .zip archive to mitk-gem source code directory Plugins/ch.zhaw.graphcut/src/internal/lib/GraphCut3D/lib/gridcut
3. Build make -j 8

FAQ

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

The compile process has stopped at 'Updating MITK'

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.

CMake Error: Found unsuitable Qt version "" from NOTFOUND

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

License

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 maxflow.
• Volume Mesher: GPLv3 because of tetgen.