diff --git a/CMakeExternals/CppUnit.cmake b/CMakeExternals/CppUnit.cmake
index 085e5f3597..df12ec1583 100644
--- a/CMakeExternals/CppUnit.cmake
+++ b/CMakeExternals/CppUnit.cmake
@@ -1,50 +1,50 @@
 #-----------------------------------------------------------------------------
 # CppUnit
 #-----------------------------------------------------------------------------
 
 # Sanity checks
 if(DEFINED CppUnit_DIR AND NOT EXISTS ${CppUnit_DIR})
   message(FATAL_ERROR "CppUnit_DIR variable is defined but corresponds to non-existing directory")
 endif()
 
 set(proj CppUnit)
 set(proj_DEPENDENCIES )
 set(${proj}_DEPENDS ${proj})
 
 if(NOT DEFINED CppUnit_DIR)
 
   set(additional_args )
   if(CTEST_USE_LAUNCHERS)
     list(APPEND additional_args
       "-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake"
     )
   endif()
 
   ExternalProject_Add(${proj}
      LIST_SEPARATOR ${sep}
      URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/cppunit-1.12.1.tar.gz
      URL_MD5 bd30e9cf5523cdfc019b94f5e1d7fd19
      PATCH_COMMAND
-       ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/CppUnit-1.12.1.patch
+       ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/CppUnit-1.12.1.patch --binary
        COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_LIST_DIR}/${proj}config.h.cmake <SOURCE_DIR>/config/config.h.cmake
        COMMAND ${CMAKE_COMMAND} -Dproj=${proj} -Dproj_target:STRING=cppunit -P ${CMAKE_CURRENT_LIST_DIR}/GenerateDefaultCMakeBuildSystem.cmake
      CMAKE_GENERATOR ${gen}
      CMAKE_GENERATOR_PLATFORM ${gen_platform}
      CMAKE_ARGS
        ${ep_common_args}
        ${additional_args}
      CMAKE_CACHE_ARGS
        ${ep_common_cache_args}
      CMAKE_CACHE_DEFAULT_ARGS
        ${ep_common_cache_default_args}
      DEPENDS ${proj_DEPENDENCIES}
     )
 
   set(${proj}_DIR ${ep_prefix}/lib/cmake/CppUnit)
   mitkFunctionInstallExternalCMakeProject(${proj})
 
 else()
 
   mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
 
 endif()
diff --git a/CMakeExternals/Eigen.cmake b/CMakeExternals/Eigen.cmake
index effd8026f9..6dad2695d2 100644
--- a/CMakeExternals/Eigen.cmake
+++ b/CMakeExternals/Eigen.cmake
@@ -1,44 +1,44 @@
 #-----------------------------------------------------------------------------
 # Eigen
 #-----------------------------------------------------------------------------
 
 if(MITK_USE_Eigen)
 
   # Sanity checks
   if(DEFINED Eigen_DIR AND NOT EXISTS ${Eigen_DIR})
     message(FATAL_ERROR "Eigen_DIR variable is defined but corresponds to non-existing directory")
   endif()
 
   set(proj Eigen)
   set(proj_DEPENDENCIES )
   set(Eigen_DEPENDS ${proj})
 
   if(NOT DEFINED Eigen_DIR)
 
     ExternalProject_Add(${proj}
       LIST_SEPARATOR ${sep}
       URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/eigen-eigen-07105f7124f9.tar.bz2
       URL_MD5 9e3bfaaab3db18253cfd87ea697b3ab1
-      PATCH_COMMAND ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/Eigen.patch
+      PATCH_COMMAND ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/Eigen.patch --binary
       CMAKE_GENERATOR ${gen}
       CMAKE_GENERATOR_PLATFORM ${gen_platform}
       CMAKE_ARGS
         ${ep_common_args}
         -DBUILD_TESTING:BOOL=ON
         -DEIGEN_BUILD_PKGCONFIG:BOOL=OFF
       CMAKE_CACHE_ARGS
         ${ep_common_cache_args}
       CMAKE_CACHE_DEFAULT_ARGS
         ${ep_common_cache_default_args}
     )
 
     set(Eigen_DIR ${ep_prefix})
     mitkFunctionInstallExternalCMakeProject(${proj})
 
   else()
 
     mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
 
   endif()
 
 endif()
diff --git a/CMakeExternals/GDCM.cmake b/CMakeExternals/GDCM.cmake
index 25a9e9d517..5d8ba3e084 100644
--- a/CMakeExternals/GDCM.cmake
+++ b/CMakeExternals/GDCM.cmake
@@ -1,71 +1,71 @@
 #-----------------------------------------------------------------------------
 # GDCM
 #-----------------------------------------------------------------------------
 
 # Sanity checks
 if(DEFINED GDCM_DIR AND NOT EXISTS ${GDCM_DIR})
   message(FATAL_ERROR "GDCM_DIR variable is defined but corresponds to non-existing directory")
 endif()
 
 # Check if an external ITK build tree was specified.
 # If yes, use the GDCM from ITK, otherwise ITK will complain
 if(ITK_DIR)
   find_package(ITK)
   if(ITK_GDCM_DIR)
     set(GDCM_DIR ${ITK_GDCM_DIR})
   endif()
 endif()
 
 
 set(proj GDCM)
 set(proj_DEPENDENCIES )
 set(GDCM_DEPENDS ${proj})
 
 if(NOT DEFINED GDCM_DIR)
 
   set(additional_args )
   if(CTEST_USE_LAUNCHERS)
     list(APPEND additional_args
       "-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake"
     )
   endif()
 
   # On Mac some assertions fail that prevent reading certain DICOM files. Bug #19995
   if(APPLE)
     list(APPEND additional_args
       "-DCMAKE_CXX_FLAGS_DEBUG:STRING=${CMAKE_CXX_FLAGS_DEBUG} -DNDEBUG"
     )
   endif()
 
   mitk_query_custom_ep_vars()
 
   ExternalProject_Add(${proj}
      LIST_SEPARATOR ${sep}
      URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/gdcm-2.6.3.tar.bz2
      URL_MD5 52d398f48e672f1949914f6b3e2d528c
-     PATCH_COMMAND ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/GDCM.patch
+     PATCH_COMMAND ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/GDCM.patch --binary
      CMAKE_GENERATOR ${gen}
      CMAKE_GENERATOR_PLATFORM ${gen_platform}
      CMAKE_ARGS
        ${ep_common_args}
        ${additional_args}
        -DGDCM_BUILD_SHARED_LIBS:BOOL=ON
        ${${proj}_CUSTOM_CMAKE_ARGS}
      CMAKE_CACHE_ARGS
        ${ep_common_cache_args}
        ${${proj}_CUSTOM_CMAKE_CACHE_ARGS}
      CMAKE_CACHE_DEFAULT_ARGS
        ${ep_common_cache_default_args}
        ${${proj}_CUSTOM_CMAKE_CACHE_DEFAULT_ARGS}
      DEPENDS ${proj_DEPENDENCIES}
     )
   set(GDCM_DIR ${ep_prefix})
   mitkFunctionInstallExternalCMakeProject(${proj})
 
 else()
 
   mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
 
   find_package(GDCM)
 
 endif()
diff --git a/CMakeExternals/OpenIGTLink.cmake b/CMakeExternals/OpenIGTLink.cmake
index 62611eafa8..b77e445bb5 100644
--- a/CMakeExternals/OpenIGTLink.cmake
+++ b/CMakeExternals/OpenIGTLink.cmake
@@ -1,58 +1,58 @@
 #-----------------------------------------------------------------------------
 # OpenIGTLink
 #-----------------------------------------------------------------------------
 if(MITK_USE_OpenIGTLink)
 
   # Sanity checks
   if(DEFINED OpenIGTLink_DIR AND NOT EXISTS ${OpenIGTLink_DIR})
     message(FATAL_ERROR "OpenIGTLink_DIR variable is defined but corresponds to non-existing directory")
   endif()
 
   set(proj OpenIGTLink)
   set(proj_DEPENDENCIES )
   set(${proj}_DEPENDS ${proj})
 
   if(NOT DEFINED OpenIGTLink_DIR)
 
     set(additional_cmake_args )
 
     if(CTEST_USE_LAUNCHERS)
       set(additional_cmake_args
         "-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake"
       )
     endif()
 
     mitk_query_custom_ep_vars()
 
     ExternalProject_Add(${proj}
        URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/OpenIGTLink-release-3.0.tar.gz
        URL_MD5 0a759655da037f6df2087dd2690d1ae2
-       PATCH_COMMAND ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/OpenIGTLink-92bc3d7b.patch
+       PATCH_COMMAND ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/OpenIGTLink-92bc3d7b.patch --binary
        CMAKE_GENERATOR ${gen}
        CMAKE_GENERATOR_PLATFORM ${gen_platform}
        CMAKE_ARGS
          ${ep_common_args}
          ${additional_cmake_args}
          -DBUILD_EXAMPLES:BOOL=OFF
          -DOpenIGTLink_PROTOCOL_VERSION_2:BOOL=ON
          -DOpenIGTLink_INSTALL_LIB_DIR:STRING=lib
          -DOpenIGTLink_INSTALL_PACKAGE_DIR:STRING=lib/cmake/OpenIGTLink
          -DOpenIGTLink_INSTALL_NO_DOCUMENTATION:BOOL=ON
          ${${proj}_CUSTOM_CMAKE_ARGS}
        CMAKE_CACHE_ARGS
          ${ep_common_cache_args}
          ${${proj}_CUSTOM_CMAKE_CACHE_ARGS}
        CMAKE_CACHE_DEFAULT_ARGS
          ${ep_common_cache_default_args}
          ${${proj}_CUSTOM_CMAKE_CACHE_DEFAULT_ARGS}
        DEPENDS ${proj_DEPENDENCIES}
       )
 
     set(OpenIGTLink_DIR "${ep_prefix}/lib/cmake/OpenIGTLink")
 
   else()
 
     mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
 
   endif()
 endif()
diff --git a/CMakeExternals/Qwt.cmake b/CMakeExternals/Qwt.cmake
index b397f9e042..9252f0aa24 100644
--- a/CMakeExternals/Qwt.cmake
+++ b/CMakeExternals/Qwt.cmake
@@ -1,62 +1,62 @@
 #-----------------------------------------------------------------------------
 # Qwt
 #-----------------------------------------------------------------------------
 
 if(MITK_USE_Qwt)
 
 # Sanity checks
 if(DEFINED Qwt_DIR AND NOT EXISTS ${Qwt_DIR})
   message(FATAL_ERROR "Qwt_DIR variable is defined but corresponds to non-existing directory")
 endif()
 
 set(proj Qwt)
 set(proj_DEPENDENCIES )
 set(${proj}_DEPENDS ${proj})
 
 if(NOT DEFINED ${proj}_DIR)
 
   set(patch_cmd ${CMAKE_COMMAND} -Dproj:STRING=${proj} -Dproj_target:STRING=qwt -P ${CMAKE_CURRENT_LIST_DIR}/GenerateDefaultCMakeBuildSystem.cmake)
   set(qt54patch_cmd ${CMAKE_COMMAND} -DTEMPLATE_FILE:FILEPATH=${MITK_SOURCE_DIR}/CMakeExternals/EmptyFileForPatching.dummy -P ${MITK_SOURCE_DIR}/CMakeExternals/PatchQwt-6.1.0.cmake)
 
   set(additional_cmake_args
   "-DQt5Svg_DIR:PATH=${Qt5Svg_DIR}"
   "-DQt5OpenGL_DIR:PATH=${Qt5OpenGL_DIR}"
   "-DQt5PrintSupport_DIR:PATH=${Qt5PrintSupport_DIR}"
   "-DQt5Concurrent_DIR:PATH=${Qt5Concurrent_DIR}"
   "-DQt5Designer_DIR:PATH=${Qt5_DIR}Designer"
   )
   if(CTEST_USE_LAUNCHERS)
     list(APPEND additional_cmake_args
       "-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake"
     )
   endif()
 
   ExternalProject_Add(${proj}
      LIST_SEPARATOR ${sep}
      URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/qwt-6.1.0.tar.bz2
      URL_MD5 aef0437b37f191067a6a9dc01c30ba64
-     PATCH_COMMAND ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/Qwt-6.1.0.patch
+     PATCH_COMMAND ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/Qwt-6.1.0.patch --binary
        COMMAND ${CMAKE_COMMAND} -Dproj=${proj} -Dproj_target:STRING=qwt -P ${CMAKE_CURRENT_LIST_DIR}/GenerateDefaultCMakeBuildSystem.cmake
      CMAKE_GENERATOR ${gen}
      CMAKE_GENERATOR_PLATFORM ${gen_platform}
      CMAKE_ARGS
        ${ep_common_args}
        ${additional_cmake_args}
        ${qt_project_args}
      CMAKE_CACHE_ARGS
        ${ep_common_cache_args}
      CMAKE_CACHE_DEFAULT_ARGS
        ${ep_common_cache_default_args}
      DEPENDS ${proj_DEPENDENCIES}
     )
 
   set(${proj}_DIR ${ep_prefix})
   mitkFunctionInstallExternalCMakeProject(${proj})
 
 else()
 
   mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
 
 endif()
 
 endif()
diff --git a/CMakeExternals/Raptor2.cmake b/CMakeExternals/Raptor2.cmake
index 5fed212c3e..5b4e5ca3ec 100644
--- a/CMakeExternals/Raptor2.cmake
+++ b/CMakeExternals/Raptor2.cmake
@@ -1,72 +1,72 @@
 #-----------------------------------------------------------------------------
 # raptor2
 #-----------------------------------------------------------------------------
 
 if(MITK_USE_Raptor2)
 
 # Sanity checks
 if(DEFINED Raptor2_DIR AND NOT EXISTS ${Raptor2_DIR})
   message(FATAL_ERROR "Raptor2_DIR variable is defined but corresponds to non-existing directory")
 endif()
 
 set(proj Raptor2)
 set(proj_DEPENDENCIES )
 set(${proj}_DEPENDS ${proj})
 
 if(NOT DEFINED Raptor2_DIR)
 
   set(additional_cmake_args )
   if(CTEST_USE_LAUNCHERS)
     list(APPEND additional_cmake_args
       "-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake"
     )
   endif()
 
   ExternalProject_Add(${proj}
      LIST_SEPARATOR ${sep}
      URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/raptor2-2.0.15.tar.gz
      URL_MD5 a39f6c07ddb20d7dd2ff1f95fa21e2cd
-     PATCH_COMMAND ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/Raptor2-2.0.15.patch
+     PATCH_COMMAND ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/Raptor2-2.0.15.patch --binary
      CMAKE_GENERATOR ${gen}
      CMAKE_GENERATOR_PLATFORM ${gen_platform}
      CMAKE_ARGS
        ${ep_common_args}
        ${additional_cmake_args}
        -DRAPTOR_ENABLE_TESTING:BOOL=OFF
        -DRAPTOR_PARSER_GRDDL:BOOL=OFF
        -DRAPTOR_PARSER_GUESS:BOOL=OFF
        -DRAPTOR_PARSER_JSON:BOOL=OFF
        -DRAPTOR_PARSER_NQUADS:BOOL=ON
        -DRAPTOR_PARSER_NTRIPLES:BOOL=ON
        -DRAPTOR_PARSER_RDFA:BOOL=OFF
        -DRAPTOR_PARSER_RDFXML:BOOL=OFF
        -DRAPTOR_PARSER_RSS:BOOL=OFF
        -DRAPTOR_PARSER_TRIG:BOOL=OFF
        -DRAPTOR_PARSER_TURTLE:BOOL=ON
        -DRAPTOR_SERIALIZER_ATOM:BOOL=OFF
        -DRAPTOR_SERIALIZER_DOT:BOOL=OFF
        -DRAPTOR_SERIALIZER_HTML:BOOL=OFF
        -DRAPTOR_SERIALIZER_JSON:BOOL=OFF
        -DRAPTOR_SERIALIZER_NQUADS:BOOL=ON
        -DRAPTOR_SERIALIZER_NTRIPLES:BOOL=ON
        -DRAPTOR_SERIALIZER_RDFXML:BOOL=OFF
        -DRAPTOR_SERIALIZER_RDFXML_ABBREV:BOOL=OFF
        -DRAPTOR_SERIALIZER_RSS_1_0:BOOL=OFF
        -DRAPTOR_SERIALIZER_TURTLE:BOOL=ON
      CMAKE_CACHE_ARGS
        ${ep_common_cache_args}
      CMAKE_CACHE_DEFAULT_ARGS
        ${ep_common_cache_default_args}
      DEPENDS ${proj_DEPENDENCIES}
     )
 
   set(${proj}_DIR ${ep_prefix}/lib/raptor2/cmake)
   mitkFunctionInstallExternalCMakeProject(${proj})
 
 else()
 
   mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
 
 endif()
 
 endif()
diff --git a/CMakeExternals/Rasqal.cmake b/CMakeExternals/Rasqal.cmake
index e89464272e..342d017249 100644
--- a/CMakeExternals/Rasqal.cmake
+++ b/CMakeExternals/Rasqal.cmake
@@ -1,56 +1,56 @@
 #-----------------------------------------------------------------------------
 # rasqal
 #-----------------------------------------------------------------------------
 
 if(MITK_USE_Rasqal)
 
 # Sanity checks
 if(DEFINED Rasqal_DIR AND NOT EXISTS ${Rasqal_DIR})
   message(FATAL_ERROR "Rasqal_DIR variable is defined but corresponds to non-existing directory")
 endif()
 
 set(proj Rasqal)
 set(proj_DEPENDENCIES ${Raptor2_DEPENDS} ${PCRE_DEPENDS})
 set(${proj}_DEPENDS ${proj})
 
 if(NOT DEFINED Rasqal_DIR)
 
   set(additional_cmake_args )
   if(CTEST_USE_LAUNCHERS)
     list(APPEND additional_cmake_args
       "-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake"
     )
   endif()
 
   ExternalProject_Add(${proj}
      LIST_SEPARATOR ${sep}
      URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/rasqal-0.9.32.tar.gz
      URL_MD5 dc7c6107de00c47f85f6ab7db164a136
-     PATCH_COMMAND ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/Rasqal-0.9.32.patch
+     PATCH_COMMAND ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/Rasqal-0.9.32.patch --binary
      LIST_SEPARATOR ${sep}
      CMAKE_GENERATOR ${gen}
      CMAKE_GENERATOR_PLATFORM ${gen_platform}
      CMAKE_ARGS
        ${ep_common_args}
        ${additional_cmake_args}
        "-DCMAKE_C_FLAGS:STRING=-DPCRE_STATIC ${CMAKE_C_FLAGS}"
        -DRASQAL_REGEX:STRING=pcre
        -DCMAKE_PREFIX_PATH:STRING=${PCRE_DIR}^^${REDLAND_INSTALL_DIR}
        -DPCRE_INCLUDE_DIR:PATH=${PCRE_DIR}/include
      CMAKE_CACHE_ARGS
        ${ep_common_cache_args}
      CMAKE_CACHE_DEFAULT_ARGS
        ${ep_common_cache_default_args}
      DEPENDS ${proj_DEPENDENCIES}
     )
 
   set(${proj}_DIR ${ep_prefix}/lib/rasqal/cmake)
   mitkFunctionInstallExternalCMakeProject(${proj})
 
 else()
 
   mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
 
 endif()
 
 endif()
diff --git a/CMakeExternals/Redland.cmake b/CMakeExternals/Redland.cmake
index 6ba7d5dac3..78cfecbefd 100644
--- a/CMakeExternals/Redland.cmake
+++ b/CMakeExternals/Redland.cmake
@@ -1,52 +1,52 @@
 #-----------------------------------------------------------------------------
 # redland
 #-----------------------------------------------------------------------------
 
 if(MITK_USE_Redland)
 
 # Sanity checks
 if(DEFINED Redland_DIR AND NOT EXISTS ${Redland_DIR})
   message(FATAL_ERROR "Redland_DIR variable is defined but corresponds to non-existing directory")
 endif()
 
 set(proj Redland)
 set(proj_DEPENDENCIES ${Raptor2_DEPENDS} ${Rasqal_DEPENDS})
 set(${proj}_DEPENDS ${proj})
 
 if(NOT DEFINED Redland_DIR)
 
   set(additional_cmake_args )
   if(CTEST_USE_LAUNCHERS)
     list(APPEND additional_cmake_args
       "-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake"
     )
   endif()
 
   ExternalProject_Add(${proj}
      LIST_SEPARATOR ${sep}
      URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/redland-1.0.17.tar.gz
      URL_MD5 e5be03eda13ef68aabab6e42aa67715e
-     PATCH_COMMAND ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/Redland-1.0.17.patch
+     PATCH_COMMAND ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/Redland-1.0.17.patch --binary
      CMAKE_GENERATOR ${gen}
      CMAKE_GENERATOR_PLATFORM ${gen_platform}
      CMAKE_ARGS
        ${ep_common_args}
        ${additional_cmake_args}
        -DWITH_THREADS:BOOL=OFF
      CMAKE_CACHE_ARGS
        ${ep_common_cache_args}
      CMAKE_CACHE_DEFAULT_ARGS
        ${ep_common_cache_default_args}
      DEPENDS ${proj_DEPENDENCIES}
     )
 
   set(${proj}_DIR ${ep_prefix}/lib/redland/cmake)
   mitkFunctionInstallExternalCMakeProject(${proj})
 
 else()
 
   mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
 
 endif()
 
 endif()
diff --git a/CMakeExternals/Vigra.cmake b/CMakeExternals/Vigra.cmake
index 80e0fd99ee..ccb791aac3 100644
--- a/CMakeExternals/Vigra.cmake
+++ b/CMakeExternals/Vigra.cmake
@@ -1,65 +1,65 @@
 #-----------------------------------------------------------------------------
 # VIGRA
 #-----------------------------------------------------------------------------
 
 if(MITK_USE_Vigra)
 
   # Sanity checks
   if(DEFINED Vigra_DIR AND NOT EXISTS ${Vigra_DIR})
     message(FATAL_ERROR "Vigra_DIR variable is defined but corresponds to non-existing directory")
   endif()
 
   if(NOT ${MITK_USE_HDF5})
     message(FATAL_ERROR "HDF5 is required for Vigra. Please enable it.")
   endif()
 
   set(proj Vigra)
   set(proj_DEPENDENCIES HDF5)
   set(Vigra_DEPENDS ${proj})
 
   # If a mac ports installation is present some imaging-io-libraries may interfere with the vigra build.
   # Hence, we exclude them here.
   set(mac_additional_cmake_args)
   if(APPLE)
     set(mac_additional_cmake_args -DJPEG_INCLUDE_DIR= -DJPEG_LIBRARY= -DTIFF_INCLUDE_DIR= -DTIFF_LIBRARY= -DPNG_LIBRARY_RELEASE= -DPNG_PNG_INCLUDE_DIR= )
   endif()
 
   if(NOT DEFINED Vigra_DIR)
 
     set(additional_cmake_args )
     if(CTEST_USE_LAUNCHERS)
       list(APPEND additional_cmake_args
         "-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake"
       )
     endif()
 
     ExternalProject_Add(${proj}
        URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/vigra-1.10.0-src.tar.gz
        URL_MD5 4f963f0be4fcb8b06271c2aa40baa9be
-       PATCH_COMMAND ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/Vigra.patch
+       PATCH_COMMAND ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/Vigra.patch --binary
        CMAKE_GENERATOR ${gen}
        CMAKE_GENERATOR_PLATFORM ${gen_platform}
        CMAKE_ARGS
          ${ep_common_args}
          ${additional_cmake_args}
          ${mac_additional_cmake_args}
          -DAUTOEXEC_TESTS:BOOL=OFF
          -DWITH_VIGRANUMPY:BOOL=OFF
          -DHDF5_DIR:PATH=${HDF5_DIR}
          -DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=TRUE
          -DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR>
        CMAKE_CACHE_ARGS
          ${ep_common_cache_args}
        CMAKE_CACHE_DEFAULT_ARGS
          ${ep_common_cache_default_args}
        DEPENDS ${proj_DEPENDENCIES}
       )
 
     set(Vigra_DIR ${ep_prefix})
 
   else()
 
     mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
 
   endif()
 endif(MITK_USE_Vigra)
diff --git a/CMakeExternals/tinyxml.cmake b/CMakeExternals/tinyxml.cmake
index 74391bee27..3194143829 100644
--- a/CMakeExternals/tinyxml.cmake
+++ b/CMakeExternals/tinyxml.cmake
@@ -1,52 +1,52 @@
 #-----------------------------------------------------------------------------
 # tinyxml
 #-----------------------------------------------------------------------------
 
 # Sanity checks
 if(DEFINED tinyxml_DIR AND NOT EXISTS ${tinyxml_DIR})
   message(FATAL_ERROR "tinyxml_DIR variable is defined but corresponds to non-existing directory")
 endif()
 
 set(proj tinyxml)
 set(proj_DEPENDENCIES )
 set(${proj}_DEPENDS ${proj})
 
 if(NOT DEFINED tinyxml_DIR)
 
   set(additional_cmake_args )
   if(WIN32)
     set(additional_cmake_args -DBUILD_SHARED_LIBS:BOOL=OFF)
   endif()
 
   if(CTEST_USE_LAUNCHERS)
     list(APPEND additional_cmake_args
       "-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake"
     )
   endif()
 
   ExternalProject_Add(${proj}
      LIST_SEPARATOR ${sep}
      URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/tinyxml_2_6_2.tar.gz
      URL_MD5 c1b864c96804a10526540c664ade67f0
-     PATCH_COMMAND ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/tinyxml-2.6.2.patch
+     PATCH_COMMAND ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/tinyxml-2.6.2.patch --binary
        COMMAND ${CMAKE_COMMAND} -Dproj=${proj} -Dproj_target:STRING=tinyxml -P ${CMAKE_CURRENT_LIST_DIR}/GenerateDefaultCMakeBuildSystem.cmake
      CMAKE_GENERATOR ${gen}
      CMAKE_GENERATOR_PLATFORM ${gen_platform}
      CMAKE_ARGS
        ${ep_common_args}
        ${additional_cmake_args}
      CMAKE_CACHE_ARGS
        ${ep_common_cache_args}
      CMAKE_CACHE_DEFAULT_ARGS
        ${ep_common_cache_default_args}
      DEPENDS ${proj_DEPENDENCIES}
     )
 
   set(${proj}_DIR ${ep_prefix})
   mitkFunctionInstallExternalCMakeProject(${proj})
 
 else()
 
   mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
 
 endif()