BIC-MNI · Copilot · Mar 6, 2026 · Mar 6, 2026
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -3,9 +3,9 @@
 # Andrew Janke - a.janke@gmail.com
 # Vladimir S. FONOV - vladimir.fonov@gmail.com
 
-cmake_minimum_required(VERSION 3.10...4.2)
+cmake_minimum_required(VERSION 3.22...4.2)
 
-project(LIBMINC)
+project(LIBMINC LANGUAGES C CXX)
 
 set(LIBMINC_PACKAGE_VERSION_MAJOR 2)
 set(LIBMINC_PACKAGE_VERSION_MINOR 4)
@@ -34,7 +34,7 @@ set(LIBMINC_BUILD_V2 ON)
 
 if(NOT LIBMINC_EXTERNALLY_CONFIGURED)
   # Allowing User to configure parameters
-  set(CMAKE_MODULE_PATH "${CMAKE_MODULE_PATH}" "${CMAKE_CURRENT_SOURCE_DIR}/cmake-modules")
+  list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake-modules")
 
   set(CPACK_GENERATOR TGZ)
   set(CPACK_PACKAGE_VERSION_MAJOR ${LIBMINC_PACKAGE_VERSION_MAJOR})
@@ -109,8 +109,7 @@ endif()
 
 # add for building relocatable library
 if(UNIX)
-  set(CMAKE_C_FLAGS   "${CMAKE_C_FLAGS}   -fPIC")
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC")
+  set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 endif()
 
 
@@ -202,10 +201,9 @@ CHECK_INCLUDE_FILES(pwd.h       HAVE_PWD_H)
 CHECK_INCLUDE_FILES(sys/select.h    HAVE_SYS_SELECT_H)
 
 
-add_definitions(-DHAVE_CONFIG_H)
-add_definitions(-DMINC2=1)
+set(MINC_COMPILE_DEFINITIONS HAVE_CONFIG_H MINC2=1)
 if(NOT APPLE)
-add_definitions(-D_XOPEN_SOURCE=500)
+  list(APPEND MINC_COMPILE_DEFINITIONS _XOPEN_SOURCE=500)
 endif()
 # aliases
 set(VERSION "${LIBMINC_EXTERNAL_LIB_PREFIX}${LIBMINC_PACKAGE_VERSION}")
@@ -214,14 +212,14 @@ set(HAVE_MINC2 ON)
 set(MINC2 "1")
 
 if(LIBMINC_MINC1_SUPPORT)
- add_definitions(-DHAVE_MINC1=1)
+ list(APPEND MINC_COMPILE_DEFINITIONS HAVE_MINC1=1)
 endif()
 
 if(LIBMINC_BUILD_EZMINC)
   set(LIBMINC_INCLUDE_DIRS_CONFIG
     ${CMAKE_CURRENT_SOURCE_DIR}/ezminc
   )
-  include_directories(
+  list(APPEND MINC_INCLUDE_DIRS
     ${CMAKE_CURRENT_SOURCE_DIR}/ezminc
    )
 endif()
@@ -242,22 +240,21 @@ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/config.h.cmake ${CMAKE_CURRENT_BINARY
 #configure_file(${CMAKE_CURRENT_SOURCE_DIR}/epm-header.in ${CMAKE_CURRENT_BINARY_DIR}/epm-header)
 
 # set the master INCLUDE directories
-include_directories(
+list(APPEND MINC_INCLUDE_DIRS
    ${CMAKE_CURRENT_SOURCE_DIR}
    ${CMAKE_CURRENT_BINARY_DIR}
    ${CMAKE_CURRENT_SOURCE_DIR}/libcommon
    ${CMAKE_CURRENT_SOURCE_DIR}/libsrc2
    ${CMAKE_CURRENT_SOURCE_DIR}/libsrc
    ${CMAKE_CURRENT_SOURCE_DIR}/volume_io/Include
-   ${HDF5_INCLUDE_DIRS}
    )
 
 if(LIBMINC_BUILD_EZMINC AND LIBMINC_MINC1_SUPPORT)
-  include_directories( ${CMAKE_CURRENT_SOURCE_DIR}/ezminc )
+  list(APPEND MINC_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/ezminc)
 endif()
 
 if(LIBMINC_NIFTI_SUPPORT)
-    include_directories(
+    list(APPEND MINC_INCLUDE_DIRS
         ${NIFTI_INCLUDE_DIR}
     )
 endif()
@@ -456,6 +453,9 @@ set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR})
 
 add_library(${LIBMINC_LIBRARY} ${LIBRARY_TYPE} ${minc_LIB_SRCS} ${minc_HEADERS} ${volume_io_LIB_SRCS} ${volume_io_HEADERS} )
 
+target_include_directories(${LIBMINC_LIBRARY} PUBLIC ${MINC_INCLUDE_DIRS} ${HDF5_INCLUDE_DIRS})
+target_compile_definitions(${LIBMINC_LIBRARY} PUBLIC ${MINC_COMPILE_DEFINITIONS})
+
 if(NIFTI_FOUND AND NOT LIBMINC_USE_SYSTEM_NIFTI)
     add_dependencies(${LIBMINC_LIBRARY} NIFTI)
 endif()
@@ -464,7 +464,7 @@ endif()
 target_link_libraries(${LIBMINC_LIBRARY} ${HDF5_LIBRARY} ${NIFTI_LIBRARIES} ${ZLIB_LIBRARY} ${RT_LIBRARY}) #
 
 if(LIBMINC_MINC1_SUPPORT)
-  include_directories(${NETCDF_INCLUDE_DIR})
+  target_include_directories(${LIBMINC_LIBRARY} PUBLIC ${NETCDF_INCLUDE_DIR})
   target_link_libraries(${LIBMINC_LIBRARY} ${NETCDF_LIBRARY})
   get_filename_component(NETCDF_LIBRARY_NAME "${NETCDF_LIBRARY}" NAME)
 else()
@@ -482,6 +482,8 @@ if(UNIX)
 
   if(LIBMINC_BUILD_SHARED_LIBS)
     add_library(${LIBMINC_LIBRARY_STATIC} STATIC ${minc_LIB_SRCS} ${minc_HEADERS} ${volume_io_LIB_SRCS} ${volume_io_HEADERS} )
+    target_include_directories(${LIBMINC_LIBRARY_STATIC} PUBLIC ${MINC_INCLUDE_DIRS} ${HDF5_INCLUDE_DIRS})
+    target_compile_definitions(${LIBMINC_LIBRARY_STATIC} PUBLIC ${MINC_COMPILE_DEFINITIONS})
     target_link_libraries(${LIBMINC_LIBRARY_STATIC} ${HDF5_LIBRARY} ${NIFTI_LIBRARIES} ${ZLIB_LIBRARY} ${RT_LIBRARY} m ${CMAKE_DL_LIBS} )
     if(LIBMINC_MINC1_SUPPORT)
       target_link_libraries(${LIBMINC_LIBRARY} ${NETCDF_LIBRARY})

diff --git a/UseLIBMINC.cmake.in b/UseLIBMINC.cmake.in
@@ -1,16 +1,16 @@
-include_directories(${LIBMINC_INCLUDE_DIRS})
+# Usage: Downstream projects should prefer using target_link_libraries()
+# with the imported LIBMINC targets. This file provides backward-compatible
+# variable-based configuration.
+
+# Legacy include/link directory variables for projects not using
+# target-based dependencies directly:
+# LIBMINC_INCLUDE_DIRS, LIBMINC_LIBRARY_DIRS, LIBMINC_LIBRARIES
 
 if(HAVE_MINC1)
   add_definitions( -DHAVE_MINC1=1)
-
-  include_directories(${NETCDF_INCLUDE_DIR})
 endif()
 
 if(HAVE_MINC2)
   set(MINC2 "1")
   add_definitions( -DMINC2=1 -DHAVE_MINC2=1)
-
-  include_directories(${HDF5_INCLUDE_DIR})
 endif()
-
-link_directories(${LIBMINC_LIBRARY_DIRS})
diff --git a/cmake-modules/FindNETCDF.cmake b/cmake-modules/FindNETCDF.cmake
@@ -1,23 +1,15 @@
 # FindNetCDF.cmake module
 
+include(FindPackageHandleStandardArgs)
 
-find_path(NETCDF_INCLUDE_DIR netcdf.h /usr/include /usr/local/include /usr/local/bic/include)
+find_path(NETCDF_INCLUDE_DIR netcdf.h)
 
-find_library(NETCDF_LIBRARY NAMES netcdf PATHS /usr/lib /usr/local/lib /usr/local/bic/lib)
+find_library(NETCDF_LIBRARY NAMES netcdf)
 
+find_package_handle_standard_args(NETCDF
+  REQUIRED_VARS NETCDF_LIBRARY NETCDF_INCLUDE_DIR
+)
 
-if (NETCDF_INCLUDE_DIR AND NETCDF_LIBRARY)
-   set(NETCDF_FOUND TRUE)
-endif ()
-
-
-if (NETCDF_FOUND)
-   if (NOT NETCDF_FIND_QUIETLY)
-      message(STATUS "Found NetCDF headers: ${NETCDF_INCLUDE_DIR}")
-      message(STATUS "Found NetCDF library: ${NETCDF_LIBRARY}")
-   endif ()
-else ()
-   if (NETCDF_FIND_REQUIRED)
-      message(FATAL_ERROR "Could not find NetCDF")
-   endif ()
-endif ()
+if(NETCDF_FOUND)
+  mark_as_advanced(NETCDF_INCLUDE_DIR NETCDF_LIBRARY)
+endif()
diff --git a/cmake-modules/FindNIFTI.cmake b/cmake-modules/FindNIFTI.cmake
@@ -1,29 +1,19 @@
 # FindNIFTI.cmake module
 
+include(FindPackageHandleStandardArgs)
 
-find_path(NIFTI_INCLUDE_DIR nifti1_io.h /usr/include /usr/local/include /usr/local/bic/include)
+find_path(NIFTI_INCLUDE_DIR nifti1_io.h)
 
-find_library(NIFTI_LIBRARY NAMES niftiio PATHS /usr/lib /usr/local/lib /usr/local/bic/lib)
+find_library(NIFTI_LIBRARY NAMES niftiio)
 
-find_path(ZNZ_INCLUDE_DIR znzlib.h /usr/include /usr/local/include /usr/local/bic/include)
+find_path(ZNZ_INCLUDE_DIR znzlib.h)
 
-find_library(ZNZ_LIBRARY NAMES znz PATHS /usr/lib /usr/local/lib /usr/local/bic/lib)
+find_library(ZNZ_LIBRARY NAMES znz)
 
+find_package_handle_standard_args(NIFTI
+  REQUIRED_VARS NIFTI_LIBRARY NIFTI_INCLUDE_DIR ZNZ_LIBRARY ZNZ_INCLUDE_DIR
+)
 
-if (NIFTI_INCLUDE_DIR AND NIFTI_LIBRARY AND ZNZ_INCLUDE_DIR AND ZNZ_LIBRARY)
-   set(NIFTI_FOUND TRUE)
-endif ()
-
-
-if (NIFTI_FOUND)
-   if (NOT NIFTI_FIND_QUIETLY)
-      message(STATUS "Found NetCDF headers: ${NIFTI_INCLUDE_DIR}")
-      message(STATUS "Found NetCDF library: ${NIFTI_LIBRARY}")
-      message(STATUS "Found znzlib headers: ${ZNZ_INCLUDE_DIR}")
-      message(STATUS "Found znzlib library: ${ZNZ_LIBRARY}")
-   endif ()
-else ()
-   if (NIFTI_FIND_REQUIRED)
-      message(FATAL_ERROR "Could not find NIfTI-1 I/O library")
-   endif ()
-endif ()
+if(NIFTI_FOUND)
+  mark_as_advanced(NIFTI_INCLUDE_DIR NIFTI_LIBRARY ZNZ_INCLUDE_DIR ZNZ_LIBRARY)
+endif()
diff --git a/ezminc/CMakeLists.txt b/ezminc/CMakeLists.txt
@@ -1,5 +1,5 @@
 if(LIBMINC_BUILD_V2)
-  add_definitions( -DMINC2 )
+  set(MINC_IO_DEFINITIONS MINC2)
 endif()
 
 
@@ -18,8 +18,9 @@ set( MINC_IO_SRC
     minc_1_simple_rw.cpp
   )
 
-include_directories( ${CMAKE_CURRENT_SOURCE_DIR})
 add_library( minc_io ${LIBRARY_TYPE} ${MINC_IO_HEADERS} ${MINC_IO_SRC})
+target_include_directories(minc_io PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
+target_compile_definitions(minc_io PUBLIC ${MINC_IO_DEFINITIONS})
 target_link_libraries(minc_io ${LIBMINC_LIBRARIES})
 
 set_target_properties(minc_io

diff --git a/ezminc/examples/CMakeLists.txt b/ezminc/examples/CMakeLists.txt
@@ -1,6 +1,8 @@
-link_libraries(minc_io)
-
 add_executable(trilinear_resample trilinear_resample.cpp)
+target_link_libraries(trilinear_resample minc_io)
 add_executable(volume_avg volume_avg.cpp)
+target_link_libraries(volume_avg minc_io)
 add_executable(volume_msq_dist volume_msq_dist.cpp)
+target_link_libraries(volume_msq_dist minc_io)
 add_executable(create_grid_file create_grid_file.cpp)
+target_link_libraries(create_grid_file minc_io)
diff --git a/ezminc/tests/CMakeLists.txt b/ezminc/tests/CMakeLists.txt
@@ -1,11 +1,11 @@
-link_libraries(minc_io ${LIBMINC_LIBRARIES})
-
 add_executable(ezminc_rw_test ezminc_rw_test.cpp)
+target_link_libraries(ezminc_rw_test minc_io ${LIBMINC_LIBRARIES})
 #add_executable(ezminc_stats   ezminc_stats.cpp)
 
 add_test(ezminc_rw_test ezminc_rw_test ${CMAKE_CURRENT_BINARY_DIR})
 
 add_executable(ezminc_rw_test2 minc_rw_test2.cpp)
+target_link_libraries(ezminc_rw_test2 minc_io ${LIBMINC_LIBRARIES})
 
 
 if(MINC_TEST_ENVIRONMENT)

diff --git a/testdir/CMakeLists.txt b/testdir/CMakeLists.txt
@@ -1,6 +1,3 @@
-link_libraries(${LIBMINC_LIBRARIES})
-
-
 macro(minc_test cmd)
   # minc 1 version
   if(HAVE_MINC1)
@@ -64,6 +61,11 @@ if(LIBMINC_MINC1_SUPPORT)
   add_executable(minc_long_attr minc_long_attr.c)
   add_executable(minc_conversion minc_conversion.c)
 
+  foreach(_target minc_tst icv icv_vec icv_dim1 icv_dim icv_fillvalue icv_range
+                  mincapi minc_types test_mconv minc_long_attr minc_conversion)
+    target_link_libraries(${_target} ${LIBMINC_LIBRARIES})
+  endforeach()
+
   # running tests
   minc_test(minc_types)
   minc_test(icv_dim1)
@@ -94,9 +96,11 @@ endif()
 
 # Volume IO tests
 add_executable(volume_test volume_test.c)
+target_link_libraries(volume_test ${LIBMINC_LIBRARIES})
 add_test(volume_test-1 volume_test)
 
 add_executable(multidim_test multidim_test.c)
+target_link_libraries(multidim_test ${LIBMINC_LIBRARIES})
 add_test(volume_multidim_test multidim_test)
 
 add_executable(test_xfm   vio_xfm_test/test-xfm.c)
@@ -151,6 +155,7 @@ set_property(TEST verify_xfm_2 APPEND PROPERTY DEPENDS copy_xfm)
 
 #common tests
 add_executable(test_arg_parse test_arg_parse.c)
+target_link_libraries(test_arg_parse ${LIBMINC_LIBRARIES})
 add_minc_test(test_arg_parse test_arg_parse)
 
 
@@ -179,6 +184,15 @@ add_executable(minc2-read-metadata minc2-read-metadata.c)
 add_executable(minc2-leak-test minc2-leak-test.c)
 add_executable(minc2-float-voxel-test minc2-float-voxel-test.c)
 
+foreach(_target minc2-convert-test minc2-create-test-images-2 minc2-create-test-images
+                minc2-datatype-test minc2-large-attribute minc2-dimension-test
+                minc2-full-test minc2-grpattr-test minc2-hyper-test-2 minc2-hyper-test
+                minc2-label-test minc2-multires-test minc2-record-test minc2-slice-test
+                minc2-valid-test minc2-vector_dimension-test minc2-volprops-test
+                minc2-read-rgb minc2-read-metadata minc2-leak-test minc2-float-voxel-test)
+  target_link_libraries(${_target} ${LIBMINC_LIBRARIES})
+endforeach()
+
 add_minc_test(minc2-convert-test          minc2-convert-test)
 add_minc_test(minc2-create-test-images    minc2-create-test-images
                                           ${CMAKE_CURRENT_BINARY_DIR}/2D_minc2.mnc