diff --git a/BEaST b/BEaST
index f7f196c..9556820 160000
--- a/BEaST
+++ b/BEaST
@@ -1 +1 @@
-Subproject commit f7f196ca1e268c9302a1041c777246950e252ed6
+Subproject commit 955682091cef1c52ee541d0285c512069dbe0a3b
diff --git a/BEaST_library b/BEaST_library
index 03b69f9..11d2088 160000
--- a/BEaST_library
+++ b/BEaST_library
@@ -1 +1 @@
-Subproject commit 03b69f9788bab3da6564887ff260453ce2755ef0
+Subproject commit 11d2088e118f1c11938ced4d291b459ae826f563
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 17984b3..5e9bf72 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,397 +1,404 @@
-project(minc-toolkit)
-enable_language(C)
-enable_language(CXX)
-
-cmake_minimum_required(VERSION 2.6)
-
-SET(MINC_TOOLKIT_PACKAGE_VERSION_MAJOR 0)
-SET(MINC_TOOLKIT_PACKAGE_VERSION_MINOR 3)
-SET(MINC_TOOLKIT_PACKAGE_VERSION_PATCH 16)
-SET(MINC_TOOLKIT_RELEASE_DATE "20121113")
-
-SET(MINC_TOOLKIT_VERSION_FULL "${MINC_TOOLKIT_PACKAGE_VERSION_MAJOR}.${MINC_TOOLKIT_PACKAGE_VERSION_MINOR}.${MINC_TOOLKIT_PACKAGE_VERSION_PATCH}-${MINC_TOOLKIT_RELEASE_DATE}")
-
-#SET(CPACK_GENERATOR DEB)
-SET(CPACK_PACKAGE_NAME "minc-toolkit")
-SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "minc image processing toolkit")
-SET(CPACK_PACKAGE_VENDOR "Brain Imaging Center, Montreal Neurological Institute, McGill University")
-SET(CPACK_PACKAGE_VERSION_MAJOR ${MINC_TOOLKIT_PACKAGE_VERSION_MAJOR})
-SET(CPACK_PACKAGE_VERSION_MINOR ${MINC_TOOLKIT_PACKAGE_VERSION_MINOR})
-SET(CPACK_PACKAGE_VERSION_PATCH ${MINC_TOOLKIT_PACKAGE_VERSION_PATCH})
-SET(CPACK_PACKAGE_CONTACT "Vladimir Fonov <vladmir.fonov@gmail.com>")
-SET(CPACK_PACKAGE_INSTALL_DIRECTORY "minc-toolkit-${MINC_TOOLKIT_VERSION_FULL}")
-SET(CPACK_MONOLITHIC_INSTALL ON)
-SET(CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_SOURCE_DIR}/README.md")
-SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
-
-#IF (CMAKE_SYSTEM_PROCESSOR MATCHES "unknown")
-EXEC_PROGRAM(uname ARGS "-m" OUTPUT_VARIABLE CMAKE_SYSTEM_PROCESSOR)
-#ENDIF (CMAKE_SYSTEM_PROCESSOR MATCHES "unknown")
-
-IF(NOT DEFINED CPACK_SYSTEM_NAME)
-  SET(MT_SYSTEM_NAME ${CMAKE_SYSTEM_NAME}-${CMAKE_SYSTEM_PROCESSOR})
-ENDIF(NOT DEFINED CPACK_SYSTEM_NAME)
-
-IF(${CMAKE_SYSTEM_NAME} MATCHES Windows)
-  IF(CMAKE_CL_64)
-    SET(MT_SYSTEM_NAME win64-${CMAKE_SYSTEM_PROCESSOR})
-  ELSE(CMAKE_CL_64)
-    SET(MT_SYSTEM_NAME win32-${CMAKE_SYSTEM_PROCESSOR})
-  ENDIF(CMAKE_CL_64)
-ELSE(${CMAKE_SYSTEM_NAME} MATCHES Windows)
-  IF(${CMAKE_SYSTEM_NAME} MATCHES Linux )
-    EXEC_PROGRAM(lsb_release ARGS "-s -i" OUTPUT_VARIABLE SYSTEM_ID)
-    EXEC_PROGRAM(lsb_release ARGS "-s -r" OUTPUT_VARIABLE SYSTEM_RELEASE)
-    SET(MT_SYSTEM_NAME "${SYSTEM_ID}_${SYSTEM_RELEASE}-${CMAKE_SYSTEM_PROCESSOR}")
-  ENDIF(${CMAKE_SYSTEM_NAME} MATCHES Linux )
-ENDIF(${CMAKE_SYSTEM_NAME} MATCHES Windows)
-
-SET(CPACK_PACKAGE_FILE_NAME "minc-toolkit-${MINC_TOOLKIT_VERSION_FULL}-${MT_SYSTEM_NAME}")
-
-# register local modules
-SET(CMAKE_MODULE_PATH "${CMAKE_MODULE_PATH}" "${CMAKE_SOURCE_DIR}/cmake-modules")
-INCLUDE(PreventInSourceBuilds)
-AssureOutOfSourceBuilds(minc-toolkit)
-
-# default install directories
-SET(CMAKE_INSTALL_PREFIX ${CMAKE_CURRENT_BINARY_DIR} CACHE PATH "Install path prefix, prepended onto install directories.")
-SET(CPACK_SET_DESTDIR    ON)
-SET(CPACK_PACKAGING_INSTALL_PREFIX ${CMAKE_INSTALL_PREFIX})
-SET(CPACK_STRIP_FILES ON)
-
-# superbuild options
-OPTION(MT_BUILD_LITE         "Build lite version of minc-toolkit, without ITK or visual tools" OFF)
-OPTION(MT_BUILD_SHARED_LIBS  "Build shared libraries." OFF)
-OPTION(USE_SYSTEM_ZLIB       "Use System ZLIB "       OFF)
-OPTION(USE_SYSTEM_NETCDF     "Use System NETCDF > 3.6.3" OFF)
-OPTION(USE_SYSTEM_HDF5       "Use System HDF5 > 1.8"     OFF)
-OPTION(USE_SYSTEM_PCRE       "Use System PCRE "       OFF)
-OPTION(USE_SYSTEM_GSL        "Use System GSL "        OFF)
-OPTION(USE_SYSTEM_FFTW3F     "Use System FFTW3F "     OFF)
-OPTION(MT_BUILD_ITK_TOOLS    "Build ITK-based tools"  OFF)
-OPTION(MT_BUILD_VISUAL_TOOLS "Build visual tools (Display, Register, postf, ray_trace) requires OpenGL & Glut"  OFF)
-OPTION(USE_SYSTEM_ITK        "Use System ITK" OFF)
-
-IF(MT_BUILD_LITE)
-  SET(MT_BUILD_ITK_TOOLS OFF)
-  SET(MT_BUILD_VISUAL_TOOLS OFF)
-  SET(MT_BUILD_MINC_ANTS OFF)
-  SET(MT_BUILD_C3D OFF)
-  
-  SET(CPACK_PACKAGE_FILE_NAME "minc-toolkit-${MINC_TOOLKIT_VERSION_FULL}-${MT_SYSTEM_NAME}-lite")
-ENDIF(MT_BUILD_LITE)
-
-ENABLE_TESTING()
-INCLUDE(CTest)
-
-# provide test environement
-# CACHE INTERNAL FORCE
-SET(MINC_TEST_ENVIRONMENT 
- "PATH=${CMAKE_CURRENT_BINARY_DIR}:${CMAKE_CURRENT_BINARY_DIR}/N3:${CMAKE_CURRENT_BINARY_DIR}/classify:${CMAKE_CURRENT_BINARY_DIR}/minctools/progs:${CMAKE_CURRENT_BINARY_DIR}/mni_autoreg/mincblur:${CMAKE_CURRENT_BINARY_DIR}/mni_autoreg/make_phantom:${CMAKE_CURRENT_BINARY_DIR}/mni_autoreg/minctracc:$ENV{PATH};PERL5LIB=${CMAKE_SOURCE_DIR}/mni-perllib:${CMAKE_CURRENT_BINARY_DIR}/mni-perllib/perl:${CMAKE_CURRENT_BINARY_DIR}/perl-modules:$ENV{PERL5LIB}"
-)
-
-# for superbuild
-IF(USE_SYSTEM_ZLIB AND USE_SYSTEM_NETCDF AND USE_SYSTEM_HDF5  AND USE_SYSTEM_PCRE  AND USE_SYSTEM_GSL AND USE_SYSTEM_FFTW3F AND USE_SYSTEM_ITK)
-  SET(USE_SUPERBUILD OFF)
-ELSE(USE_SYSTEM_ZLIB AND USE_SYSTEM_NETCDF AND USE_SYSTEM_HDF5  AND USE_SYSTEM_PCRE AND USE_SYSTEM_GSL AND USE_SYSTEM_FFTW3F AND USE_SYSTEM_ITK)
-  INCLUDE(ExternalProject)
-  SET(USE_SUPERBUILD ON)
-  INCLUDE(ConfigureExternalProjects)
-ENDIF(USE_SYSTEM_ZLIB AND USE_SYSTEM_NETCDF AND USE_SYSTEM_HDF5  AND USE_SYSTEM_PCRE  AND USE_SYSTEM_GSL AND USE_SYSTEM_FFTW3F AND USE_SYSTEM_ITK)
-
-SET(SUPERBUILD_STAGING_PREFIX ${CMAKE_BINARY_DIR}/external)
-
-# required packages
-FIND_PACKAGE( Perl   REQUIRED )
-# required for minc
-IF(USE_SYSTEM_ZLIB)
-  FIND_PACKAGE( ZLIB   REQUIRED )
-ELSE(USE_SYSTEM_ZLIB)
-  INCLUDE(BuildZLIB)
-  build_zlib( ${CMAKE_INSTALL_PREFIX} ${SUPERBUILD_STAGING_PREFIX})
-ENDIF(USE_SYSTEM_ZLIB)
-
-IF(USE_SYSTEM_NETCDF)
-  FIND_PACKAGE( NETCDF REQUIRED )
-ELSE(USE_SYSTEM_NETCDF)
-  INCLUDE(BuildNETCDF)
-  build_netcdf( ${CMAKE_INSTALL_PREFIX} ${SUPERBUILD_STAGING_PREFIX})
-ENDIF(USE_SYSTEM_NETCDF)
-
-IF(USE_SYSTEM_HDF5)
-  FIND_PACKAGE( HDF5   REQUIRED )
-ELSE(USE_SYSTEM_HDF5)
-  INCLUDE(BuildHDF5)
-  build_hdf5( ${CMAKE_INSTALL_PREFIX} ${SUPERBUILD_STAGING_PREFIX} ${ZLIB_INCLUDE_DIR} ${ZLIB_LIBRARY})
-  IF(NOT USE_SYSTEM_ZLIB)
-    add_dependencies(HDF5 ZLIB)
-  ENDIF(NOT USE_SYSTEM_ZLIB)
-ENDIF(USE_SYSTEM_HDF5)
-
-#required for some minc tools
-FIND_PACKAGE( BISON )
-FIND_PACKAGE( FLEX )
-FIND_PACKAGE( Threads)
-
-#required for bicpl
-IF(USE_SYSTEM_NETPBM) # else we will use bundled libppm
-  FIND_PACKAGE( NETPBM QUIET )
-ENDIF(USE_SYSTEM_NETPBM)
-
-#required for oobicpl
-IF(USE_SYSTEM_PCRE)
-  FIND_PACKAGE( PCRE QUIET )
-ELSE(USE_SYSTEM_PCRE)
-  INCLUDE(BuildPCRE)
-  build_pcre(${CMAKE_INSTALL_PREFIX} ${SUPERBUILD_STAGING_PREFIX})
-ENDIF(USE_SYSTEM_PCRE)
-
-
-SET(MINC_TOOLKIT_BUILD ON)
-SET(MINC_TOOLKIT_BUILD_DIR   ${CMAKE_BINARY_DIR})
-SET(MINC_TOOLKIT_INSTALL_DIR ${CMAKE_INSTALL_PREFIX})
-
-#setup parameters
-#MINC2
-SET(LIBMINC_BUILD_V2           ON)
-SET(LIBMINC_FOUND              ON)
-SET(LIBMINC_BUILD_TOOLS        ON)
-SET(LIBMINC_BUILD_CONVERTERS   ON)
-SET(LIBMINC_BUILD_EZMINC       ON)
-SET(LIBMINC_BUILD_EZMINC_EXAMPLES ON)
-
-IF(MT_BUILD_SHARED_LIBS)
-  SET(LIBMINC_BUILD_SHARED_LIBS      ON)
-  #EBTKS
-  SET(EBTKS_BUILD_SHARED_LIBS      OFF)
-  #bicpl
-  SET(BICPL_BUILD_SHARED_LIBS      ON)
-  #oobicpl
-  SET(OOBICPL_BUILD_SHARED_LIBS    ON)
-  #arguments
-  SET(ARGUMENTS_BUILD_SHARED_LIBS  ON)
-  #bicgl
-  SET(BICGL_BUILD_SHARED_LIBS      ON)
-ELSE(MT_BUILD_SHARED_LIBS)
-
-  SET(LIBMINC_BUILD_SHARED_LIBS      OFF)
-  #EBTKS
-  SET(EBTKS_BUILD_SHARED_LIBS      OFF)
-  #bicpl
-  SET(BICPL_BUILD_SHARED_LIBS      OFF)
-  #oobicpl
-  SET(OOBICPL_BUILD_SHARED_LIBS    OFF)
-  #arguments
-  SET(ARGUMENTS_BUILD_SHARED_LIBS  OFF)
-  #bicgl
-  SET(BICGL_BUILD_SHARED_LIBS      OFF)
-ENDIF(MT_BUILD_SHARED_LIBS)
-
-
-#EZMINC
-SET(EZMINC_BUILD_MINCNLM  ON)
-SET(EZMINC_BUILD_DISTORTION_CORRECTION  ON)
-SET(EZMINC_BUILD_MRFSEG  ON)
-SET(EZMINC_BUILD_DD      ON)
-SET(EZMINC_BUILD_TOOLS   ON)
-
-ADD_SUBDIRECTORY(libminc)
-
-IF(NOT USE_SYSTEM_NETCDF)
-  ADD_DEPENDENCIES(minc2 NETCDF)
-ENDIF(NOT USE_SYSTEM_NETCDF)
-
-IF(NOT USE_SYSTEM_HDF5)
-  ADD_DEPENDENCIES(minc2 HDF5)
-ENDIF(NOT USE_SYSTEM_HDF5)
-
-# Setup main minc variables
-SET(LIBMINC_USE_FILE ${CMAKE_BINARY_DIR}/libminc/UseLIBMINC.cmake CACHE INTERNAL "LIBMINC use file")
-INCLUDE(${CMAKE_BINARY_DIR}/libminc/LIBMINCConfig.cmake)
-INCLUDE(${LIBMINC_USE_FILE})
-
-ADD_SUBDIRECTORY(minctools)
-ADD_SUBDIRECTORY(EBTKS)
-ADD_DEPENDENCIES(EBTKS minc2)
-
-# setup EBTKS variables
-SET(EBTKS_USE_FILE ${CMAKE_BINARY_DIR}/EBTKS/UseEBTKS.cmake CACHE INTERNAL "EBTKS use file")
-INCLUDE(${CMAKE_BINARY_DIR}/EBTKS/EBTKSConfig.cmake)
-INCLUDE(${EBTKS_USE_FILE})
-
-ADD_SUBDIRECTORY(bicpl)
-ADD_DEPENDENCIES(bicpl minc2)
-
-#setup bicpl variables
-SET(BICPL_USE_FILE ${CMAKE_BINARY_DIR}/bicpl/UseBICPL.cmake CACHE INTERNAL "BICPL use file")
-INCLUDE(${CMAKE_BINARY_DIR}/bicpl/BICPLConfig.cmake)
-INCLUDE(${BICPL_USE_FILE})
-IF(NOT USE_SYSTEM_NETPBM)
-  ADD_DEPENDENCIES(bicpl NETPBM)
-ENDIF(NOT USE_SYSTEM_NETPBM)
-
-ADD_SUBDIRECTORY(arguments)
-
-#setup arguments variables
-SET(ARGUMENTS_USE_FILE ${CMAKE_BINARY_DIR}/bicpl/UseARGUMENTS.cmake CACHE INTERNAL "ARGUMENTS use file")
-INCLUDE(${CMAKE_BINARY_DIR}/arguments/ARGUMENTSConfig.cmake)
-INCLUDE(${ARGUMENTS_USE_FILE})
-
-ADD_SUBDIRECTORY(oobicpl)
-ADD_DEPENDENCIES(oobicpl minc2 bicpl arguments)
-
-#setup oobicpl variables
-SET(OOBICPL_USE_FILE ${CMAKE_BINARY_DIR}/bicpl/UseOOBICPL.cmake CACHE INTERNAL "OOBICPL use file")
-INCLUDE(${CMAKE_BINARY_DIR}/oobicpl/OOBICPLConfig.cmake)
-INCLUDE(${OOBICPL_USE_FILE})
-
-ADD_SUBDIRECTORY(BEaST)
-ADD_SUBDIRECTORY(BEaST_library)
-ADD_SUBDIRECTORY(conglomerate)
-ADD_SUBDIRECTORY(classify)
-ADD_SUBDIRECTORY(mni-perllib)
-ADD_SUBDIRECTORY(N3)
-
-ADD_SUBDIRECTORY(glim_image)
-ADD_SUBDIRECTORY(mni_autoreg)
-ADD_SUBDIRECTORY(inormalize)
-ADD_SUBDIRECTORY(mrisim)
-ADD_SUBDIRECTORY(bic-pipelines)
-ADD_SUBDIRECTORY(perl-modules)
-
-# build tools that require ITK
-IF(MT_BUILD_ITK_TOOLS)
-
-  OPTION(MT_BUILD_MINC_ANTS "Build mincANTS " OFF)
-  OPTION(MT_BUILD_C3D "Build convert3D " OFF)
-
-  SET(HAVE_MINC4ITK  ON)
-
-  #required for minc4itk & EZminc
-  IF(USE_SYSTEM_ITK)
-    FIND_PACKAGE(ITK )
-  ELSE(USE_SYSTEM_ITK)
-    INCLUDE(BuildITKv3)  
-    build_itkv3(${CMAKE_INSTALL_PREFIX} ${SUPERBUILD_STAGING_PREFIX} )
-  ENDIF(USE_SYSTEM_ITK)
-
-  #required for EZminc
-  IF(USE_SYSTEM_GSL)
-    FIND_PACKAGE(GSL)
-  ELSE(USE_SYSTEM_GSL)  
-    INCLUDE(BuildGSL)
-    build_gsl(${CMAKE_INSTALL_PREFIX} ${SUPERBUILD_STAGING_PREFIX})
-  ENDIF(USE_SYSTEM_GSL)
-
-  IF(USE_SYSTEM_FFTW3F)
-    FIND_PACKAGE(FFTW3F)
-  ELSE(USE_SYSTEM_FFTW3)
-    INCLUDE(BuildFFTW3F)
-    build_fftw3f(${CMAKE_INSTALL_PREFIX} ${SUPERBUILD_STAGING_PREFIX})
-  ENDIF(USE_SYSTEM_FFTW3F)
-
-  # minc4itk integration library
-  ADD_SUBDIRECTORY(minc4itk)
-  INCLUDE(${CMAKE_CURRENT_BINARY_DIR}/minc4itk/MINC4ITKConfig.cmake)
-  # setup minc4itk variables
-  SET(MINC4ITK_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/minc4itk/include)
-  SET(MINC4ITK_LIBRARY_DIRS ${CMAKE_BINARY_DIR}/minc4itk/)
-  
-  ADD_DEPENDENCIES(ITKIOMINC minc2)
-  
-  IF(NOT USE_SYSTEM_ITK)
-    ADD_DEPENDENCIES(ITKIOMINC ITKv3)
-  ENDIF(NOT USE_SYSTEM_ITK)
-  
-  ADD_SUBDIRECTORY(EZminc)
-  ADD_DEPENDENCIES(minc_image_proc minc2)
-  ADD_DEPENDENCIES(mincnlm minc2)
-  ADD_DEPENDENCIES(mrfseg minc2)
-  ADD_DEPENDENCIES(mrflib minc2)
-  
-  IF(MT_BUILD_MINC_ANTS)
-    ADD_SUBDIRECTORY(mincANTS)
-    ADD_DEPENDENCIES(mincANTS ITKIOMINC minc2)
-  ENDIF(MT_BUILD_MINC_ANTS)
-  
-  IF(MT_BUILD_C3D)
-    ADD_SUBDIRECTORY(c3d)
-    ADD_DEPENDENCIES(c3d ITKIOMINC minc2)
-    ADD_DEPENDENCIES(c2d ITKIOMINC minc2)
-  ENDIF(MT_BUILD_C3D)
-  
-  
-  IF(NOT USE_SYSTEM_ITK)
-    ADD_DEPENDENCIES(ITKIOMINC ITKv3)
-  ENDIF(NOT USE_SYSTEM_ITK)
-  
-  IF(NOT USE_SYSTEM_GSL)
-    ADD_DEPENDENCIES(minc_image_proc GSL)
-  ENDIF(NOT USE_SYSTEM_GSL)
-  
-  IF(NOT USE_SYSTEM_FFTW3F)
-    ADD_DEPENDENCIES(minc_image_proc FFTW3F)
-  ENDIF(NOT USE_SYSTEM_FFTW3F)
-ENDIF(MT_BUILD_ITK_TOOLS)
-
-# build tools that require OpenGL and GLUT
-IF(MT_BUILD_VISUAL_TOOLS)
-  FIND_PACKAGE( OpenGL REQUIRED )
-  FIND_PACKAGE( GLUT REQUIRED )
-  FIND_PACKAGE( X11 QUIET )
-
-  ADD_SUBDIRECTORY(bicgl)
-  INCLUDE(${CMAKE_BINARY_DIR}/bicgl/BICGLConfig.cmake)
-  
-  ADD_SUBDIRECTORY(ray_trace)
-  ADD_DEPENDENCIES(ray_trace bicgl minc2 bicpl)
-
-  ADD_SUBDIRECTORY(Display)
-  ADD_DEPENDENCIES(Display bicgl minc2 bicpl)
-  
-  ADD_SUBDIRECTORY(Register)
-  ADD_DEPENDENCIES(register bicgl minc2 bicpl)
-
-  IF(X11_FOUND)
-    ADD_SUBDIRECTORY(postf)
-    ADD_DEPENDENCIES(postf minc2)
-  ENDIF(X11_FOUND)
-ENDIF(MT_BUILD_VISUAL_TOOLS)
-
-# DO nothing?
-IF(USE_SUPERBUILD)
-  #install external dependencies to final destination
-  INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/bin
-        DESTINATION . 
-        PATTERN *
-        PERMISSIONS OWNER_EXECUTE OWNER_READ OWNER_WRITE GROUP_EXECUTE GROUP_READ WORLD_READ WORLD_EXECUTE )
-  
-  INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}
-        DESTINATION .)
-  
-  INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/include
-        DESTINATION .)
-  
-  # do we really need to install share?
-  INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/share
-        DESTINATION .)
-ENDIF(USE_SUPERBUILD)
-
-# write configuration information
-IF(UNIX)
-  CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/minc-toolkit-config.unix.sh.cmake ${CMAKE_CURRENT_BINARY_DIR}/minc-toolkit-config.sh @ONLY)
-  CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/minc-toolkit-config.unix.csh.cmake ${CMAKE_CURRENT_BINARY_DIR}/minc-toolkit-config.csh @ONLY)
-ENDIF(UNIX)
-
-IF(APPLE)
-  CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/minc-toolkit-config.apple.sh.cmake ${CMAKE_CURRENT_BINARY_DIR}/minc-toolkit-config.sh @ONLY)
-  CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/minc-toolkit-config.apple.csh.cmake ${CMAKE_CURRENT_BINARY_DIR}/minc-toolkit-config.csh @ONLY)
-ENDIF(APPLE)
-
-INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/minc-toolkit-config.sh ${CMAKE_CURRENT_BINARY_DIR}/minc-toolkit-config.csh DESTINATION .)
-
-# setup additional variables for making Debian package
-INCLUDE(DebianPackageAddons)
-
-# according to http://www.cmake.org/pipermail/cmake/2011-November/047137.html it's better to put this in the end
-INCLUDE(CPack)
+project(minc-toolkit)
+enable_language(C)
+enable_language(CXX)
+
+cmake_minimum_required(VERSION 2.6)
+
+SET(MINC_TOOLKIT_PACKAGE_VERSION_MAJOR 0)
+SET(MINC_TOOLKIT_PACKAGE_VERSION_MINOR 3)
+SET(MINC_TOOLKIT_PACKAGE_VERSION_PATCH 17)
+SET(MINC_TOOLKIT_RELEASE_DATE "20130307")
+
+SET(MINC_TOOLKIT_VERSION_FULL "${MINC_TOOLKIT_PACKAGE_VERSION_MAJOR}.${MINC_TOOLKIT_PACKAGE_VERSION_MINOR}.${MINC_TOOLKIT_PACKAGE_VERSION_PATCH}-${MINC_TOOLKIT_RELEASE_DATE}")
+
+#SET(CPACK_GENERATOR DEB)
+SET(CPACK_PACKAGE_NAME "minc-toolkit")
+SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "minc image processing toolkit")
+SET(CPACK_PACKAGE_VENDOR "Brain Imaging Center, Montreal Neurological Institute, McGill University")
+SET(CPACK_PACKAGE_VERSION_MAJOR ${MINC_TOOLKIT_PACKAGE_VERSION_MAJOR})
+SET(CPACK_PACKAGE_VERSION_MINOR ${MINC_TOOLKIT_PACKAGE_VERSION_MINOR})
+SET(CPACK_PACKAGE_VERSION_PATCH ${MINC_TOOLKIT_PACKAGE_VERSION_PATCH})
+SET(CPACK_PACKAGE_CONTACT "Vladimir Fonov <vladmir.fonov@gmail.com>")
+SET(CPACK_PACKAGE_INSTALL_DIRECTORY "minc-toolkit-${MINC_TOOLKIT_VERSION_FULL}")
+SET(CPACK_MONOLITHIC_INSTALL ON)
+SET(CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_SOURCE_DIR}/README.md")
+SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
+
+#IF (CMAKE_SYSTEM_PROCESSOR MATCHES "unknown")
+EXEC_PROGRAM(uname ARGS "-m" OUTPUT_VARIABLE CMAKE_SYSTEM_PROCESSOR)
+#ENDIF (CMAKE_SYSTEM_PROCESSOR MATCHES "unknown")
+
+IF(NOT DEFINED CPACK_SYSTEM_NAME)
+  SET(MT_SYSTEM_NAME ${CMAKE_SYSTEM_NAME}-${CMAKE_SYSTEM_PROCESSOR})
+ENDIF(NOT DEFINED CPACK_SYSTEM_NAME)
+
+IF(${CMAKE_SYSTEM_NAME} MATCHES Windows)
+  IF(CMAKE_CL_64)
+    SET(MT_SYSTEM_NAME win64-${CMAKE_SYSTEM_PROCESSOR})
+  ELSE(CMAKE_CL_64)
+    SET(MT_SYSTEM_NAME win32-${CMAKE_SYSTEM_PROCESSOR})
+  ENDIF(CMAKE_CL_64)
+ELSE(${CMAKE_SYSTEM_NAME} MATCHES Windows)
+  IF(${CMAKE_SYSTEM_NAME} MATCHES Linux )
+    EXEC_PROGRAM(lsb_release ARGS "-s -i" OUTPUT_VARIABLE SYSTEM_ID)
+    EXEC_PROGRAM(lsb_release ARGS "-s -r" OUTPUT_VARIABLE SYSTEM_RELEASE)
+    SET(MT_SYSTEM_NAME "${SYSTEM_ID}_${SYSTEM_RELEASE}-${CMAKE_SYSTEM_PROCESSOR}")
+  ENDIF(${CMAKE_SYSTEM_NAME} MATCHES Linux )
+ENDIF(${CMAKE_SYSTEM_NAME} MATCHES Windows)
+
+SET(CPACK_PACKAGE_FILE_NAME "minc-toolkit-${MINC_TOOLKIT_VERSION_FULL}-${MT_SYSTEM_NAME}")
+
+# register local modules
+SET(CMAKE_MODULE_PATH "${CMAKE_MODULE_PATH}" "${CMAKE_SOURCE_DIR}/cmake-modules")
+INCLUDE(PreventInSourceBuilds)
+AssureOutOfSourceBuilds(minc-toolkit)
+
+# default install directories
+SET(CMAKE_INSTALL_PREFIX ${CMAKE_CURRENT_BINARY_DIR} CACHE PATH "Install path prefix, prepended onto install directories.")
+SET(CPACK_SET_DESTDIR    ON)
+SET(CPACK_PACKAGING_INSTALL_PREFIX ${CMAKE_INSTALL_PREFIX})
+SET(CPACK_STRIP_FILES ON)
+
+# superbuild options
+OPTION(MT_BUILD_LITE         "Build lite version of minc-toolkit, without ITK or visual tools" OFF)
+OPTION(MT_BUILD_SHARED_LIBS  "Build shared libraries." OFF)
+OPTION(USE_SYSTEM_ZLIB       "Use System ZLIB "       OFF)
+OPTION(USE_SYSTEM_NETCDF     "Use System NETCDF > 3.6.3" OFF)
+OPTION(USE_SYSTEM_HDF5       "Use System HDF5 > 1.8"     OFF)
+OPTION(USE_SYSTEM_PCRE       "Use System PCRE "       OFF)
+OPTION(USE_SYSTEM_GSL        "Use System GSL "        OFF)
+OPTION(USE_SYSTEM_FFTW3F     "Use System FFTW3F "     OFF)
+OPTION(MT_BUILD_ITK_TOOLS    "Build ITK-based tools"  OFF)
+OPTION(MT_BUILD_VISUAL_TOOLS "Build visual tools (Display, Register, postf, ray_trace) requires OpenGL & Glut"  OFF)
+OPTION(USE_SYSTEM_ITK        "Use System ITK" OFF)
+
+IF(MT_BUILD_LITE)
+  SET(MT_BUILD_ITK_TOOLS OFF)
+  SET(MT_BUILD_VISUAL_TOOLS OFF)
+  SET(MT_BUILD_MINC_ANTS OFF)
+  SET(MT_BUILD_C3D OFF)
+
+  SET(CPACK_PACKAGE_FILE_NAME "minc-toolkit-${MINC_TOOLKIT_VERSION_FULL}-${MT_SYSTEM_NAME}-lite")
+ENDIF(MT_BUILD_LITE)
+
+ENABLE_TESTING()
+INCLUDE(CTest)
+
+# provide test environement
+# CACHE INTERNAL FORCE
+SET(MINC_TEST_ENVIRONMENT
+ "PATH=${CMAKE_CURRENT_BINARY_DIR}:${CMAKE_CURRENT_BINARY_DIR}/N3:${CMAKE_CURRENT_BINARY_DIR}/classify:${CMAKE_CURRENT_BINARY_DIR}/minctools/progs:${CMAKE_CURRENT_BINARY_DIR}/mni_autoreg/mincblur:${CMAKE_CURRENT_BINARY_DIR}/mni_autoreg/make_phantom:${CMAKE_CURRENT_BINARY_DIR}/mni_autoreg/minctracc:$ENV{PATH};PERL5LIB=${CMAKE_SOURCE_DIR}/mni-perllib:${CMAKE_CURRENT_BINARY_DIR}/mni-perllib/perl:${CMAKE_CURRENT_BINARY_DIR}/perl-modules:$ENV{PERL5LIB}"
+)
+
+# for superbuild
+IF(USE_SYSTEM_ZLIB AND USE_SYSTEM_NETCDF AND USE_SYSTEM_HDF5  AND USE_SYSTEM_PCRE  AND USE_SYSTEM_GSL AND USE_SYSTEM_FFTW3F AND USE_SYSTEM_ITK)
+  SET(USE_SUPERBUILD OFF)
+ELSE(USE_SYSTEM_ZLIB AND USE_SYSTEM_NETCDF AND USE_SYSTEM_HDF5  AND USE_SYSTEM_PCRE AND USE_SYSTEM_GSL AND USE_SYSTEM_FFTW3F AND USE_SYSTEM_ITK)
+  INCLUDE(ExternalProject)
+  SET(USE_SUPERBUILD ON)
+  INCLUDE(ConfigureExternalProjects)
+ENDIF(USE_SYSTEM_ZLIB AND USE_SYSTEM_NETCDF AND USE_SYSTEM_HDF5  AND USE_SYSTEM_PCRE  AND USE_SYSTEM_GSL AND USE_SYSTEM_FFTW3F AND USE_SYSTEM_ITK)
+
+SET(SUPERBUILD_STAGING_PREFIX ${CMAKE_BINARY_DIR}/external)
+
+# required packages
+FIND_PACKAGE( Perl   REQUIRED )
+# required for minc
+IF(USE_SYSTEM_ZLIB)
+  FIND_PACKAGE( ZLIB   REQUIRED )
+ELSE(USE_SYSTEM_ZLIB)
+  INCLUDE(BuildZLIB)
+  build_zlib( ${CMAKE_INSTALL_PREFIX} ${SUPERBUILD_STAGING_PREFIX})
+ENDIF(USE_SYSTEM_ZLIB)
+
+IF(USE_SYSTEM_NETCDF)
+  FIND_PACKAGE( NETCDF REQUIRED )
+ELSE(USE_SYSTEM_NETCDF)
+  INCLUDE(BuildNETCDF)
+  build_netcdf( ${CMAKE_INSTALL_PREFIX} ${SUPERBUILD_STAGING_PREFIX})
+ENDIF(USE_SYSTEM_NETCDF)
+
+IF(USE_SYSTEM_HDF5)
+  FIND_PACKAGE( HDF5   REQUIRED )
+ELSE(USE_SYSTEM_HDF5)
+  INCLUDE(BuildHDF5)
+  build_hdf5( ${CMAKE_INSTALL_PREFIX} ${SUPERBUILD_STAGING_PREFIX} ${ZLIB_INCLUDE_DIR} ${ZLIB_LIBRARY})
+  IF(NOT USE_SYSTEM_ZLIB)
+    add_dependencies(HDF5 ZLIB)
+  ENDIF(NOT USE_SYSTEM_ZLIB)
+ENDIF(USE_SYSTEM_HDF5)
+
+#required for some minc tools
+FIND_PACKAGE( BISON )
+FIND_PACKAGE( FLEX )
+FIND_PACKAGE( Threads)
+
+#required for bicpl
+IF(USE_SYSTEM_NETPBM) # else we will use bundled libppm
+  FIND_PACKAGE( NETPBM QUIET )
+ENDIF(USE_SYSTEM_NETPBM)
+
+#required for oobicpl
+IF(USE_SYSTEM_PCRE)
+  FIND_PACKAGE( PCRE QUIET )
+ELSE(USE_SYSTEM_PCRE)
+  INCLUDE(BuildPCRE)
+  build_pcre(${CMAKE_INSTALL_PREFIX} ${SUPERBUILD_STAGING_PREFIX})
+ENDIF(USE_SYSTEM_PCRE)
+
+
+SET(MINC_TOOLKIT_BUILD ON)
+SET(MINC_TOOLKIT_BUILD_DIR   ${CMAKE_BINARY_DIR})
+SET(MINC_TOOLKIT_INSTALL_DIR ${CMAKE_INSTALL_PREFIX})
+
+#setup parameters
+#MINC2
+SET(LIBMINC_BUILD_V2           ON)
+SET(LIBMINC_MINC1_SUPPORT      ON)
+SET(LIBMINC_FOUND              ON)
+SET(LIBMINC_BUILD_TOOLS        ON)
+SET(LIBMINC_BUILD_CONVERTERS   ON)
+SET(LIBMINC_BUILD_EZMINC       ON)
+SET(LIBMINC_BUILD_EZMINC_EXAMPLES ON)
+SET(LIBMINC_INTEGRATE_VOLUME_IO OFF)
+# we have both MINC1 API
+SET(HAVE_MINC1 ON)
+# and MINC2 API
+SET(HAVE_MINC2 ON)
+
+
+IF(MT_BUILD_SHARED_LIBS)
+  SET(LIBMINC_BUILD_SHARED_LIBS    OFF)
+  #EBTKS
+  SET(EBTKS_BUILD_SHARED_LIBS      OFF)
+  #bicpl
+  SET(BICPL_BUILD_SHARED_LIBS      ON)
+  #oobicpl
+  SET(OOBICPL_BUILD_SHARED_LIBS    ON)
+  #arguments
+  SET(ARGUMENTS_BUILD_SHARED_LIBS  ON)
+  #bicgl
+  SET(BICGL_BUILD_SHARED_LIBS      ON)
+ELSE(MT_BUILD_SHARED_LIBS)
+
+  SET(LIBMINC_BUILD_SHARED_LIBS      OFF)
+  #EBTKS
+  SET(EBTKS_BUILD_SHARED_LIBS      OFF)
+  #bicpl
+  SET(BICPL_BUILD_SHARED_LIBS      OFF)
+  #oobicpl
+  SET(OOBICPL_BUILD_SHARED_LIBS    OFF)
+  #arguments
+  SET(ARGUMENTS_BUILD_SHARED_LIBS  OFF)
+  #bicgl
+  SET(BICGL_BUILD_SHARED_LIBS      OFF)
+ENDIF(MT_BUILD_SHARED_LIBS)
+
+
+#EZMINC
+SET(EZMINC_BUILD_MINCNLM  ON)
+SET(EZMINC_BUILD_DISTORTION_CORRECTION  ON)
+SET(EZMINC_BUILD_MRFSEG  ON)
+SET(EZMINC_BUILD_DD      ON)
+SET(EZMINC_BUILD_TOOLS   ON)
+
+ADD_SUBDIRECTORY(libminc)
+
+IF(NOT USE_SYSTEM_NETCDF)
+  ADD_DEPENDENCIES(minc2 NETCDF)
+ENDIF(NOT USE_SYSTEM_NETCDF)
+
+IF(NOT USE_SYSTEM_HDF5)
+  ADD_DEPENDENCIES(minc2 HDF5)
+ENDIF(NOT USE_SYSTEM_HDF5)
+
+# Setup main minc variables
+SET(LIBMINC_USE_FILE ${CMAKE_BINARY_DIR}/libminc/UseLIBMINC.cmake CACHE INTERNAL "LIBMINC use file")
+INCLUDE(${CMAKE_BINARY_DIR}/libminc/LIBMINCConfig.cmake)
+INCLUDE(${LIBMINC_USE_FILE})
+
+ADD_SUBDIRECTORY(minctools)
+ADD_SUBDIRECTORY(EBTKS)
+ADD_DEPENDENCIES(EBTKS minc2)
+
+# setup EBTKS variables
+SET(EBTKS_USE_FILE ${CMAKE_BINARY_DIR}/EBTKS/UseEBTKS.cmake CACHE INTERNAL "EBTKS use file")
+INCLUDE(${CMAKE_BINARY_DIR}/EBTKS/EBTKSConfig.cmake)
+INCLUDE(${EBTKS_USE_FILE})
+
+ADD_SUBDIRECTORY(bicpl)
+ADD_DEPENDENCIES(bicpl minc2)
+
+#setup bicpl variables
+SET(BICPL_USE_FILE ${CMAKE_BINARY_DIR}/bicpl/UseBICPL.cmake CACHE INTERNAL "BICPL use file")
+INCLUDE(${CMAKE_BINARY_DIR}/bicpl/BICPLConfig.cmake)
+INCLUDE(${BICPL_USE_FILE})
+IF(NOT USE_SYSTEM_NETPBM)
+  ADD_DEPENDENCIES(bicpl NETPBM)
+ENDIF(NOT USE_SYSTEM_NETPBM)
+
+ADD_SUBDIRECTORY(arguments)
+
+#setup arguments variables
+SET(ARGUMENTS_USE_FILE ${CMAKE_BINARY_DIR}/bicpl/UseARGUMENTS.cmake CACHE INTERNAL "ARGUMENTS use file")
+INCLUDE(${CMAKE_BINARY_DIR}/arguments/ARGUMENTSConfig.cmake)
+INCLUDE(${ARGUMENTS_USE_FILE})
+
+ADD_SUBDIRECTORY(oobicpl)
+ADD_DEPENDENCIES(oobicpl minc2 bicpl arguments)
+
+#setup oobicpl variables
+SET(OOBICPL_USE_FILE ${CMAKE_BINARY_DIR}/bicpl/UseOOBICPL.cmake CACHE INTERNAL "OOBICPL use file")
+INCLUDE(${CMAKE_BINARY_DIR}/oobicpl/OOBICPLConfig.cmake)
+INCLUDE(${OOBICPL_USE_FILE})
+
+ADD_SUBDIRECTORY(BEaST)
+#ADD_SUBDIRECTORY(BEaST_library)
+ADD_SUBDIRECTORY(conglomerate)
+ADD_SUBDIRECTORY(classify)
+ADD_SUBDIRECTORY(mni-perllib)
+ADD_SUBDIRECTORY(N3)
+
+ADD_SUBDIRECTORY(glim_image)
+ADD_SUBDIRECTORY(mni_autoreg)
+ADD_SUBDIRECTORY(inormalize)
+ADD_SUBDIRECTORY(mrisim)
+ADD_SUBDIRECTORY(bic-pipelines)
+ADD_SUBDIRECTORY(perl-modules)
+
+# build tools that require ITK
+IF(MT_BUILD_ITK_TOOLS)
+
+  OPTION(MT_BUILD_MINC_ANTS "Build mincANTS " OFF)
+  OPTION(MT_BUILD_C3D "Build convert3D " OFF)
+
+  SET(HAVE_MINC4ITK  ON)
+
+  #required for minc4itk & EZminc
+  IF(USE_SYSTEM_ITK)
+    FIND_PACKAGE(ITK )
+  ELSE(USE_SYSTEM_ITK)
+    INCLUDE(BuildITKv3)
+    build_itkv3(${CMAKE_INSTALL_PREFIX} ${SUPERBUILD_STAGING_PREFIX} )
+  ENDIF(USE_SYSTEM_ITK)
+
+  #required for EZminc
+  IF(USE_SYSTEM_GSL)
+    FIND_PACKAGE(GSL)
+  ELSE(USE_SYSTEM_GSL)
+    INCLUDE(BuildGSL)
+    build_gsl(${CMAKE_INSTALL_PREFIX} ${SUPERBUILD_STAGING_PREFIX})
+  ENDIF(USE_SYSTEM_GSL)
+
+  IF(USE_SYSTEM_FFTW3F)
+    FIND_PACKAGE(FFTW3F)
+  ELSE(USE_SYSTEM_FFTW3)
+    INCLUDE(BuildFFTW3F)
+    build_fftw3f(${CMAKE_INSTALL_PREFIX} ${SUPERBUILD_STAGING_PREFIX})
+  ENDIF(USE_SYSTEM_FFTW3F)
+
+  # minc4itk integration library
+  ADD_SUBDIRECTORY(minc4itk)
+  INCLUDE(${CMAKE_CURRENT_BINARY_DIR}/minc4itk/MINC4ITKConfig.cmake)
+  # setup minc4itk variables
+  SET(MINC4ITK_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/minc4itk/include)
+  SET(MINC4ITK_LIBRARY_DIRS ${CMAKE_BINARY_DIR}/minc4itk/)
+
+  ADD_DEPENDENCIES(ITKIOMINC minc2)
+
+  IF(NOT USE_SYSTEM_ITK)
+    ADD_DEPENDENCIES(ITKIOMINC ITKv3)
+  ENDIF(NOT USE_SYSTEM_ITK)
+
+  ADD_SUBDIRECTORY(EZminc)
+  ADD_DEPENDENCIES(minc_image_proc minc2)
+  ADD_DEPENDENCIES(mincnlm minc2)
+  ADD_DEPENDENCIES(mrfseg minc2)
+  ADD_DEPENDENCIES(mrflib minc2)
+
+  IF(MT_BUILD_MINC_ANTS)
+    ADD_SUBDIRECTORY(mincANTS)
+    ADD_DEPENDENCIES(mincANTS ITKIOMINC minc2)
+  ENDIF(MT_BUILD_MINC_ANTS)
+
+  IF(MT_BUILD_C3D)
+    ADD_SUBDIRECTORY(c3d)
+    ADD_DEPENDENCIES(c3d ITKIOMINC minc2)
+    ADD_DEPENDENCIES(c2d ITKIOMINC minc2)
+  ENDIF(MT_BUILD_C3D)
+
+
+  IF(NOT USE_SYSTEM_ITK)
+    ADD_DEPENDENCIES(ITKIOMINC ITKv3)
+  ENDIF(NOT USE_SYSTEM_ITK)
+
+  IF(NOT USE_SYSTEM_GSL)
+    ADD_DEPENDENCIES(minc_image_proc GSL)
+  ENDIF(NOT USE_SYSTEM_GSL)
+
+  IF(NOT USE_SYSTEM_FFTW3F)
+    ADD_DEPENDENCIES(minc_image_proc FFTW3F)
+  ENDIF(NOT USE_SYSTEM_FFTW3F)
+ENDIF(MT_BUILD_ITK_TOOLS)
+
+# build tools that require OpenGL and GLUT
+IF(MT_BUILD_VISUAL_TOOLS)
+  FIND_PACKAGE( OpenGL REQUIRED )
+  FIND_PACKAGE( GLUT REQUIRED )
+  FIND_PACKAGE( X11 QUIET )
+
+  ADD_SUBDIRECTORY(bicgl)
+  INCLUDE(${CMAKE_BINARY_DIR}/bicgl/BICGLConfig.cmake)
+
+  ADD_SUBDIRECTORY(ray_trace)
+  ADD_DEPENDENCIES(ray_trace bicgl minc2 bicpl)
+
+  ADD_SUBDIRECTORY(Display)
+  ADD_DEPENDENCIES(Display bicgl minc2 bicpl)
+
+  ADD_SUBDIRECTORY(Register)
+  ADD_DEPENDENCIES(register bicgl minc2 bicpl)
+
+  IF(X11_FOUND)
+    ADD_SUBDIRECTORY(postf)
+    ADD_DEPENDENCIES(postf minc2)
+  ENDIF(X11_FOUND)
+ENDIF(MT_BUILD_VISUAL_TOOLS)
+
+# DO nothing?
+IF(USE_SUPERBUILD)
+  #install external dependencies to final destination
+  INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/bin
+        DESTINATION .
+        PATTERN *
+        PERMISSIONS OWNER_EXECUTE OWNER_READ OWNER_WRITE GROUP_EXECUTE GROUP_READ WORLD_READ WORLD_EXECUTE )
+
+  INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}
+        DESTINATION .)
+
+  INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/include
+        DESTINATION .)
+
+  # do we really need to install share?
+  INSTALL(DIRECTORY ${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/share
+        DESTINATION .)
+ENDIF(USE_SUPERBUILD)
+
+# write configuration information
+IF(UNIX)
+  CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/minc-toolkit-config.unix.sh.cmake ${CMAKE_CURRENT_BINARY_DIR}/minc-toolkit-config.sh @ONLY)
+  CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/minc-toolkit-config.unix.csh.cmake ${CMAKE_CURRENT_BINARY_DIR}/minc-toolkit-config.csh @ONLY)
+ENDIF(UNIX)
+
+IF(APPLE)
+  CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/minc-toolkit-config.apple.sh.cmake ${CMAKE_CURRENT_BINARY_DIR}/minc-toolkit-config.sh @ONLY)
+  CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/minc-toolkit-config.apple.csh.cmake ${CMAKE_CURRENT_BINARY_DIR}/minc-toolkit-config.csh @ONLY)
+ENDIF(APPLE)
+
+INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/minc-toolkit-config.sh ${CMAKE_CURRENT_BINARY_DIR}/minc-toolkit-config.csh DESTINATION .)
+
+# setup additional variables for making Debian package
+INCLUDE(DebianPackageAddons)
+
+# according to http://www.cmake.org/pipermail/cmake/2011-November/047137.html it's better to put this in the end
+INCLUDE(CPack)
diff --git a/EBTKS b/EBTKS
index 90158c8..51822e4 160000
--- a/EBTKS
+++ b/EBTKS
@@ -1 +1 @@
-Subproject commit 90158c88c7807b4da76a67bc46d78f8e1f9fec0d
+Subproject commit 51822e44ea8fe698459eb04cf8ef740dff82c004
diff --git a/EZminc b/EZminc
index 3d86117..1bb2aa8 160000
--- a/EZminc
+++ b/EZminc
@@ -1 +1 @@
-Subproject commit 3d861173aca24960624ec78c7fd5eb062d527734
+Subproject commit 1bb2aa8d2b5c1b5a338333ea27a2cd47cad2198f
diff --git a/N3 b/N3
index fd6854a..4bfa5c5 160000
--- a/N3
+++ b/N3
@@ -1 +1 @@
-Subproject commit fd6854aac2dc107fe0f9b91af37a55fb27c32f1c
+Subproject commit 4bfa5c5d0eaae7184d29e13bf2740fb89c05e7d9
diff --git a/bic-pipelines b/bic-pipelines
index 165a559..1f53362 160000
--- a/bic-pipelines
+++ b/bic-pipelines
@@ -1 +1 @@
-Subproject commit 165a559885dec34686fa4b6724e8152a1ee8cc7b
+Subproject commit 1f53362e4ac384075e7a3e34233add0d11348e2f
diff --git a/bicgl b/bicgl
index 78fbbbd..cfe3ae8 160000
--- a/bicgl
+++ b/bicgl
@@ -1 +1 @@
-Subproject commit 78fbbbd4fa50a334a7e57b39f004dfed2aee302a
+Subproject commit cfe3ae823b1e8d1a4287371361facb726da88cbb
diff --git a/bicpl b/bicpl
index a5255b3..ed9282e 160000
--- a/bicpl
+++ b/bicpl
@@ -1 +1 @@
-Subproject commit a5255b3e25ccd4c8b438f0d086187f36e359be6e
+Subproject commit ed9282e1797b8d2ed22a7e4aa2e5e43c0183dfec
diff --git a/c3d b/c3d
index fa89c4c..5288dee 160000
--- a/c3d
+++ b/c3d
@@ -1 +1 @@
-Subproject commit fa89c4ca36fdebbe4468b00909b747a1b2454508
+Subproject commit 5288dee993a240fc32b2c4881c14e5a7735bae26
diff --git a/cmake-modules/BuildFFTW3F.cmake b/cmake-modules/BuildFFTW3F.cmake
index 26d1950..000626d 100644
--- a/cmake-modules/BuildFFTW3F.cmake
+++ b/cmake-modules/BuildFFTW3F.cmake
@@ -8,7 +8,7 @@ ExternalProject_Add(FFTW3F
         INSTALL_DIR     "${staging_prefix}"
         BUILD_COMMAND   make 
         INSTALL_COMMAND make DESTDIR=${staging_prefix} install 
-        CONFIGURE_COMMAND ./configure --prefix=${install_prefix} --with-pic --disable-shared --enable-float 
+        CONFIGURE_COMMAND ./configure --prefix=${install_prefix} --with-pic --disable-shared --enable-float
 #        INSTALL_DIR ${CMAKE_CURRENT_BINARY_DIR}/external
       )
 
diff --git a/cmake-modules/BuildGSL.cmake b/cmake-modules/BuildGSL.cmake
index 9f516c1..3a98952 100644
--- a/cmake-modules/BuildGSL.cmake
+++ b/cmake-modules/BuildGSL.cmake
@@ -8,7 +8,7 @@ ExternalProject_Add(GSL
         INSTALL_DIR     "${CMAKE_BINARY_DIR}/external"
         BUILD_COMMAND   make 
         INSTALL_COMMAND make DESTDIR=${CMAKE_BINARY_DIR}/external install 
-        CONFIGURE_COMMAND ./configure --prefix=${install_prefix} --with-pic --disable-shared --enable-static
+        CONFIGURE_COMMAND ./configure --prefix=${install_prefix} --with-pic --disable-shared --enable-static 
 #        INSTALL_DIR ${CMAKE_CURRENT_BINARY_DIR}/external
       )
 
diff --git a/cmake-modules/BuildHDF5.cmake b/cmake-modules/BuildHDF5.cmake
index 07b3505..6f178f1 100644
--- a/cmake-modules/BuildHDF5.cmake
+++ b/cmake-modules/BuildHDF5.cmake
@@ -4,8 +4,8 @@ get_filename_component(zlib_library_dir ${zlib_library} PATH)
 
 ExternalProject_Add(HDF5
   SOURCE_DIR HDF5
-  URL "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.8/src/hdf5-1.8.8.tar.gz"
-  URL_MD5 "1196e668f5592bfb50d1de162eb16cff"
+  URL "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.10/src/hdf5-1.8.10-patch1.tar.gz"
+  URL_MD5 "2147a289fb33c887464ad2b6c5a8ae4c"
   BUILD_IN_SOURCE 1
   INSTALL_DIR     "${CMAKE_BINARY_DIR}/external"
   BUILD_COMMAND   make 
diff --git a/cmake-modules/BuildPCRE.cmake b/cmake-modules/BuildPCRE.cmake
index fd282d0..344a7fc 100644
--- a/cmake-modules/BuildPCRE.cmake
+++ b/cmake-modules/BuildPCRE.cmake
@@ -8,7 +8,7 @@ ExternalProject_Add(PCRE
   INSTALL_DIR     "${staging_prefix}"
   BUILD_COMMAND   make 
   INSTALL_COMMAND make DESTDIR=${staging_prefix} install 
-  CONFIGURE_COMMAND ./configure --prefix=${install_prefix} --with-pic --disable-shared --enable-cpp 
+  CONFIGURE_COMMAND ./configure --prefix=${install_prefix} --with-pic --disable-shared --enable-cpp
 )
 
 SET(PCRE_INCLUDE_DIR  ${staging_prefix}/${install_prefix}/include )
diff --git a/libminc b/libminc
index 087f05d..5004fc2 160000
--- a/libminc
+++ b/libminc
@@ -1 +1 @@
-Subproject commit 087f05d467574f621138d2ac99af554325bbab5d
+Subproject commit 5004fc285ee06a4c36200ce0460982430318e8e2
diff --git a/minc4itk b/minc4itk
index 24be7f1..5b9a8cd 160000
--- a/minc4itk
+++ b/minc4itk
@@ -1 +1 @@
-Subproject commit 24be7f12d0b5647e9f2f1c3ed93f31ff13abc797
+Subproject commit 5b9a8cd6d4c08aed305fc9b3f3952a9548cb0bef
diff --git a/mni_autoreg b/mni_autoreg
index 8de4371..c22e920 160000
--- a/mni_autoreg
+++ b/mni_autoreg
@@ -1 +1 @@
-Subproject commit 8de43718a8e82d49c8d5969dda7e419575f0cdb6
+Subproject commit c22e9207de22a5efd782aec1d52798622b9fc2be
diff --git a/oobicpl b/oobicpl
index 0d4f7a6..7119ad1 160000
--- a/oobicpl
+++ b/oobicpl
@@ -1 +1 @@
-Subproject commit 0d4f7a65e62abebd4fdede3ef5a27feee0073777
+Subproject commit 7119ad16fd048a48f2cd8a0513cc0e7bda03d4b5