-INCLUDE_DIRECTORIES(${PROJECT_SOURCE_DIR}/ilr/base)
-INCLUDE_DIRECTORIES(${PROJECT_SOURCE_DIR}/ilr/grid)
-INCLUDE_DIRECTORIES(${PROJECT_SOURCE_DIR}/ilr/gridtools)
-INCLUDE_DIRECTORIES(${PROJECT_SOURCE_DIR}/ilr/signal)
-INCLUDE_DIRECTORIES(${PROJECT_SOURCE_DIR}/ilr/pose)
-INCLUDE_DIRECTORIES(${PROJECT_SOURCE_DIR}/ilr/shearwarp)
-INCLUDE_DIRECTORIES(${PROJECT_SOURCE_DIR}/ilr/synergy)
-INCLUDE_DIRECTORIES(${PROJECT_SOURCE_DIR}/ilr/reconstruction)
-INCLUDE_DIRECTORIES(${PROJECT_SOURCE_DIR}/ilr/register)
-INCLUDE_DIRECTORIES(${PROJECT_SOURCE_DIR}/ilr/deformableregistration)
-INCLUDE_DIRECTORIES(${PROJECT_SOURCE_DIR}/ilr/optim)
-INCLUDE_DIRECTORIES(${PROJECT_SOURCE_DIR}/common)
-#INCLUDE_DIRECTORIES(${PROJECT_SOURCE_DIR}/tests)
-INCLUDE_DIRECTORIES(${PROJECT_SOURCE_DIR}/tools)
+INCLUDE_DIRECTORIES(${PROJECT_BINARY_DIR}/tools) #For _ggo.h includes from other directories
+INCLUDE_DIRECTORIES(${PROJECT_BINARY_DIR}/segmentation) #For _ggo.h includes from other directories
+INCLUDE_DIRECTORIES(${PROJECT_BINARY_DIR}/registration) #For _ggo.h includes from other directories
+#=========================================================
+
+#=========================================================
+# Building in the source tree is forbidden
+IF(PROJECT_BINARY_DIR STREQUAL ${PROJECT_SOURCE_DIR})
+ MESSAGE(FATAL_ERROR "Building in the source tree is not allowed ! Quit; remove the file 'CMakeCache.txt' and the folder 'CMakeFiles' an
+d build outside the sources (for example 'mkdir build ; cmake <CLITK_DIR>'.")
+ENDIF(PROJECT_BINARY_DIR STREQUAL ${PROJECT_SOURCE_DIR})
+#=========================================================
+
+#=========================================================
+# Remove some MS Visual c++ flags
+IF(MSVC)
+ ADD_DEFINITIONS(-D_CRT_SECURE_NO_WARNINGS -D_CRT_NONSTDC_NO_DEPRECATE -D_SCL_SECURE_NO_WARNINGS)
+ENDIF(MSVC)