As [badly] explained in the ML, CTK fails to build on Windows. The actual error is
13>CMake Error at CMake/ctkMacroSetupQt.cmake:76 (else): 13> A duplicate ELSE command was found inside an IF block.
This error seems to have been fixed in may 2017. I tried fixing it myself to see if it would compile but all my changes are overwritten by cmake, so I'm not sure if there are other errors after.
What version of MITK do you use? We are constantly building MITK on Windows without any such issues. Should only happen with rather old versions of MITK in combination with new CMake versions. Did you already try 2018.04 beta? The branch is T25191-v2018.04-beta here on Phabricator (https://phabricator.mitk.org/source/mitk.git).
I thought I used the current master but I tried again this morning and everthing is fine. I probably mistyped the source folder name and picked an old version. My bad.
It seems I can't close my own tasks. You can close this task :)