If you use MITK as an external project, the MITK-build/bin link directory is missing in the library search paths list of the application executable. Other bin directories of VTK, ITK and GDCM are working.
For us adding
LINK_DIRECTORIES( /mes/bin/MITK/MITK-build/bin )
to the application CMakeList.txt temporarily works
The application is a "small tool", a command line version of the server using no QT, only MITK and MES.
Adding to our CMakeList.txt of the application the missing line:
LINK_DIRECTORIES( ${ALL_LIBRARY_DIRS} )fixes all. That CMake variable seems to be build up in MITK_USE_MODULE macro.
The CMakeList.txt we are using was copied from another small tool (mbi/Modules/FatSegmentation/MiniApps) and modified to our needs. No idea why the original CMakeList.txt is linking without the line, and ours not.