• 64bit system, it won't work on 32bit.
• git 2.21.0.windows.1 (version not important unless the interface changes)
• cmake 3.12.2
• MITK v2018.04.2, more instructions on this below
• Qt 5.11.1: Download and install using open-source license. This version is slightly old even now, so look for it in the archive when installing. We need the following components: "Desktop gcc (or msvc2017) 64-bit", "Qt WebEngine", and "Qt Script". On Windows install in short path, like C:\Qt. On linux you can install it wherever you want, but /home/YOUR_USERNAME/Work/Qt is a good place to be reduce clutter in accordance to what happens below.

Note: Use short paths for everything. This is a limitation of Windows. To be sure, it's better to use the exact paths listed below.

• Visual Studio 2017 (Community - aka free - edition is fine). This needs the 2017 c++ toolset. I wasn't able to make it work with the VS2019 generator. I think it is not supported by MITK. After/During install make sure the "Desktop development with C++" workload is installed. The default enabled checkboxes should be fine but make sure that "VC++ 2017 ... tools" and "Visual C++ tools for CMake" are installed.
• NSIS 2.51. Make sure it's available in path, you can do this by installing nsis-2.51-setup.exe. Don't use version 3+.

cd C:\
git clone https://github.com/MITK/MITK
git clone https://github.com/CBICA/MITK-Workshop-Project

cd C:\MITK
git fetch --all --tags
git checkout v2018.04.2 -b v2018.04.2-branch

Important note: Even though we are on Windows, use '/' as a path separator and not '\' in cmake!

• Open cmake-gui.
• Put C:/MITK at "Where is the source code" (notice the forward slashes in the path)
• Put C:/MITK-sb at "Where to build the binaries" (say yes if it asks to create the folder) (notice the forward slashes in the path)
• Click configure.
• If it comes up with an "error" that it can't find Qt, find the Qt5_DIR variable and set it to "C:/Qt/5.11.1/msvc2017_64/lib/cmake/Qt5" (notice the forward slashes)
• Click configure
• Set "CMAKE_INSTALL_PREFIX" to "C:/MITK-sb/install"
• Set "MITK_USE_OpenCV" to true (check the box).
• Set "MITK_EXTENSION_DIRS" to "C:/MITK-Workshop-Project" (notice the forward slashes)
• Configure (and then configure again until there are no more red variables)
• Click Generate
• Click "Open Project" - that should open Visual Studio

• In Visual Studio there will be a combobox that says "Solution Configurations" when you hover over it and will probably say "Debug" by default. Set it to "Release". * SEE COMMENT ON THIS BELOW
• In the "Solution Explorer" on the right, right-click "ALL_BUILD" and click "Build".

This will take 1+ hour(s) depending on the system.

* Release means that the program will run fast, just the way we distribute it. You can choose to build the superbuild+build in "Debug" too. That way you can use a debugger to figure out issues in the code, but note that it will - for obvious reasons - run slower.

Note: To distinguish between the two, the superbuild resides in "C:/MITK-sb" and the build in "C:/MITK-sb/MITK-build". It is obvious that the superbuild kind of contains the build even now without doing anything else. MITK Workbench - the GUI - will run even without doing anything in the build. But we need to enable two more plugins that work with our own.

Note: Close the "old" project in Visual Studio to not make things confusing.

• Open CMake again
• Put the "build" path in "Where to build the binaries". The path is "C:/MITK-sb/MITK-build".
• Locate "MITK_BUILD_org.mitk.gui.qt.segmentation" and set it to true
• Locate "MITK_BUILD_org.mitk.gui.qt.multilabelsegmentation" and set it to true
• They would be enabled, but for reference: our plugin is enabled/disabled by "MITK_BUILD_upenn.cbica.captk.example1" and MITK Workbench - the GUI - by "MITK_BUILD_APP_Workbench".
• Configure
• Generate
• Open Project

In Visual Studio, on your new "build" project and NOT the superbuild one:

• There will be a combobox that says "Solution Configurations" when you hover over it and will probably say "Debug" by default. Set it to "Release". * SEE COMMENT ON THIS BELOW
• In the "Solution Explorer" on the right, right-click "MitkWorkbench" and click "Build".

This will take 1+ hour(s) depending on the system.

* Release means that the program will run fast, just the way we distribute it. You can choose to build the superbuild+build in "Debug" too. That way you can use a debugger to figure out issues in the code, but note that it will - for obvious reasons - run slower.

You can run the program by running the bat files in C:\MITK-sb\MITK-build\bin.

• startMitkWorkbench_release.bat starts the program.
• startMitkWorkbench_debug.bat starts the program in debug mode, if that was build.

Packaging means making a zip file of the program + an installer. To do all this in the "build" project in visual studio, and only when in "Release" mode, find the "PACKAGE" project in "Solution Explorer". Right-click it and click build. That will create:

• C:\MITK-sb\MITK-build\_CPack_Packages\win64\ZIP\MITK-v2018.04.2-windows-x86_64.zip the zip package

This allows the program to run without installing. Just unzip and run bin\MitkWorkbench.exe. For some very old systems, running thirdpartyinstallers\vc_redist.x64.exe might be needed first.

• C:\MITK-sb\MITK-build\_CPack_Packages\win64\NSIS\MITK-v2018.04.2-windows-x86_64.exe the installer

This allows the program to be installed like a regular windows program. After that it will be available as MITK Workbench.

Note: This list was compiled in Ubuntu 18.04 and it might be slightly different if you are from the future.

• Run: sudo apt install -y build-essential mesa-common-dev libglu1-mesa-dev libtiff5-dev libwrap0-dev libxt-dev libxi-dev g++ git gitk git-gui

You are free to choose whichever paths you want, but for the instruction purposes everything will happen in $HOME/Work ($HOME aka ~ is your home directory, i.e. /home/YOUR_USERNAME)

mkdir -p ~/Work
cd ~/Work
git clone https://github.com/MITK/MITK
git clone https://github.com/CBICA/MITK-Workshop-Project

cd ~/Work/MITK
git fetch --all --tags
git checkout v2018.04.2 -b v2018.04.2-branch

These instructions are for a "Release" superbuild. Replace all instances of "Release" with "Debug" for a "Debug" superbuild. Release means that the program will run fast, just the way we distribute it. You can choose to build the superbuild+build in "Debug" too. That way you can use a debugger to figure out issues in the code, but note that it will - for obvious reasons - run slower.

• Open cmake-gui.
• Put /home/YOUR_USERNAME/Work/MITK at "Where is the source code"
• Put /home/YOUR_USERNAME/Work/MITK-sb/Release at "Where to build the binaries" (say yes if it asks to create the directory)
• Click configure.
• If it comes up with an "error" that it can't find Qt: If you installed Qt in /home/YOUR_USERNAME/Work/Qt then find the Qt5_DIR variable and set it to /home/YOUR_USERNAME/Work/Qt/5.11.1/gcc_64/lib/cmake/Qt5 (obviously replace the first part if you installed somewhere else)
• Click configure
• Set "CMAKE_INSTALL_PREFIX" to "/home/YOUR_USERNAME/Work/MITK-sb/Release/install"
• Set "MITK_USE_OpenCV" to true (check the box).
• Set "MITK_EXTENSION_DIRS" to "/home/YOUR_USERNAME/Work/MITK-Workshop-Project"
• Set CMAKE_BUILD_TYPE to "Release"
• Set CMAKE_EXPORT_COMPILE_COMMANDS to true
• Configure (and then configure again until there are no more red variables)
• Click Generate

cd ~/Work/MITK-sb/Release
make -j4

(If you do a debug build, navigate to ~/Work/MITK-sb/Debug)

Note: You can replace make -j4 with make -j8 if your system is decent and it has 16+GB of RAM. If you get a compiler error related to RAM, just run make instead.

This will take 1+ hour(s) depending on the system.

Note: To distinguish between the two, the superbuild resides in "/home/YOUR_USERNAME/Work/MITK-sb/Release" and the build in "/home/YOUR_USERNAME/Work/MITK-sb/Release/MITK-build". It is obvious that the superbuild kind of contains the build even now without doing anything else. MITK Workbench - the GUI - will run even without doing anything in the build. But we need to enable two more plugins that work with our own.

Note: Change all instances of "Release" to "Debug" for a "Debug" build.

• Open CMake again
• Put the "build" path in "Where to build the binaries". The path is "/home/YOUR_USERNAME/Work/MITK-sb/Release/MITK-build".
• Locate "MITK_BUILD_org.mitk.gui.qt.segmentation" and set it to true
• Locate "MITK_BUILD_org.mitk.gui.qt.multilabelsegmentation" and set it to true
• They would be enabled, but for reference: our plugin is enabled/disabled by "MITK_BUILD_upenn.cbica.captk.example1" and MITK Workbench - the GUI - by "MITK_BUILD_APP_Workbench".
• Set CMAKE_EXPORT_COMPILE_COMMANDS to true (this can help visual studio code and other IDEs pick up the headers.
• Configure
• Generate

cd ~/Work/MITK-sb/Release/MITK-build
make -j4

(If you do a debug build, navigate to ~/Work/MITK-sb/Debug/MITK-build)

Note: You can replace make -j4 with make -j8 if your system is decent and it has 16+GB of RAM. If you get a compiler error related to RAM, just run make instead.

You can run the program by running ~/Work/MITK-sb/Release/MITK-build/bin/MitkWorkbench.

(If you build debug, run ~/Work/MITK-sb/Debug/MITK-build/bin/MitkWorkbench with your debugger)

Release only!

cd ~/Work/MITK-sb/Release/MITK-build
make package