diff --git a/.github/workflows/checks.yml b/.github/workflows/checks.yml
index 24ebb4ebee..3a97284642 100644
--- a/.github/workflows/checks.yml
+++ b/.github/workflows/checks.yml
@@ -158,6 +158,7 @@ jobs:
         -B build
         -G Ninja
         -D CMAKE_BUILD_TYPE=Release
+        -D CMAKE_FIND_FRAMEWORK=LAST
         -D MRTRIX_BUILD_TESTS=ON
         -D MRTRIX_STL_DEBUGGING=ON
         -D MRTRIX_USE_PCH=OFF
diff --git a/CMakeLists.txt b/CMakeLists.txt
index ec4e36e39c..871b431545 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -23,7 +23,7 @@ option(MRTRIX_BUILD_TESTS "Build tests executables" OFF)
 option(MRTRIX_STRIP_CONDA "Strip ananconda/mininconda from PATH to avoid conflicts" ON)
 option(MRTRIX_USE_PCH "Use precompiled headers" ON)
 option(MRTRIX_PYTHON_SOFTLINK "Build directory softlink to Python source code rather than copying" ON)
-option(MRTRIX_BUILD_NON_CORE_STATIC "Build MRtrix's non-core code as a static library" OFF)
+option(MRTRIX_BUILD_STATIC "Build MRtrix's library statically" OFF)
 option(MRTRIX_USE_LLD "Use lld as the linker" OFF)
 
 set(MRTRIX_DEPENDENCIES_DIR "" CACHE PATH
@@ -73,16 +73,6 @@ file(RELATIVE_PATH relDir
 set(CMAKE_INSTALL_RPATH ${base} ${base}/${relDir})
 
 include(BuildType)
-include(LinkerSetup)
-include(FindFFTW)
-include(CompilerCache)
-include(ECMEnableSanitizers)
-include(Dependencies)
-if(CMAKE_SYSTEM_NAME MATCHES "Darwin")
-    include(MacOSBundle)
-endif()
-
-use_compiler_cache()
 
 if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/.git AND NOT EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/.git/hooks/pre-commit)
     message(WARNING
@@ -91,37 +81,6 @@ if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/.git AND NOT EXISTS ${CMAKE_CURRENT_SOURCE
         "and then run `pre-commit install` from the ${CMAKE_CURRENT_SOURCE_DIR} directory.")
 endif()
 
-add_library(mrtrix-common INTERFACE)
-add_library(mrtrix::common ALIAS mrtrix-common)
-target_compile_definitions(mrtrix-common INTERFACE
-    MRTRIX_BUILD_TYPE="${CMAKE_BUILD_TYPE}"
-    $<$<PLATFORM_ID:Windows>:MRTRIX_WINDOWS>
-    $<$<PLATFORM_ID:Darwin>:MRTRIX_MACOSX>
-    $<$<PLATFORM_ID:FreeBSD>:MRTRIX_FREEBSD>
-)
-
-if(MRTRIX_STL_DEBUGGING AND NOT CMAKE_BUILD_TYPE STREQUAL "Debug")
-    message(STATUS "Enabling STL debug mode")
-    target_compile_definitions(mrtrix-common INTERFACE
-        $<$<CXX_COMPILER_ID:MSVC>:_ITERATOR_DEBUG_LEVEL=1>
-        $<$<CXX_COMPILER_ID:GNU>:_GLIBCXX_DEBUG _GLIBCXX_DEBUG_PEDANTIC>
-        $<$<CXX_COMPILER_ID:Clang>:_LIBCPP_DEBUG=1>
-    )
-endif()
-
-if(MRTRIX_WARNINGS_AS_ERRORS)
-    message(STATUS "Enabling warnings as errors")
-    target_compile_options(mrtrix-common INTERFACE
-        $<$<CXX_COMPILER_ID:MSVC>:/WX>
-        $<$<CXX_COMPILER_ID:GNU,Clang>:-Werror>
-    )
-endif()
-
-# Allow compilation of big object of files in debug mode on MINGW
-if(MINGW AND CMAKE_BUILD_TYPE MATCHES "Debug")
-    target_compile_options(mrtrix-common INTERFACE -Wa,-mbig-obj)
-endif()
-
 
 if(MRTRIX_STRIP_CONDA AND DEFINED ENV{CONDA_PREFIX})
     message(WARNING "CONDA_PREFIX is set to ${CONDA_PREFIX}, adding conda diretories to CMAKE_IGNORE_PATH to avoid conflicts.\n"
@@ -145,11 +104,9 @@ if(COMPILER_PATH MATCHES "fsl/bin" OR LINKER_PATH MATCHES "fsl/bin")
     )
 endif()
 
-add_subdirectory(cmd)
-add_subdirectory(core)
+add_subdirectory(cpp)
 add_subdirectory(python)
 add_subdirectory(share)
-add_subdirectory(src)
 
 if(PROJECT_IS_TOP_LEVEL AND MRTRIX_BUILD_TESTS)
     add_subdirectory(testing)
diff --git a/clang-format-all b/clang-format-all
index b5a5649c28..3ed85526e0 100755
--- a/clang-format-all
+++ b/clang-format-all
@@ -34,11 +34,10 @@ parser.add_argument(
 
 args = parser.parse_args()
 clang_format = args.executable
-paths = ['core', 'cmd', 'src', 'testing']
+paths = ['cpp', 'testing']
 extensions = ['.h', '.cpp']
-exclusion_list = ['core/file/nifti1.h',
-                  'core/file/nifti2.h',
-                  'core/file/json.h']
+exclusion_list = ['cpp/gui/opengl/gl_core_3_3.h',
+                  'cpp/gui/opengl/gl_core_3_3.cpp']
 
 # if clang-format path contains spaces, wrap it in quotes
 if ' ' in clang_format and not clang_format.startswith('"'):
diff --git a/cmake/MacOSBundle.cmake b/cmake/MacOSBundle.cmake
index 42bb702a7d..d90e7358af 100644
--- a/cmake/MacOSBundle.cmake
+++ b/cmake/MacOSBundle.cmake
@@ -1,7 +1,7 @@
 function(set_bundle_properties executable_name)
-    set(icon_files ${CMAKE_CURRENT_SOURCE_DIR}/../icons/macos/${executable_name}.icns)
+    set(icon_files ${PROJECT_SOURCE_DIR}/icons/macos/${executable_name}.icns)
     if(${executable_name} STREQUAL "mrview")
-        list(APPEND icon_files ${CMAKE_CURRENT_SOURCE_DIR}/../icons/macos/mrview_doc.icns)
+        list(APPEND icon_files ${PROJECT_SOURCE_DIR}/icons/macos/mrview_doc.icns)
     endif()
 
     string(TIMESTAMP CURRENT_YEAR "%Y")
@@ -10,14 +10,14 @@ function(set_bundle_properties executable_name)
     target_sources(${executable_name} PRIVATE ${icon_files})
     set_target_properties(${executable_name} PROPERTIES
         MACOSX_BUNDLE TRUE
-        MACOSX_BUNDLE_INFO_PLIST "${CMAKE_CURRENT_SOURCE_DIR}/../packaging/macos/bundle/${executable_name}.plist.in"
+        MACOSX_BUNDLE_INFO_PLIST "${PROJECT_SOURCE_DIR}/packaging/macos/bundle/${executable_name}.plist.in"
         RESOURCE "${icon_files}"
         INSTALL_RPATH "@executable_path/../../../../lib"
     )
 endfunction()
 
 function(install_bundle_wrapper_scripts executable_name)
-    set(wrapper_script ${CMAKE_CURRENT_SOURCE_DIR}/../packaging/macos/bundle/wrapper_launcher.sh.in)
+    set(wrapper_script ${PROJECT_SOURCE_DIR}/packaging/macos/bundle/wrapper_launcher.sh.in)
     configure_file(${wrapper_script} ${PROJECT_BINARY_DIR}/bin/${executable_name}
         FILE_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
         @ONLY
diff --git a/core/version.cpp.in b/core/version.cpp.in
deleted file mode 100644
index 2143df497a..0000000000
--- a/core/version.cpp.in
+++ /dev/null
@@ -1,8 +0,0 @@
-#include "version.h"
-
-namespace MR {
-    namespace App {
-        const char *mrtrix_version = "@MRTRIX_VERSION@";
-        const char *build_date = __DATE__;
-    }
-}
diff --git a/core/version.h b/core/version.h
deleted file mode 100644
index a5aafdfb51..0000000000
--- a/core/version.h
+++ /dev/null
@@ -1,4 +0,0 @@
-#pragma once
-
-extern const char *mrtrix_version;
-extern const char *build_date;
diff --git a/cpp/CMakeLists.txt b/cpp/CMakeLists.txt
new file mode 100644
index 0000000000..0319494577
--- /dev/null
+++ b/cpp/CMakeLists.txt
@@ -0,0 +1,41 @@
+include(LinkerSetup)
+include(FindFFTW)
+include(ECMEnableSanitizers)
+include(Dependencies)
+include(CompilerCache)
+use_compiler_cache()
+
+add_library(mrtrix-common INTERFACE)
+add_library(mrtrix::common ALIAS mrtrix-common)
+target_compile_definitions(mrtrix-common INTERFACE
+    MRTRIX_BUILD_TYPE="${CMAKE_BUILD_TYPE}"
+    $<$<PLATFORM_ID:Windows>:MRTRIX_WINDOWS>
+    $<$<PLATFORM_ID:Darwin>:MRTRIX_MACOSX>
+    $<$<PLATFORM_ID:FreeBSD>:MRTRIX_FREEBSD>
+)
+
+if(MRTRIX_STL_DEBUGGING AND NOT CMAKE_BUILD_TYPE STREQUAL "Debug")
+    message(STATUS "Enabling STL debug mode")
+    target_compile_definitions(mrtrix-common INTERFACE
+        $<$<CXX_COMPILER_ID:MSVC>:_ITERATOR_DEBUG_LEVEL=1>
+        $<$<CXX_COMPILER_ID:GNU>:_GLIBCXX_DEBUG _GLIBCXX_DEBUG_PEDANTIC>
+        $<$<CXX_COMPILER_ID:Clang>:_LIBCPP_DEBUG=1>
+    )
+endif()
+
+if(MRTRIX_WARNINGS_AS_ERRORS)
+    message(STATUS "Enabling warnings as errors")
+    target_compile_options(mrtrix-common INTERFACE
+        $<$<CXX_COMPILER_ID:MSVC>:/WX>
+        $<$<CXX_COMPILER_ID:GNU,Clang>:-Werror>
+    )
+endif()
+
+# Allow compilation of big object of files in debug mode on MINGW
+if(MINGW AND CMAKE_BUILD_TYPE MATCHES "Debug")
+    target_compile_options(mrtrix-common INTERFACE -Wa,-mbig-obj)
+endif()
+
+add_subdirectory(cmd)
+add_subdirectory(core)
+add_subdirectory(gui)
diff --git a/cmd/5tt2gmwmi.cpp b/cpp/cmd/5tt2gmwmi.cpp
similarity index 100%
rename from cmd/5tt2gmwmi.cpp
rename to cpp/cmd/5tt2gmwmi.cpp
diff --git a/cmd/5tt2vis.cpp b/cpp/cmd/5tt2vis.cpp
similarity index 100%
rename from cmd/5tt2vis.cpp
rename to cpp/cmd/5tt2vis.cpp
diff --git a/cmd/5ttcheck.cpp b/cpp/cmd/5ttcheck.cpp
similarity index 100%
rename from cmd/5ttcheck.cpp
rename to cpp/cmd/5ttcheck.cpp
diff --git a/cmd/5ttedit.cpp b/cpp/cmd/5ttedit.cpp
similarity index 100%
rename from cmd/5ttedit.cpp
rename to cpp/cmd/5ttedit.cpp
diff --git a/cmd/CMakeLists.txt b/cpp/cmd/CMakeLists.txt
similarity index 93%
rename from cmd/CMakeLists.txt
rename to cpp/cmd/CMakeLists.txt
index e6ede5619b..0ec13f4241 100644
--- a/cmd/CMakeLists.txt
+++ b/cpp/cmd/CMakeLists.txt
@@ -1,3 +1,7 @@
+if(CMAKE_SYSTEM_NAME MATCHES "Darwin")
+    include(MacOSBundle)
+endif()
+
 set(GUI_CMD_SRCS mrview.cpp shview.cpp)
 
 file(GLOB HEADLESS_CMD_SRCS *.cpp)
@@ -26,8 +30,8 @@ function(add_cmd CMD_SRC IS_GUI)
     get_filename_component(CMD_NAME ${CMD_SRC} NAME_WE)
     add_executable(${CMD_NAME} ${CMD_SRC})
     target_link_libraries(${CMD_NAME} PRIVATE
-        $<IF:$<BOOL:${IS_GUI}>,mrtrix::gui,mrtrix::headless>
-        mrtrix::exec-version-lib
+        $<IF:$<BOOL:${IS_GUI}>,mrtrix::gui,mrtrix::core>
+        mrtrix::executable-version
     )
     set_target_properties(${CMD_NAME} PROPERTIES
         LINK_DEPENDS_NO_SHARED true
diff --git a/cmd/afdconnectivity.cpp b/cpp/cmd/afdconnectivity.cpp
similarity index 99%
rename from cmd/afdconnectivity.cpp
rename to cpp/cmd/afdconnectivity.cpp
index 617a242679..5d0023d63d 100644
--- a/cmd/afdconnectivity.cpp
+++ b/cpp/cmd/afdconnectivity.cpp
@@ -23,7 +23,7 @@
 #include "dwi/tractography/mapping/mapping.h"
 #include "dwi/tractography/properties.h"
 #include "memory.h"
-#include "version.h"
+#include "mrtrix_version.h"
 
 using namespace MR;
 using namespace MR::DWI;
diff --git a/cmd/amp2response.cpp b/cpp/cmd/amp2response.cpp
similarity index 100%
rename from cmd/amp2response.cpp
rename to cpp/cmd/amp2response.cpp
diff --git a/cmd/amp2sh.cpp b/cpp/cmd/amp2sh.cpp
similarity index 100%
rename from cmd/amp2sh.cpp
rename to cpp/cmd/amp2sh.cpp
diff --git a/cmd/connectome2tck.cpp b/cpp/cmd/connectome2tck.cpp
similarity index 100%
rename from cmd/connectome2tck.cpp
rename to cpp/cmd/connectome2tck.cpp
diff --git a/cmd/connectomeedit.cpp b/cpp/cmd/connectomeedit.cpp
similarity index 100%
rename from cmd/connectomeedit.cpp
rename to cpp/cmd/connectomeedit.cpp
diff --git a/cmd/connectomestats.cpp b/cpp/cmd/connectomestats.cpp
similarity index 100%
rename from cmd/connectomestats.cpp
rename to cpp/cmd/connectomestats.cpp
diff --git a/cmd/dcmedit.cpp b/cpp/cmd/dcmedit.cpp
similarity index 100%
rename from cmd/dcmedit.cpp
rename to cpp/cmd/dcmedit.cpp
diff --git a/cmd/dcminfo.cpp b/cpp/cmd/dcminfo.cpp
similarity index 100%
rename from cmd/dcminfo.cpp
rename to cpp/cmd/dcminfo.cpp
diff --git a/cmd/dirflip.cpp b/cpp/cmd/dirflip.cpp
similarity index 100%
rename from cmd/dirflip.cpp
rename to cpp/cmd/dirflip.cpp
diff --git a/cmd/dirgen.cpp b/cpp/cmd/dirgen.cpp
similarity index 100%
rename from cmd/dirgen.cpp
rename to cpp/cmd/dirgen.cpp
diff --git a/cmd/dirmerge.cpp b/cpp/cmd/dirmerge.cpp
similarity index 100%
rename from cmd/dirmerge.cpp
rename to cpp/cmd/dirmerge.cpp
diff --git a/cmd/dirorder.cpp b/cpp/cmd/dirorder.cpp
similarity index 100%
rename from cmd/dirorder.cpp
rename to cpp/cmd/dirorder.cpp
diff --git a/cmd/dirrotate.cpp b/cpp/cmd/dirrotate.cpp
similarity index 100%
rename from cmd/dirrotate.cpp
rename to cpp/cmd/dirrotate.cpp
diff --git a/cmd/dirsplit.cpp b/cpp/cmd/dirsplit.cpp
similarity index 100%
rename from cmd/dirsplit.cpp
rename to cpp/cmd/dirsplit.cpp
diff --git a/cmd/dirstat.cpp b/cpp/cmd/dirstat.cpp
similarity index 100%
rename from cmd/dirstat.cpp
rename to cpp/cmd/dirstat.cpp
diff --git a/cmd/dwi2adc.cpp b/cpp/cmd/dwi2adc.cpp
similarity index 100%
rename from cmd/dwi2adc.cpp
rename to cpp/cmd/dwi2adc.cpp
diff --git a/cmd/dwi2fod.cpp b/cpp/cmd/dwi2fod.cpp
similarity index 100%
rename from cmd/dwi2fod.cpp
rename to cpp/cmd/dwi2fod.cpp
diff --git a/cmd/dwi2tensor.cpp b/cpp/cmd/dwi2tensor.cpp
similarity index 100%
rename from cmd/dwi2tensor.cpp
rename to cpp/cmd/dwi2tensor.cpp
diff --git a/cmd/dwidenoise.cpp b/cpp/cmd/dwidenoise.cpp
similarity index 100%
rename from cmd/dwidenoise.cpp
rename to cpp/cmd/dwidenoise.cpp
diff --git a/cmd/dwiextract.cpp b/cpp/cmd/dwiextract.cpp
similarity index 100%
rename from cmd/dwiextract.cpp
rename to cpp/cmd/dwiextract.cpp
diff --git a/cmd/fixel2peaks.cpp b/cpp/cmd/fixel2peaks.cpp
similarity index 100%
rename from cmd/fixel2peaks.cpp
rename to cpp/cmd/fixel2peaks.cpp
diff --git a/cmd/fixel2sh.cpp b/cpp/cmd/fixel2sh.cpp
similarity index 100%
rename from cmd/fixel2sh.cpp
rename to cpp/cmd/fixel2sh.cpp
diff --git a/cmd/fixel2tsf.cpp b/cpp/cmd/fixel2tsf.cpp
similarity index 100%
rename from cmd/fixel2tsf.cpp
rename to cpp/cmd/fixel2tsf.cpp
diff --git a/cmd/fixel2voxel.cpp b/cpp/cmd/fixel2voxel.cpp
similarity index 100%
rename from cmd/fixel2voxel.cpp
rename to cpp/cmd/fixel2voxel.cpp
diff --git a/cmd/fixelcfestats.cpp b/cpp/cmd/fixelcfestats.cpp
similarity index 100%
rename from cmd/fixelcfestats.cpp
rename to cpp/cmd/fixelcfestats.cpp
diff --git a/cmd/fixelconnectivity.cpp b/cpp/cmd/fixelconnectivity.cpp
similarity index 100%
rename from cmd/fixelconnectivity.cpp
rename to cpp/cmd/fixelconnectivity.cpp
diff --git a/cmd/fixelconvert.cpp b/cpp/cmd/fixelconvert.cpp
similarity index 100%
rename from cmd/fixelconvert.cpp
rename to cpp/cmd/fixelconvert.cpp
diff --git a/cmd/fixelcorrespondence.cpp b/cpp/cmd/fixelcorrespondence.cpp
similarity index 100%
rename from cmd/fixelcorrespondence.cpp
rename to cpp/cmd/fixelcorrespondence.cpp
diff --git a/cmd/fixelcrop.cpp b/cpp/cmd/fixelcrop.cpp
similarity index 100%
rename from cmd/fixelcrop.cpp
rename to cpp/cmd/fixelcrop.cpp
diff --git a/cmd/fixelfilter.cpp b/cpp/cmd/fixelfilter.cpp
similarity index 100%
rename from cmd/fixelfilter.cpp
rename to cpp/cmd/fixelfilter.cpp
diff --git a/cmd/fixelreorient.cpp b/cpp/cmd/fixelreorient.cpp
similarity index 100%
rename from cmd/fixelreorient.cpp
rename to cpp/cmd/fixelreorient.cpp
diff --git a/cmd/fod2dec.cpp b/cpp/cmd/fod2dec.cpp
similarity index 100%
rename from cmd/fod2dec.cpp
rename to cpp/cmd/fod2dec.cpp
diff --git a/cmd/fod2fixel.cpp b/cpp/cmd/fod2fixel.cpp
similarity index 100%
rename from cmd/fod2fixel.cpp
rename to cpp/cmd/fod2fixel.cpp
diff --git a/cmd/label2colour.cpp b/cpp/cmd/label2colour.cpp
similarity index 100%
rename from cmd/label2colour.cpp
rename to cpp/cmd/label2colour.cpp
diff --git a/cmd/label2mesh.cpp b/cpp/cmd/label2mesh.cpp
similarity index 100%
rename from cmd/label2mesh.cpp
rename to cpp/cmd/label2mesh.cpp
diff --git a/cmd/labelconvert.cpp b/cpp/cmd/labelconvert.cpp
similarity index 99%
rename from cmd/labelconvert.cpp
rename to cpp/cmd/labelconvert.cpp
index 0c6cbc4152..de59687d03 100644
--- a/cmd/labelconvert.cpp
+++ b/cpp/cmd/labelconvert.cpp
@@ -18,8 +18,8 @@
 #include "image.h"
 #include "image_helpers.h"
 #include "mrtrix.h"
+#include "mrtrix_version.h"
 #include "transform.h"
-#include "version.h"
 
 #include "algo/loop.h"
 #include "file/path.h"
diff --git a/cmd/labelstats.cpp b/cpp/cmd/labelstats.cpp
similarity index 100%
rename from cmd/labelstats.cpp
rename to cpp/cmd/labelstats.cpp
diff --git a/cmd/maskdump.cpp b/cpp/cmd/maskdump.cpp
similarity index 100%
rename from cmd/maskdump.cpp
rename to cpp/cmd/maskdump.cpp
diff --git a/cmd/maskfilter.cpp b/cpp/cmd/maskfilter.cpp
similarity index 100%
rename from cmd/maskfilter.cpp
rename to cpp/cmd/maskfilter.cpp
diff --git a/cmd/mesh2voxel.cpp b/cpp/cmd/mesh2voxel.cpp
similarity index 100%
rename from cmd/mesh2voxel.cpp
rename to cpp/cmd/mesh2voxel.cpp
diff --git a/cmd/meshconvert.cpp b/cpp/cmd/meshconvert.cpp
similarity index 100%
rename from cmd/meshconvert.cpp
rename to cpp/cmd/meshconvert.cpp
diff --git a/cmd/meshfilter.cpp b/cpp/cmd/meshfilter.cpp
similarity index 100%
rename from cmd/meshfilter.cpp
rename to cpp/cmd/meshfilter.cpp
diff --git a/cmd/mraverageheader.cpp b/cpp/cmd/mraverageheader.cpp
similarity index 100%
rename from cmd/mraverageheader.cpp
rename to cpp/cmd/mraverageheader.cpp
diff --git a/cmd/mrcalc.cpp b/cpp/cmd/mrcalc.cpp
similarity index 100%
rename from cmd/mrcalc.cpp
rename to cpp/cmd/mrcalc.cpp
diff --git a/cmd/mrcat.cpp b/cpp/cmd/mrcat.cpp
similarity index 100%
rename from cmd/mrcat.cpp
rename to cpp/cmd/mrcat.cpp
diff --git a/cmd/mrcentroid.cpp b/cpp/cmd/mrcentroid.cpp
similarity index 100%
rename from cmd/mrcentroid.cpp
rename to cpp/cmd/mrcentroid.cpp
diff --git a/cmd/mrcheckerboardmask.cpp b/cpp/cmd/mrcheckerboardmask.cpp
similarity index 100%
rename from cmd/mrcheckerboardmask.cpp
rename to cpp/cmd/mrcheckerboardmask.cpp
diff --git a/cmd/mrclusterstats.cpp b/cpp/cmd/mrclusterstats.cpp
similarity index 100%
rename from cmd/mrclusterstats.cpp
rename to cpp/cmd/mrclusterstats.cpp
diff --git a/cmd/mrcolour.cpp b/cpp/cmd/mrcolour.cpp
similarity index 100%
rename from cmd/mrcolour.cpp
rename to cpp/cmd/mrcolour.cpp
diff --git a/cmd/mrconvert.cpp b/cpp/cmd/mrconvert.cpp
similarity index 100%
rename from cmd/mrconvert.cpp
rename to cpp/cmd/mrconvert.cpp
diff --git a/cmd/mrdegibbs.cpp b/cpp/cmd/mrdegibbs.cpp
similarity index 100%
rename from cmd/mrdegibbs.cpp
rename to cpp/cmd/mrdegibbs.cpp
diff --git a/cmd/mrdump.cpp b/cpp/cmd/mrdump.cpp
similarity index 100%
rename from cmd/mrdump.cpp
rename to cpp/cmd/mrdump.cpp
diff --git a/cmd/mredit.cpp b/cpp/cmd/mredit.cpp
similarity index 100%
rename from cmd/mredit.cpp
rename to cpp/cmd/mredit.cpp
diff --git a/cmd/mrfilter.cpp b/cpp/cmd/mrfilter.cpp
similarity index 100%
rename from cmd/mrfilter.cpp
rename to cpp/cmd/mrfilter.cpp
diff --git a/cmd/mrgrid.cpp b/cpp/cmd/mrgrid.cpp
similarity index 100%
rename from cmd/mrgrid.cpp
rename to cpp/cmd/mrgrid.cpp
diff --git a/cmd/mrhistmatch.cpp b/cpp/cmd/mrhistmatch.cpp
similarity index 100%
rename from cmd/mrhistmatch.cpp
rename to cpp/cmd/mrhistmatch.cpp
diff --git a/cmd/mrhistogram.cpp b/cpp/cmd/mrhistogram.cpp
similarity index 100%
rename from cmd/mrhistogram.cpp
rename to cpp/cmd/mrhistogram.cpp
diff --git a/cmd/mrinfo.cpp b/cpp/cmd/mrinfo.cpp
similarity index 100%
rename from cmd/mrinfo.cpp
rename to cpp/cmd/mrinfo.cpp
diff --git a/cmd/mrmath.cpp b/cpp/cmd/mrmath.cpp
similarity index 100%
rename from cmd/mrmath.cpp
rename to cpp/cmd/mrmath.cpp
diff --git a/cmd/mrmetric.cpp b/cpp/cmd/mrmetric.cpp
similarity index 100%
rename from cmd/mrmetric.cpp
rename to cpp/cmd/mrmetric.cpp
diff --git a/cmd/mrregister.cpp b/cpp/cmd/mrregister.cpp
similarity index 100%
rename from cmd/mrregister.cpp
rename to cpp/cmd/mrregister.cpp
diff --git a/cmd/mrstats.cpp b/cpp/cmd/mrstats.cpp
similarity index 100%
rename from cmd/mrstats.cpp
rename to cpp/cmd/mrstats.cpp
diff --git a/cmd/mrthreshold.cpp b/cpp/cmd/mrthreshold.cpp
similarity index 100%
rename from cmd/mrthreshold.cpp
rename to cpp/cmd/mrthreshold.cpp
diff --git a/cmd/mrtransform.cpp b/cpp/cmd/mrtransform.cpp
similarity index 100%
rename from cmd/mrtransform.cpp
rename to cpp/cmd/mrtransform.cpp
diff --git a/cmd/mrview.cpp b/cpp/cmd/mrview.cpp
similarity index 94%
rename from cmd/mrview.cpp
rename to cpp/cmd/mrview.cpp
index d45aef8a60..62cf5f4a54 100644
--- a/cmd/mrview.cpp
+++ b/cpp/cmd/mrview.cpp
@@ -15,16 +15,16 @@
  */
 
 // clang-format off
-#include "gui/gui.h"
+#include "gui.h"
 #include "command.h"
 // clang-format on
 
-#include "gui/mrview/icons.h"
-#include "gui/mrview/mode/list.h"
-#include "gui/mrview/sync/syncmanager.h"
-#include "gui/mrview/tool/list.h"
-#include "gui/mrview/window.h"
 #include "memory.h"
+#include "mrview/icons.h"
+#include "mrview/mode/list.h"
+#include "mrview/sync/syncmanager.h"
+#include "mrview/tool/list.h"
+#include "mrview/window.h"
 #include "progressbar.h"
 
 using namespace MR;
@@ -75,7 +75,7 @@ void usage() {
   MR::GUI::MRView::Tool::classname::add_commandline_options(OPTIONS);
   {
     using namespace MR::GUI::MRView::Tool;
-#include "gui/mrview/tool/list.h"
+#include "mrview/tool/list.h"
   }
 
   REQUIRES_AT_LEAST_ONE_ARGUMENT = false;
diff --git a/cmd/mtnormalise.cpp b/cpp/cmd/mtnormalise.cpp
similarity index 100%
rename from cmd/mtnormalise.cpp
rename to cpp/cmd/mtnormalise.cpp
diff --git a/cmd/peaks2amp.cpp b/cpp/cmd/peaks2amp.cpp
similarity index 100%
rename from cmd/peaks2amp.cpp
rename to cpp/cmd/peaks2amp.cpp
diff --git a/cmd/peaks2fixel.cpp b/cpp/cmd/peaks2fixel.cpp
similarity index 100%
rename from cmd/peaks2fixel.cpp
rename to cpp/cmd/peaks2fixel.cpp
diff --git a/cmd/sh2amp.cpp b/cpp/cmd/sh2amp.cpp
similarity index 100%
rename from cmd/sh2amp.cpp
rename to cpp/cmd/sh2amp.cpp
diff --git a/cmd/sh2peaks.cpp b/cpp/cmd/sh2peaks.cpp
similarity index 100%
rename from cmd/sh2peaks.cpp
rename to cpp/cmd/sh2peaks.cpp
diff --git a/cmd/sh2power.cpp b/cpp/cmd/sh2power.cpp
similarity index 100%
rename from cmd/sh2power.cpp
rename to cpp/cmd/sh2power.cpp
diff --git a/cmd/sh2response.cpp b/cpp/cmd/sh2response.cpp
similarity index 100%
rename from cmd/sh2response.cpp
rename to cpp/cmd/sh2response.cpp
diff --git a/cmd/shbasis.cpp b/cpp/cmd/shbasis.cpp
similarity index 100%
rename from cmd/shbasis.cpp
rename to cpp/cmd/shbasis.cpp
diff --git a/cmd/shconv.cpp b/cpp/cmd/shconv.cpp
similarity index 100%
rename from cmd/shconv.cpp
rename to cpp/cmd/shconv.cpp
diff --git a/cmd/shview.cpp b/cpp/cmd/shview.cpp
similarity index 95%
rename from cmd/shview.cpp
rename to cpp/cmd/shview.cpp
index ffa21c2098..91c427130a 100644
--- a/cmd/shview.cpp
+++ b/cpp/cmd/shview.cpp
@@ -15,15 +15,15 @@
  */
 
 // clang-format off
-#include "gui/gui.h"
+#include "gui.h"
 #include "command.h"
 // clang-format on
 
 #include "file/path.h"
-#include "gui/shview/icons.h"
-#include "gui/shview/render_window.h"
 #include "math/SH.h"
 #include "progressbar.h"
+#include "shview/icons.h"
+#include "shview/render_window.h"
 
 using namespace MR;
 using namespace App;
diff --git a/cmd/tck2connectome.cpp b/cpp/cmd/tck2connectome.cpp
similarity index 100%
rename from cmd/tck2connectome.cpp
rename to cpp/cmd/tck2connectome.cpp
diff --git a/cmd/tck2fixel.cpp b/cpp/cmd/tck2fixel.cpp
similarity index 100%
rename from cmd/tck2fixel.cpp
rename to cpp/cmd/tck2fixel.cpp
diff --git a/cmd/tckconvert.cpp b/cpp/cmd/tckconvert.cpp
similarity index 100%
rename from cmd/tckconvert.cpp
rename to cpp/cmd/tckconvert.cpp
diff --git a/cmd/tckdfc.cpp b/cpp/cmd/tckdfc.cpp
similarity index 100%
rename from cmd/tckdfc.cpp
rename to cpp/cmd/tckdfc.cpp
diff --git a/cmd/tckedit.cpp b/cpp/cmd/tckedit.cpp
similarity index 100%
rename from cmd/tckedit.cpp
rename to cpp/cmd/tckedit.cpp
diff --git a/cmd/tckgen.cpp b/cpp/cmd/tckgen.cpp
similarity index 100%
rename from cmd/tckgen.cpp
rename to cpp/cmd/tckgen.cpp
diff --git a/cmd/tckglobal.cpp b/cpp/cmd/tckglobal.cpp
similarity index 99%
rename from cmd/tckglobal.cpp
rename to cpp/cmd/tckglobal.cpp
index eb8dc81afd..ceb5fa7096 100644
--- a/cmd/tckglobal.cpp
+++ b/cpp/cmd/tckglobal.cpp
@@ -22,8 +22,8 @@
 #include "file/matrix.h"
 #include "image.h"
 #include "math/SH.h"
+#include "mrtrix_version.h"
 #include "thread.h"
-#include "version.h"
 
 #include "dwi/tractography/GT/externalenergy.h"
 #include "dwi/tractography/GT/gt.h"
diff --git a/cmd/tckinfo.cpp b/cpp/cmd/tckinfo.cpp
similarity index 100%
rename from cmd/tckinfo.cpp
rename to cpp/cmd/tckinfo.cpp
diff --git a/cmd/tckmap.cpp b/cpp/cmd/tckmap.cpp
similarity index 100%
rename from cmd/tckmap.cpp
rename to cpp/cmd/tckmap.cpp
diff --git a/cmd/tckresample.cpp b/cpp/cmd/tckresample.cpp
similarity index 100%
rename from cmd/tckresample.cpp
rename to cpp/cmd/tckresample.cpp
diff --git a/cmd/tcksample.cpp b/cpp/cmd/tcksample.cpp
similarity index 100%
rename from cmd/tcksample.cpp
rename to cpp/cmd/tcksample.cpp
diff --git a/cmd/tcksift.cpp b/cpp/cmd/tcksift.cpp
similarity index 100%
rename from cmd/tcksift.cpp
rename to cpp/cmd/tcksift.cpp
diff --git a/cmd/tcksift2.cpp b/cpp/cmd/tcksift2.cpp
similarity index 100%
rename from cmd/tcksift2.cpp
rename to cpp/cmd/tcksift2.cpp
diff --git a/cmd/tckstats.cpp b/cpp/cmd/tckstats.cpp
similarity index 100%
rename from cmd/tckstats.cpp
rename to cpp/cmd/tckstats.cpp
diff --git a/cmd/tcktransform.cpp b/cpp/cmd/tcktransform.cpp
similarity index 100%
rename from cmd/tcktransform.cpp
rename to cpp/cmd/tcktransform.cpp
diff --git a/cmd/tensor2metric.cpp b/cpp/cmd/tensor2metric.cpp
similarity index 100%
rename from cmd/tensor2metric.cpp
rename to cpp/cmd/tensor2metric.cpp
diff --git a/cmd/transformcalc.cpp b/cpp/cmd/transformcalc.cpp
similarity index 100%
rename from cmd/transformcalc.cpp
rename to cpp/cmd/transformcalc.cpp
diff --git a/cmd/transformcompose.cpp b/cpp/cmd/transformcompose.cpp
similarity index 100%
rename from cmd/transformcompose.cpp
rename to cpp/cmd/transformcompose.cpp
diff --git a/cmd/transformconvert.cpp b/cpp/cmd/transformconvert.cpp
similarity index 100%
rename from cmd/transformconvert.cpp
rename to cpp/cmd/transformconvert.cpp
diff --git a/cmd/tsfdivide.cpp b/cpp/cmd/tsfdivide.cpp
similarity index 100%
rename from cmd/tsfdivide.cpp
rename to cpp/cmd/tsfdivide.cpp
diff --git a/cmd/tsfinfo.cpp b/cpp/cmd/tsfinfo.cpp
similarity index 100%
rename from cmd/tsfinfo.cpp
rename to cpp/cmd/tsfinfo.cpp
diff --git a/cmd/tsfmult.cpp b/cpp/cmd/tsfmult.cpp
similarity index 100%
rename from cmd/tsfmult.cpp
rename to cpp/cmd/tsfmult.cpp
diff --git a/cmd/tsfsmooth.cpp b/cpp/cmd/tsfsmooth.cpp
similarity index 100%
rename from cmd/tsfsmooth.cpp
rename to cpp/cmd/tsfsmooth.cpp
diff --git a/cmd/tsfthreshold.cpp b/cpp/cmd/tsfthreshold.cpp
similarity index 100%
rename from cmd/tsfthreshold.cpp
rename to cpp/cmd/tsfthreshold.cpp
diff --git a/cmd/tsfvalidate.cpp b/cpp/cmd/tsfvalidate.cpp
similarity index 100%
rename from cmd/tsfvalidate.cpp
rename to cpp/cmd/tsfvalidate.cpp
diff --git a/cmd/vectorstats.cpp b/cpp/cmd/vectorstats.cpp
similarity index 100%
rename from cmd/vectorstats.cpp
rename to cpp/cmd/vectorstats.cpp
diff --git a/cmd/voxel2fixel.cpp b/cpp/cmd/voxel2fixel.cpp
similarity index 100%
rename from cmd/voxel2fixel.cpp
rename to cpp/cmd/voxel2fixel.cpp
diff --git a/cmd/voxel2mesh.cpp b/cpp/cmd/voxel2mesh.cpp
similarity index 100%
rename from cmd/voxel2mesh.cpp
rename to cpp/cmd/voxel2mesh.cpp
diff --git a/cmd/warp2metric.cpp b/cpp/cmd/warp2metric.cpp
similarity index 100%
rename from cmd/warp2metric.cpp
rename to cpp/cmd/warp2metric.cpp
diff --git a/cmd/warpconvert.cpp b/cpp/cmd/warpconvert.cpp
similarity index 100%
rename from cmd/warpconvert.cpp
rename to cpp/cmd/warpconvert.cpp
diff --git a/cmd/warpcorrect.cpp b/cpp/cmd/warpcorrect.cpp
similarity index 100%
rename from cmd/warpcorrect.cpp
rename to cpp/cmd/warpcorrect.cpp
diff --git a/cmd/warpinit.cpp b/cpp/cmd/warpinit.cpp
similarity index 100%
rename from cmd/warpinit.cpp
rename to cpp/cmd/warpinit.cpp
diff --git a/cmd/warpinvert.cpp b/cpp/cmd/warpinvert.cpp
similarity index 100%
rename from cmd/warpinvert.cpp
rename to cpp/cmd/warpinvert.cpp
diff --git a/core/CMakeLists.txt b/cpp/core/CMakeLists.txt
similarity index 52%
rename from core/CMakeLists.txt
rename to cpp/core/CMakeLists.txt
index 6b4211f625..a09046350a 100644
--- a/core/CMakeLists.txt
+++ b/cpp/core/CMakeLists.txt
@@ -1,7 +1,4 @@
 include(CheckSymbolExists)
-
-file(GLOB_RECURSE CORE_SRCS *.cpp *.h)
-
 find_package(ZLIB REQUIRED)
 find_package(FFTW REQUIRED)
 find_package(Git QUIET)
@@ -12,9 +9,6 @@ if(PNG_FOUND)
     message(STATUS "Found PNG: ${PNG_LIBRARIES}")
 endif()
 
-add_library(mrtrix-core SHARED ${CORE_SRCS})
-add_library(mrtrix::core ALIAS mrtrix-core)
-
 # Check to see if we can use lgamma_r() function in custom Math::betaincreg()
 # The function is defined under _REENTRANT on some systems (e.g. MacOS)
 list(APPEND CMAKE_REQUIRED_DEFINITIONS -D_REENTRANT)
@@ -25,33 +19,61 @@ if(NOT MRTRIX_HAVE_LGAMMA_R)
     message(STATUS "No lgamma_r() function found; statistical inference may have poorer multi-threading performance")
 endif()
 
-# On Windows, the library need to be in the same directory as the executables
-if(WIN32)
-    set_target_properties(mrtrix-core PROPERTIES
-        RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/bin
-    )
-endif()
+file(GLOB_RECURSE HEADLESS_SOURCES *.h *.cpp)
 
-set(CORE_VERSION_CPP ${CMAKE_CURRENT_BINARY_DIR}/version.cpp)
+find_package(Git QUIET)
+
+# Create version target and library
+set(MRTRIX_VERSION_CPP ${CMAKE_CURRENT_BINARY_DIR}/mrtrix_version.cpp)
+set(CMD_VERSION_CPP ${CMAKE_CURRENT_BINARY_DIR}/executable_version.cpp)
+
+add_custom_target(mrtrix-executable-version-target ALL
+    COMMAND ${CMAKE_COMMAND}
+        -D GIT_EXECUTABLE=${GIT_EXECUTABLE}
+        -D MRTRIX_BASE_VERSION=${MRTRIX_BASE_VERSION}
+        -D DST=${CMD_VERSION_CPP}
+        -D SRC=${CMAKE_CURRENT_SOURCE_DIR}/executable_version.cpp.in
+        -P ${PROJECT_SOURCE_DIR}/cmake/FindVersion.cmake
+    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+    COMMENT "Generating executable_version.cpp"
+    BYPRODUCTS ${CMD_VERSION_CPP}
+    VERBATIM
+)
 
-add_custom_target(core-version-target ALL
+add_custom_target(mrtrix-version-target ALL
     COMMAND ${CMAKE_COMMAND}
         -D GIT_EXECUTABLE=${GIT_EXECUTABLE}
         -D MRTRIX_BASE_VERSION=${MRTRIX_BASE_VERSION}
-        -D DST=${CMAKE_CURRENT_BINARY_DIR}/version.cpp
-        -D SRC=${CMAKE_CURRENT_SOURCE_DIR}/version.cpp.in
-        -P ${CMAKE_CURRENT_SOURCE_DIR}/../cmake/FindVersion.cmake
+        -D DST=${MRTRIX_VERSION_CPP}
+        -D SRC=${CMAKE_CURRENT_SOURCE_DIR}/mrtrix_version.cpp.in
+        -P ${PROJECT_SOURCE_DIR}/cmake/FindVersion.cmake
     WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-    COMMENT "Generating version.cpp for core library"
-    BYPRODUCTS ${CORE_VERSION_CPP}
+    COMMENT "Generating mrtrix_version.cpp"
+    BYPRODUCTS ${MRTRIX_VERSION_CPP}
     VERBATIM
 )
 
-add_library(mrtrix-core-version-lib STATIC ${CORE_VERSION_CPP})
-add_library(mrtrix::core-version-lib ALIAS mrtrix-core-version-lib)
-add_dependencies(mrtrix-core-version-lib core-version-target)
+add_library(mrtrix-version STATIC ${MRTRIX_VERSION_CPP})
+add_library(mrtrix::version ALIAS mrtrix-version)
+target_include_directories(mrtrix-version PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
+add_dependencies(mrtrix-version mrtrix-version-target)
 
-target_include_directories(mrtrix-core-version-lib PRIVATE
+add_library(mrtrix-executable-version STATIC ${CMD_VERSION_CPP})
+add_library(mrtrix::executable-version ALIAS mrtrix-executable-version)
+target_include_directories(mrtrix-executable-version PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
+add_dependencies(mrtrix-executable-version mrtrix-executable-version-target)
+
+
+if(MRTRIX_BUILD_STATIC)
+    set(MRTRIX_LIBRARY_TYPE STATIC)
+else()
+    set(MRTRIX_LIBRARY_TYPE SHARED)
+endif()
+
+add_library(mrtrix-core ${MRTRIX_LIBRARY_TYPE} ${HEADLESS_SOURCES})
+add_library(mrtrix::core ALIAS mrtrix-core)
+
+target_include_directories(mrtrix-core PUBLIC
     ${CMAKE_CURRENT_SOURCE_DIR}
 )
 
@@ -59,6 +81,7 @@ if(MRTRIX_USE_PCH)
     target_precompile_headers(mrtrix-core PRIVATE
         [["exception.h"]]
         <fstream>
+        <complex>
     )
 endif()
 
@@ -82,20 +105,22 @@ target_link_libraries(mrtrix-core PUBLIC
     Eigen3::Eigen
     ZLIB::ZLIB
     ${FFTW_LIBRARIES}
-    mrtrix::core-version-lib
     mrtrix::common
+    mrtrix::version
     Threads::Threads
-    ${FFTW_LIBRARIES}
     nlohmann_json::nlohmann_json
     nifti::nifti
     half::half
 )
 
-target_include_directories(mrtrix-core PUBLIC
-    ${CMAKE_CURRENT_SOURCE_DIR} ${FFTW_INCLUDES}
-)
+# On Windows, the libraries need to be in the same directory as the executables
+if(WIN32)
+    set_target_properties(mrtrix-core PROPERTIES
+        RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/bin
+    )
+endif()
 
 install(TARGETS mrtrix-core
     RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
     LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-)
+)
\ No newline at end of file
diff --git a/core/adapter/base.h b/cpp/core/adapter/base.h
similarity index 100%
rename from core/adapter/base.h
rename to cpp/core/adapter/base.h
diff --git a/core/adapter/extract.h b/cpp/core/adapter/extract.h
similarity index 100%
rename from core/adapter/extract.h
rename to cpp/core/adapter/extract.h
diff --git a/core/adapter/gaussian1D.h b/cpp/core/adapter/gaussian1D.h
similarity index 100%
rename from core/adapter/gaussian1D.h
rename to cpp/core/adapter/gaussian1D.h
diff --git a/core/adapter/gradient1D.h b/cpp/core/adapter/gradient1D.h
similarity index 100%
rename from core/adapter/gradient1D.h
rename to cpp/core/adapter/gradient1D.h
diff --git a/core/adapter/gradient3D.h b/cpp/core/adapter/gradient3D.h
similarity index 100%
rename from core/adapter/gradient3D.h
rename to cpp/core/adapter/gradient3D.h
diff --git a/core/adapter/jacobian.h b/cpp/core/adapter/jacobian.h
similarity index 100%
rename from core/adapter/jacobian.h
rename to cpp/core/adapter/jacobian.h
diff --git a/core/adapter/median.h b/cpp/core/adapter/median.h
similarity index 100%
rename from core/adapter/median.h
rename to cpp/core/adapter/median.h
diff --git a/core/adapter/neighbourhood3D.h b/cpp/core/adapter/neighbourhood3D.h
similarity index 100%
rename from core/adapter/neighbourhood3D.h
rename to cpp/core/adapter/neighbourhood3D.h
diff --git a/core/adapter/normalise3D.h b/cpp/core/adapter/normalise3D.h
similarity index 100%
rename from core/adapter/normalise3D.h
rename to cpp/core/adapter/normalise3D.h
diff --git a/core/adapter/permute_axes.h b/cpp/core/adapter/permute_axes.h
similarity index 100%
rename from core/adapter/permute_axes.h
rename to cpp/core/adapter/permute_axes.h
diff --git a/core/adapter/regrid.h b/cpp/core/adapter/regrid.h
similarity index 100%
rename from core/adapter/regrid.h
rename to cpp/core/adapter/regrid.h
diff --git a/core/adapter/replicate.h b/cpp/core/adapter/replicate.h
similarity index 100%
rename from core/adapter/replicate.h
rename to cpp/core/adapter/replicate.h
diff --git a/core/adapter/reslice.cpp b/cpp/core/adapter/reslice.cpp
similarity index 100%
rename from core/adapter/reslice.cpp
rename to cpp/core/adapter/reslice.cpp
diff --git a/core/adapter/reslice.h b/cpp/core/adapter/reslice.h
similarity index 100%
rename from core/adapter/reslice.h
rename to cpp/core/adapter/reslice.h
diff --git a/core/adapter/subset.h b/cpp/core/adapter/subset.h
similarity index 100%
rename from core/adapter/subset.h
rename to cpp/core/adapter/subset.h
diff --git a/core/adapter/warp.h b/cpp/core/adapter/warp.h
similarity index 100%
rename from core/adapter/warp.h
rename to cpp/core/adapter/warp.h
diff --git a/core/algo/copy.h b/cpp/core/algo/copy.h
similarity index 100%
rename from core/algo/copy.h
rename to cpp/core/algo/copy.h
diff --git a/core/algo/histogram.cpp b/cpp/core/algo/histogram.cpp
similarity index 100%
rename from core/algo/histogram.cpp
rename to cpp/core/algo/histogram.cpp
diff --git a/core/algo/histogram.h b/cpp/core/algo/histogram.h
similarity index 100%
rename from core/algo/histogram.h
rename to cpp/core/algo/histogram.h
diff --git a/core/algo/iterator.h b/cpp/core/algo/iterator.h
similarity index 100%
rename from core/algo/iterator.h
rename to cpp/core/algo/iterator.h
diff --git a/core/algo/loop.h b/cpp/core/algo/loop.h
similarity index 100%
rename from core/algo/loop.h
rename to cpp/core/algo/loop.h
diff --git a/core/algo/min_max.h b/cpp/core/algo/min_max.h
similarity index 100%
rename from core/algo/min_max.h
rename to cpp/core/algo/min_max.h
diff --git a/core/algo/neighbourhooditerator.h b/cpp/core/algo/neighbourhooditerator.h
similarity index 100%
rename from core/algo/neighbourhooditerator.h
rename to cpp/core/algo/neighbourhooditerator.h
diff --git a/core/algo/random_loop.h b/cpp/core/algo/random_loop.h
similarity index 100%
rename from core/algo/random_loop.h
rename to cpp/core/algo/random_loop.h
diff --git a/core/algo/random_threaded_loop.h b/cpp/core/algo/random_threaded_loop.h
similarity index 100%
rename from core/algo/random_threaded_loop.h
rename to cpp/core/algo/random_threaded_loop.h
diff --git a/core/algo/stochastic_threaded_loop.h b/cpp/core/algo/stochastic_threaded_loop.h
similarity index 100%
rename from core/algo/stochastic_threaded_loop.h
rename to cpp/core/algo/stochastic_threaded_loop.h
diff --git a/core/algo/threaded_copy.h b/cpp/core/algo/threaded_copy.h
similarity index 100%
rename from core/algo/threaded_copy.h
rename to cpp/core/algo/threaded_copy.h
diff --git a/core/algo/threaded_loop.h b/cpp/core/algo/threaded_loop.h
similarity index 100%
rename from core/algo/threaded_loop.h
rename to cpp/core/algo/threaded_loop.h
diff --git a/core/app.cpp b/cpp/core/app.cpp
similarity index 98%
rename from core/app.cpp
rename to cpp/core/app.cpp
index b0347fa429..3594d95e79 100644
--- a/core/app.cpp
+++ b/cpp/core/app.cpp
@@ -22,8 +22,10 @@
 
 #include "app.h"
 #include "debug.h"
+#include "executable_version.h"
 #include "file/config.h"
 #include "file/path.h"
+#include "mrtrix_version.h"
 #include "progressbar.h"
 #include "signal_handler.h"
 
@@ -114,7 +116,6 @@ const std::thread::id main_thread_ID = std::this_thread::get_id();
 
 const char *project_version = nullptr;
 const char *project_build_date = nullptr;
-const char *executable_uses_mrtrix_version = nullptr;
 
 std::vector<std::string> raw_arguments_list;
 
@@ -1151,16 +1152,6 @@ void init(int cmdline_argc, const char *const *cmdline_argv) {
     NAME.erase(NAME.size() - 4);
 #endif
 
-  if (strcmp(mrtrix_version, executable_uses_mrtrix_version) != 0) {
-    Exception E("executable was compiled for a different version of the MRtrix3 library!");
-    E.push_back(std::string("  ") + NAME + " version: " + executable_uses_mrtrix_version);
-    E.push_back(std::string("  library version: ") + mrtrix_version);
-    E.push_back("You may need to erase files left over from prior MRtrix3 versions;");
-    E.push_back("eg. core/version.cpp; src/exec_version.cpp");
-    E.push_back(", and re-configure cmake");
-    throw E;
-  }
-
   auto argv_quoted = [](const std::string &s) -> std::string {
     for (size_t i = 0; i != s.size(); ++i) {
       if (!(isalnum(s[i]) || s[i] == '.' || s[i] == '_' || s[i] == '-' || s[i] == '/')) {
diff --git a/core/app.h b/cpp/core/app.h
similarity index 99%
rename from core/app.h
rename to cpp/core/app.h
index 1af93e0e74..d678d6f0c4 100644
--- a/core/app.h
+++ b/cpp/core/app.h
@@ -34,8 +34,8 @@ extern void run();
 
 namespace MR::App {
 
-extern const char *mrtrix_version;
-extern const char *build_date;
+extern const std::string mrtrix_version;
+extern const std::string build_date;
 extern int log_level;
 extern int exit_error_code;
 extern std::string NAME;
diff --git a/core/apply.h b/cpp/core/apply.h
similarity index 100%
rename from core/apply.h
rename to cpp/core/apply.h
diff --git a/core/axes.cpp b/cpp/core/axes.cpp
similarity index 100%
rename from core/axes.cpp
rename to cpp/core/axes.cpp
diff --git a/core/axes.h b/cpp/core/axes.h
similarity index 100%
rename from core/axes.h
rename to cpp/core/axes.h
diff --git a/core/cmdline_option.h b/cpp/core/cmdline_option.h
similarity index 100%
rename from core/cmdline_option.h
rename to cpp/core/cmdline_option.h
diff --git a/src/colourmap.cpp b/cpp/core/colourmap.cpp
similarity index 100%
rename from src/colourmap.cpp
rename to cpp/core/colourmap.cpp
diff --git a/src/colourmap.h b/cpp/core/colourmap.h
similarity index 100%
rename from src/colourmap.h
rename to cpp/core/colourmap.h
diff --git a/core/command.h b/cpp/core/command.h
similarity index 83%
rename from core/command.h
rename to cpp/core/command.h
index aec23d4415..59c1e924a8 100644
--- a/core/command.h
+++ b/cpp/core/command.h
@@ -21,8 +21,9 @@
 #endif
 
 #include "app.h"
-#include "exec_version.h"
+#include "executable_version.h"
 #include "mrtrix.h"
+#include "mrtrix_version.h"
 #ifdef MRTRIX_PROJECT
 namespace MR {
 namespace App {
@@ -36,7 +37,6 @@ void set_project_version();
 #ifdef MRTRIX_AS_R_LIBRARY
 
 extern "C" void R_main(int *cmdline_argc, char **cmdline_argv) {
-  ::MR::App::set_executable_uses_mrtrix_version();
 #ifdef MRTRIX_PROJECT
   ::MR::App::set_project_version();
 #endif
@@ -70,6 +70,16 @@ extern "C" void R_usage(char **output) {
 #else
 
 int main(int cmdline_argc, char **cmdline_argv) {
+  if (MR::App::mrtrix_version != MR::App::mrtrix_executable_version) {
+    MR::Exception E("executable was compiled for a different version of the MRtrix3 library!");
+    E.push_back(std::string("  ") + MR::App::NAME + " version: " + MR::App::mrtrix_executable_version);
+    E.push_back(std::string("  library version: ") + MR::App::mrtrix_version);
+    E.push_back("You may need to erase files left over from prior MRtrix3 versions;");
+    E.push_back("eg. core/version.cpp; src/exec_version.cpp");
+    E.push_back(", and re-configure cmake");
+    throw E;
+  }
+
 #ifdef FLUSH_TO_ZERO
   // use gcc switches: -msse -mfpmath=sse -ffast-math
   int mxcsr = _mm_getcsr();
@@ -79,7 +89,6 @@ int main(int cmdline_argc, char **cmdline_argv) {
   mxcsr |= (1 << 6); // denormals-are-zero
   _mm_setcsr(mxcsr);
 #endif
-  ::MR::App::set_executable_uses_mrtrix_version();
 #ifdef MRTRIX_PROJECT
   ::MR::App::set_project_version();
 #endif
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rename from src/dwi/tractography/scalar_file.h
rename to cpp/core/dwi/tractography/scalar_file.h
diff --git a/src/dwi/tractography/seeding/base.h b/cpp/core/dwi/tractography/seeding/base.h
similarity index 100%
rename from src/dwi/tractography/seeding/base.h
rename to cpp/core/dwi/tractography/seeding/base.h
diff --git a/src/dwi/tractography/seeding/basic.cpp b/cpp/core/dwi/tractography/seeding/basic.cpp
similarity index 100%
rename from src/dwi/tractography/seeding/basic.cpp
rename to cpp/core/dwi/tractography/seeding/basic.cpp
diff --git a/src/dwi/tractography/seeding/basic.h b/cpp/core/dwi/tractography/seeding/basic.h
similarity index 100%
rename from src/dwi/tractography/seeding/basic.h
rename to cpp/core/dwi/tractography/seeding/basic.h
diff --git a/src/dwi/tractography/seeding/dynamic.cpp b/cpp/core/dwi/tractography/seeding/dynamic.cpp
similarity index 100%
rename from src/dwi/tractography/seeding/dynamic.cpp
rename to cpp/core/dwi/tractography/seeding/dynamic.cpp
diff --git a/src/dwi/tractography/seeding/dynamic.h b/cpp/core/dwi/tractography/seeding/dynamic.h
similarity index 100%
rename from src/dwi/tractography/seeding/dynamic.h
rename to cpp/core/dwi/tractography/seeding/dynamic.h
diff --git a/src/dwi/tractography/seeding/gmwmi.cpp b/cpp/core/dwi/tractography/seeding/gmwmi.cpp
similarity index 100%
rename from src/dwi/tractography/seeding/gmwmi.cpp
rename to cpp/core/dwi/tractography/seeding/gmwmi.cpp
diff --git a/src/dwi/tractography/seeding/gmwmi.h b/cpp/core/dwi/tractography/seeding/gmwmi.h
similarity index 100%
rename from src/dwi/tractography/seeding/gmwmi.h
rename to cpp/core/dwi/tractography/seeding/gmwmi.h
diff --git a/src/dwi/tractography/seeding/list.cpp b/cpp/core/dwi/tractography/seeding/list.cpp
similarity index 100%
rename from src/dwi/tractography/seeding/list.cpp
rename to cpp/core/dwi/tractography/seeding/list.cpp
diff --git a/src/dwi/tractography/seeding/list.h b/cpp/core/dwi/tractography/seeding/list.h
similarity index 100%
rename from src/dwi/tractography/seeding/list.h
rename to cpp/core/dwi/tractography/seeding/list.h
diff --git a/src/dwi/tractography/seeding/seeding.cpp b/cpp/core/dwi/tractography/seeding/seeding.cpp
similarity index 100%
rename from src/dwi/tractography/seeding/seeding.cpp
rename to cpp/core/dwi/tractography/seeding/seeding.cpp
diff --git a/src/dwi/tractography/seeding/seeding.h b/cpp/core/dwi/tractography/seeding/seeding.h
similarity index 100%
rename from src/dwi/tractography/seeding/seeding.h
rename to cpp/core/dwi/tractography/seeding/seeding.h
diff --git a/src/dwi/tractography/streamline.h b/cpp/core/dwi/tractography/streamline.h
similarity index 100%
rename from src/dwi/tractography/streamline.h
rename to cpp/core/dwi/tractography/streamline.h
diff --git a/src/dwi/tractography/tracking/early_exit.cpp b/cpp/core/dwi/tractography/tracking/early_exit.cpp
similarity index 100%
rename from src/dwi/tractography/tracking/early_exit.cpp
rename to cpp/core/dwi/tractography/tracking/early_exit.cpp
diff --git a/src/dwi/tractography/tracking/early_exit.h b/cpp/core/dwi/tractography/tracking/early_exit.h
similarity index 100%
rename from src/dwi/tractography/tracking/early_exit.h
rename to cpp/core/dwi/tractography/tracking/early_exit.h
diff --git a/src/dwi/tractography/tracking/exec.h b/cpp/core/dwi/tractography/tracking/exec.h
similarity index 100%
rename from src/dwi/tractography/tracking/exec.h
rename to cpp/core/dwi/tractography/tracking/exec.h
diff --git a/src/dwi/tractography/tracking/generated_track.h b/cpp/core/dwi/tractography/tracking/generated_track.h
similarity index 100%
rename from src/dwi/tractography/tracking/generated_track.h
rename to cpp/core/dwi/tractography/tracking/generated_track.h
diff --git a/src/dwi/tractography/tracking/method.cpp b/cpp/core/dwi/tractography/tracking/method.cpp
similarity index 100%
rename from src/dwi/tractography/tracking/method.cpp
rename to cpp/core/dwi/tractography/tracking/method.cpp
diff --git a/src/dwi/tractography/tracking/method.h b/cpp/core/dwi/tractography/tracking/method.h
similarity index 100%
rename from src/dwi/tractography/tracking/method.h
rename to cpp/core/dwi/tractography/tracking/method.h
diff --git a/src/dwi/tractography/tracking/shared.cpp b/cpp/core/dwi/tractography/tracking/shared.cpp
similarity index 100%
rename from src/dwi/tractography/tracking/shared.cpp
rename to cpp/core/dwi/tractography/tracking/shared.cpp
diff --git a/src/dwi/tractography/tracking/shared.h b/cpp/core/dwi/tractography/tracking/shared.h
similarity index 100%
rename from src/dwi/tractography/tracking/shared.h
rename to cpp/core/dwi/tractography/tracking/shared.h
diff --git a/src/dwi/tractography/tracking/tractography.cpp b/cpp/core/dwi/tractography/tracking/tractography.cpp
similarity index 100%
rename from src/dwi/tractography/tracking/tractography.cpp
rename to cpp/core/dwi/tractography/tracking/tractography.cpp
diff --git a/src/dwi/tractography/tracking/tractography.h b/cpp/core/dwi/tractography/tracking/tractography.h
similarity index 100%
rename from src/dwi/tractography/tracking/tractography.h
rename to cpp/core/dwi/tractography/tracking/tractography.h
diff --git a/src/dwi/tractography/tracking/types.h b/cpp/core/dwi/tractography/tracking/types.h
similarity index 100%
rename from src/dwi/tractography/tracking/types.h
rename to cpp/core/dwi/tractography/tracking/types.h
diff --git a/src/dwi/tractography/tracking/write_kernel.cpp b/cpp/core/dwi/tractography/tracking/write_kernel.cpp
similarity index 100%
rename from src/dwi/tractography/tracking/write_kernel.cpp
rename to cpp/core/dwi/tractography/tracking/write_kernel.cpp
diff --git a/src/dwi/tractography/tracking/write_kernel.h b/cpp/core/dwi/tractography/tracking/write_kernel.h
similarity index 100%
rename from src/dwi/tractography/tracking/write_kernel.h
rename to cpp/core/dwi/tractography/tracking/write_kernel.h
diff --git a/src/dwi/tractography/weights.cpp b/cpp/core/dwi/tractography/weights.cpp
similarity index 100%
rename from src/dwi/tractography/weights.cpp
rename to cpp/core/dwi/tractography/weights.cpp
diff --git a/src/dwi/tractography/weights.h b/cpp/core/dwi/tractography/weights.h
similarity index 100%
rename from src/dwi/tractography/weights.h
rename to cpp/core/dwi/tractography/weights.h
diff --git a/core/eigen_plugins/array.h b/cpp/core/eigen_plugins/array.h
similarity index 100%
rename from core/eigen_plugins/array.h
rename to cpp/core/eigen_plugins/array.h
diff --git a/core/eigen_plugins/dense_base.h b/cpp/core/eigen_plugins/dense_base.h
similarity index 100%
rename from core/eigen_plugins/dense_base.h
rename to cpp/core/eigen_plugins/dense_base.h
diff --git a/core/eigen_plugins/matrix.h b/cpp/core/eigen_plugins/matrix.h
similarity index 100%
rename from core/eigen_plugins/matrix.h
rename to cpp/core/eigen_plugins/matrix.h
diff --git a/core/exception.cpp b/cpp/core/exception.cpp
similarity index 100%
rename from core/exception.cpp
rename to cpp/core/exception.cpp
diff --git a/core/exception.h b/cpp/core/exception.h
similarity index 100%
rename from core/exception.h
rename to cpp/core/exception.h
diff --git a/cpp/core/executable_version.cpp.in b/cpp/core/executable_version.cpp.in
new file mode 100644
index 0000000000..8f9ce69bca
--- /dev/null
+++ b/cpp/core/executable_version.cpp.in
@@ -0,0 +1,5 @@
+#include "executable_version.h"
+
+namespace MR::App {
+const std::string mrtrix_executable_version = "@MRTRIX_VERSION@";
+}
diff --git a/src/exec_version.h b/cpp/core/executable_version.h
similarity index 88%
rename from src/exec_version.h
rename to cpp/core/executable_version.h
index a5533b4271..ca85af1c7f 100644
--- a/src/exec_version.h
+++ b/cpp/core/executable_version.h
@@ -15,7 +15,8 @@
  */
 
 #pragma once
+#include <string>
 
 namespace MR::App {
-void set_executable_uses_mrtrix_version();
-}
+extern const std::string mrtrix_executable_version;
+} // namespace MR::App
diff --git a/core/fetch_store.cpp b/cpp/core/fetch_store.cpp
similarity index 100%
rename from core/fetch_store.cpp
rename to cpp/core/fetch_store.cpp
diff --git a/core/fetch_store.h b/cpp/core/fetch_store.h
similarity index 100%
rename from core/fetch_store.h
rename to cpp/core/fetch_store.h
diff --git a/core/file/config.cpp b/cpp/core/file/config.cpp
similarity index 100%
rename from core/file/config.cpp
rename to cpp/core/file/config.cpp
diff --git a/core/file/config.h b/cpp/core/file/config.h
similarity index 100%
rename from core/file/config.h
rename to cpp/core/file/config.h
diff --git a/core/file/copy.h b/cpp/core/file/copy.h
similarity index 100%
rename from core/file/copy.h
rename to cpp/core/file/copy.h
diff --git a/core/file/dicom/csa_entry.h b/cpp/core/file/dicom/csa_entry.h
similarity index 100%
rename from core/file/dicom/csa_entry.h
rename to cpp/core/file/dicom/csa_entry.h
diff --git a/core/file/dicom/definitions.h b/cpp/core/file/dicom/definitions.h
similarity index 100%
rename from core/file/dicom/definitions.h
rename to cpp/core/file/dicom/definitions.h
diff --git a/core/file/dicom/dict.cpp b/cpp/core/file/dicom/dict.cpp
similarity index 100%
rename from core/file/dicom/dict.cpp
rename to cpp/core/file/dicom/dict.cpp
diff --git a/core/file/dicom/element.cpp b/cpp/core/file/dicom/element.cpp
similarity index 100%
rename from core/file/dicom/element.cpp
rename to cpp/core/file/dicom/element.cpp
diff --git a/core/file/dicom/element.h b/cpp/core/file/dicom/element.h
similarity index 100%
rename from core/file/dicom/element.h
rename to cpp/core/file/dicom/element.h
diff --git a/core/file/dicom/image.cpp b/cpp/core/file/dicom/image.cpp
similarity index 100%
rename from core/file/dicom/image.cpp
rename to cpp/core/file/dicom/image.cpp
diff --git a/core/file/dicom/image.h b/cpp/core/file/dicom/image.h
similarity index 100%
rename from core/file/dicom/image.h
rename to cpp/core/file/dicom/image.h
diff --git a/core/file/dicom/mapper.cpp b/cpp/core/file/dicom/mapper.cpp
similarity index 100%
rename from core/file/dicom/mapper.cpp
rename to cpp/core/file/dicom/mapper.cpp
diff --git a/core/file/dicom/mapper.h b/cpp/core/file/dicom/mapper.h
similarity index 100%
rename from core/file/dicom/mapper.h
rename to cpp/core/file/dicom/mapper.h
diff --git a/core/file/dicom/patient.cpp b/cpp/core/file/dicom/patient.cpp
similarity index 100%
rename from core/file/dicom/patient.cpp
rename to cpp/core/file/dicom/patient.cpp
diff --git a/core/file/dicom/patient.h b/cpp/core/file/dicom/patient.h
similarity index 100%
rename from core/file/dicom/patient.h
rename to cpp/core/file/dicom/patient.h
diff --git a/core/file/dicom/quick_scan.cpp b/cpp/core/file/dicom/quick_scan.cpp
similarity index 100%
rename from core/file/dicom/quick_scan.cpp
rename to cpp/core/file/dicom/quick_scan.cpp
diff --git a/core/file/dicom/quick_scan.h b/cpp/core/file/dicom/quick_scan.h
similarity index 100%
rename from core/file/dicom/quick_scan.h
rename to cpp/core/file/dicom/quick_scan.h
diff --git a/core/file/dicom/select_cmdline.cpp b/cpp/core/file/dicom/select_cmdline.cpp
similarity index 100%
rename from core/file/dicom/select_cmdline.cpp
rename to cpp/core/file/dicom/select_cmdline.cpp
diff --git a/core/file/dicom/series.cpp b/cpp/core/file/dicom/series.cpp
similarity index 100%
rename from core/file/dicom/series.cpp
rename to cpp/core/file/dicom/series.cpp
diff --git a/core/file/dicom/series.h b/cpp/core/file/dicom/series.h
similarity index 100%
rename from core/file/dicom/series.h
rename to cpp/core/file/dicom/series.h
diff --git a/core/file/dicom/study.cpp b/cpp/core/file/dicom/study.cpp
similarity index 100%
rename from core/file/dicom/study.cpp
rename to cpp/core/file/dicom/study.cpp
diff --git a/core/file/dicom/study.h b/cpp/core/file/dicom/study.h
similarity index 100%
rename from core/file/dicom/study.h
rename to cpp/core/file/dicom/study.h
diff --git a/core/file/dicom/tree.cpp b/cpp/core/file/dicom/tree.cpp
similarity index 100%
rename from core/file/dicom/tree.cpp
rename to cpp/core/file/dicom/tree.cpp
diff --git a/core/file/dicom/tree.h b/cpp/core/file/dicom/tree.h
similarity index 100%
rename from core/file/dicom/tree.h
rename to cpp/core/file/dicom/tree.h
diff --git a/core/file/entry.h b/cpp/core/file/entry.h
similarity index 100%
rename from core/file/entry.h
rename to cpp/core/file/entry.h
diff --git a/core/file/gz.h b/cpp/core/file/gz.h
similarity index 100%
rename from core/file/gz.h
rename to cpp/core/file/gz.h
diff --git a/core/file/json_utils.cpp b/cpp/core/file/json_utils.cpp
similarity index 100%
rename from core/file/json_utils.cpp
rename to cpp/core/file/json_utils.cpp
diff --git a/core/file/json_utils.h b/cpp/core/file/json_utils.h
similarity index 100%
rename from core/file/json_utils.h
rename to cpp/core/file/json_utils.h
diff --git a/core/file/key_value.cpp b/cpp/core/file/key_value.cpp
similarity index 100%
rename from core/file/key_value.cpp
rename to cpp/core/file/key_value.cpp
diff --git a/core/file/key_value.h b/cpp/core/file/key_value.h
similarity index 100%
rename from core/file/key_value.h
rename to cpp/core/file/key_value.h
diff --git a/core/file/matrix.h b/cpp/core/file/matrix.h
similarity index 100%
rename from core/file/matrix.h
rename to cpp/core/file/matrix.h
diff --git a/core/file/mgh.cpp b/cpp/core/file/mgh.cpp
similarity index 100%
rename from core/file/mgh.cpp
rename to cpp/core/file/mgh.cpp
diff --git a/core/file/mgh.h b/cpp/core/file/mgh.h
similarity index 100%
rename from core/file/mgh.h
rename to cpp/core/file/mgh.h
diff --git a/core/file/mmap.cpp b/cpp/core/file/mmap.cpp
similarity index 100%
rename from core/file/mmap.cpp
rename to cpp/core/file/mmap.cpp
diff --git a/core/file/mmap.h b/cpp/core/file/mmap.h
similarity index 100%
rename from core/file/mmap.h
rename to cpp/core/file/mmap.h
diff --git a/core/file/name_parser.cpp b/cpp/core/file/name_parser.cpp
similarity index 100%
rename from core/file/name_parser.cpp
rename to cpp/core/file/name_parser.cpp
diff --git a/core/file/name_parser.h b/cpp/core/file/name_parser.h
similarity index 100%
rename from core/file/name_parser.h
rename to cpp/core/file/name_parser.h
diff --git a/core/file/nifti_utils.cpp b/cpp/core/file/nifti_utils.cpp
similarity index 100%
rename from core/file/nifti_utils.cpp
rename to cpp/core/file/nifti_utils.cpp
diff --git a/core/file/nifti_utils.h b/cpp/core/file/nifti_utils.h
similarity index 100%
rename from core/file/nifti_utils.h
rename to cpp/core/file/nifti_utils.h
diff --git a/core/file/npy.cpp b/cpp/core/file/npy.cpp
similarity index 100%
rename from core/file/npy.cpp
rename to cpp/core/file/npy.cpp
diff --git a/core/file/npy.h b/cpp/core/file/npy.h
similarity index 100%
rename from core/file/npy.h
rename to cpp/core/file/npy.h
diff --git a/core/file/ofstream.cpp b/cpp/core/file/ofstream.cpp
similarity index 100%
rename from core/file/ofstream.cpp
rename to cpp/core/file/ofstream.cpp
diff --git a/core/file/ofstream.h b/cpp/core/file/ofstream.h
similarity index 100%
rename from core/file/ofstream.h
rename to cpp/core/file/ofstream.h
diff --git a/core/file/path.h b/cpp/core/file/path.h
similarity index 100%
rename from core/file/path.h
rename to cpp/core/file/path.h
diff --git a/core/file/png.cpp b/cpp/core/file/png.cpp
similarity index 100%
rename from core/file/png.cpp
rename to cpp/core/file/png.cpp
diff --git a/core/file/png.h b/cpp/core/file/png.h
similarity index 100%
rename from core/file/png.h
rename to cpp/core/file/png.h
diff --git a/core/file/pyconfig.h b/cpp/core/file/pyconfig.h
similarity index 100%
rename from core/file/pyconfig.h
rename to cpp/core/file/pyconfig.h
diff --git a/core/file/utils.cpp b/cpp/core/file/utils.cpp
similarity index 100%
rename from core/file/utils.cpp
rename to cpp/core/file/utils.cpp
diff --git a/core/file/utils.h b/cpp/core/file/utils.h
similarity index 100%
rename from core/file/utils.h
rename to cpp/core/file/utils.h
diff --git a/core/filter/base.h b/cpp/core/filter/base.h
similarity index 100%
rename from core/filter/base.h
rename to cpp/core/filter/base.h
diff --git a/core/filter/connected_components.cpp b/cpp/core/filter/connected_components.cpp
similarity index 100%
rename from core/filter/connected_components.cpp
rename to cpp/core/filter/connected_components.cpp
diff --git a/core/filter/connected_components.h b/cpp/core/filter/connected_components.h
similarity index 100%
rename from core/filter/connected_components.h
rename to cpp/core/filter/connected_components.h
diff --git a/core/filter/dilate.h b/cpp/core/filter/dilate.h
similarity index 100%
rename from core/filter/dilate.h
rename to cpp/core/filter/dilate.h
diff --git a/core/filter/erode.h b/cpp/core/filter/erode.h
similarity index 100%
rename from core/filter/erode.h
rename to cpp/core/filter/erode.h
diff --git a/core/filter/fill.h b/cpp/core/filter/fill.h
similarity index 100%
rename from core/filter/fill.h
rename to cpp/core/filter/fill.h
diff --git a/core/filter/gradient.h b/cpp/core/filter/gradient.h
similarity index 100%
rename from core/filter/gradient.h
rename to cpp/core/filter/gradient.h
diff --git a/core/filter/mask_clean.h b/cpp/core/filter/mask_clean.h
similarity index 100%
rename from core/filter/mask_clean.h
rename to cpp/core/filter/mask_clean.h
diff --git a/core/filter/median.h b/cpp/core/filter/median.h
similarity index 100%
rename from core/filter/median.h
rename to cpp/core/filter/median.h
diff --git a/core/filter/normalise.h b/cpp/core/filter/normalise.h
similarity index 100%
rename from core/filter/normalise.h
rename to cpp/core/filter/normalise.h
diff --git a/core/filter/optimal_threshold.h b/cpp/core/filter/optimal_threshold.h
similarity index 100%
rename from core/filter/optimal_threshold.h
rename to cpp/core/filter/optimal_threshold.h
diff --git a/core/filter/resize.h b/cpp/core/filter/resize.h
similarity index 100%
rename from core/filter/resize.h
rename to cpp/core/filter/resize.h
diff --git a/core/filter/reslice.h b/cpp/core/filter/reslice.h
similarity index 100%
rename from core/filter/reslice.h
rename to cpp/core/filter/reslice.h
diff --git a/core/filter/smooth.h b/cpp/core/filter/smooth.h
similarity index 100%
rename from core/filter/smooth.h
rename to cpp/core/filter/smooth.h
diff --git a/core/filter/warp.h b/cpp/core/filter/warp.h
similarity index 100%
rename from core/filter/warp.h
rename to cpp/core/filter/warp.h
diff --git a/core/filter/zclean.h b/cpp/core/filter/zclean.h
similarity index 100%
rename from core/filter/zclean.h
rename to cpp/core/filter/zclean.h
diff --git a/src/fixel/filter/base.h b/cpp/core/fixel/filter/base.h
similarity index 100%
rename from src/fixel/filter/base.h
rename to cpp/core/fixel/filter/base.h
diff --git a/src/fixel/filter/connect.cpp b/cpp/core/fixel/filter/connect.cpp
similarity index 100%
rename from src/fixel/filter/connect.cpp
rename to cpp/core/fixel/filter/connect.cpp
diff --git a/src/fixel/filter/connect.h b/cpp/core/fixel/filter/connect.h
similarity index 100%
rename from src/fixel/filter/connect.h
rename to cpp/core/fixel/filter/connect.h
diff --git a/src/fixel/filter/smooth.cpp b/cpp/core/fixel/filter/smooth.cpp
similarity index 100%
rename from src/fixel/filter/smooth.cpp
rename to cpp/core/fixel/filter/smooth.cpp
diff --git a/src/fixel/filter/smooth.h b/cpp/core/fixel/filter/smooth.h
similarity index 100%
rename from src/fixel/filter/smooth.h
rename to cpp/core/fixel/filter/smooth.h
diff --git a/core/fixel/fixel.cpp b/cpp/core/fixel/fixel.cpp
similarity index 97%
rename from core/fixel/fixel.cpp
rename to cpp/core/fixel/fixel.cpp
index 74e75defe9..e5c8f9c085 100644
--- a/core/fixel/fixel.cpp
+++ b/cpp/core/fixel/fixel.cpp
@@ -15,7 +15,7 @@
  */
 
 #include "fixel/fixel.h"
-#include "version.h"
+#include "mrtrix_version.h"
 
 namespace MR::Fixel {
 
diff --git a/core/fixel/fixel.h b/cpp/core/fixel/fixel.h
similarity index 100%
rename from core/fixel/fixel.h
rename to cpp/core/fixel/fixel.h
diff --git a/core/fixel/helpers.h b/cpp/core/fixel/helpers.h
similarity index 100%
rename from core/fixel/helpers.h
rename to cpp/core/fixel/helpers.h
diff --git a/src/fixel/index_remapper.cpp b/cpp/core/fixel/index_remapper.cpp
similarity index 100%
rename from src/fixel/index_remapper.cpp
rename to cpp/core/fixel/index_remapper.cpp
diff --git a/src/fixel/index_remapper.h b/cpp/core/fixel/index_remapper.h
similarity index 100%
rename from src/fixel/index_remapper.h
rename to cpp/core/fixel/index_remapper.h
diff --git a/core/fixel/legacy/fixel_metric.h b/cpp/core/fixel/legacy/fixel_metric.h
similarity index 100%
rename from core/fixel/legacy/fixel_metric.h
rename to cpp/core/fixel/legacy/fixel_metric.h
diff --git a/core/fixel/legacy/image.h b/cpp/core/fixel/legacy/image.h
similarity index 100%
rename from core/fixel/legacy/image.h
rename to cpp/core/fixel/legacy/image.h
diff --git a/core/fixel/legacy/keys.h b/cpp/core/fixel/legacy/keys.h
similarity index 100%
rename from core/fixel/legacy/keys.h
rename to cpp/core/fixel/legacy/keys.h
diff --git a/core/fixel/loop.h b/cpp/core/fixel/loop.h
similarity index 100%
rename from core/fixel/loop.h
rename to cpp/core/fixel/loop.h
diff --git a/src/fixel/matrix.cpp b/cpp/core/fixel/matrix.cpp
similarity index 100%
rename from src/fixel/matrix.cpp
rename to cpp/core/fixel/matrix.cpp
diff --git a/src/fixel/matrix.h b/cpp/core/fixel/matrix.h
similarity index 100%
rename from src/fixel/matrix.h
rename to cpp/core/fixel/matrix.h
diff --git a/core/formats/dicom.cpp b/cpp/core/formats/dicom.cpp
similarity index 100%
rename from core/formats/dicom.cpp
rename to cpp/core/formats/dicom.cpp
diff --git a/core/formats/list.cpp b/cpp/core/formats/list.cpp
similarity index 100%
rename from core/formats/list.cpp
rename to cpp/core/formats/list.cpp
diff --git a/core/formats/list.h b/cpp/core/formats/list.h
similarity index 100%
rename from core/formats/list.h
rename to cpp/core/formats/list.h
diff --git a/core/formats/mgh.cpp b/cpp/core/formats/mgh.cpp
similarity index 100%
rename from core/formats/mgh.cpp
rename to cpp/core/formats/mgh.cpp
diff --git a/core/formats/mgz.cpp b/cpp/core/formats/mgz.cpp
similarity index 100%
rename from core/formats/mgz.cpp
rename to cpp/core/formats/mgz.cpp
diff --git a/core/formats/mri.cpp b/cpp/core/formats/mri.cpp
similarity index 100%
rename from core/formats/mri.cpp
rename to cpp/core/formats/mri.cpp
diff --git a/core/formats/mrtrix.cpp b/cpp/core/formats/mrtrix.cpp
similarity index 100%
rename from core/formats/mrtrix.cpp
rename to cpp/core/formats/mrtrix.cpp
diff --git a/core/formats/mrtrix_gz.cpp b/cpp/core/formats/mrtrix_gz.cpp
similarity index 100%
rename from core/formats/mrtrix_gz.cpp
rename to cpp/core/formats/mrtrix_gz.cpp
diff --git a/core/formats/mrtrix_sparse_legacy.cpp b/cpp/core/formats/mrtrix_sparse_legacy.cpp
similarity index 100%
rename from core/formats/mrtrix_sparse_legacy.cpp
rename to cpp/core/formats/mrtrix_sparse_legacy.cpp
diff --git a/core/formats/mrtrix_utils.cpp b/cpp/core/formats/mrtrix_utils.cpp
similarity index 100%
rename from core/formats/mrtrix_utils.cpp
rename to cpp/core/formats/mrtrix_utils.cpp
diff --git a/core/formats/mrtrix_utils.h b/cpp/core/formats/mrtrix_utils.h
similarity index 100%
rename from core/formats/mrtrix_utils.h
rename to cpp/core/formats/mrtrix_utils.h
diff --git a/core/formats/nifti1.cpp b/cpp/core/formats/nifti1.cpp
similarity index 100%
rename from core/formats/nifti1.cpp
rename to cpp/core/formats/nifti1.cpp
diff --git a/core/formats/nifti1_gz.cpp b/cpp/core/formats/nifti1_gz.cpp
similarity index 100%
rename from core/formats/nifti1_gz.cpp
rename to cpp/core/formats/nifti1_gz.cpp
diff --git a/core/formats/nifti2.cpp b/cpp/core/formats/nifti2.cpp
similarity index 100%
rename from core/formats/nifti2.cpp
rename to cpp/core/formats/nifti2.cpp
diff --git a/core/formats/nifti2_gz.cpp b/cpp/core/formats/nifti2_gz.cpp
similarity index 100%
rename from core/formats/nifti2_gz.cpp
rename to cpp/core/formats/nifti2_gz.cpp
diff --git a/core/formats/par.cpp b/cpp/core/formats/par.cpp
similarity index 100%
rename from core/formats/par.cpp
rename to cpp/core/formats/par.cpp
diff --git a/core/formats/pipe.cpp b/cpp/core/formats/pipe.cpp
similarity index 100%
rename from core/formats/pipe.cpp
rename to cpp/core/formats/pipe.cpp
diff --git a/core/formats/png.cpp b/cpp/core/formats/png.cpp
similarity index 100%
rename from core/formats/png.cpp
rename to cpp/core/formats/png.cpp
diff --git a/core/formats/ram.cpp b/cpp/core/formats/ram.cpp
similarity index 100%
rename from core/formats/ram.cpp
rename to cpp/core/formats/ram.cpp
diff --git a/core/formats/xds.cpp b/cpp/core/formats/xds.cpp
similarity index 100%
rename from core/formats/xds.cpp
rename to cpp/core/formats/xds.cpp
diff --git a/core/half.h b/cpp/core/half.h
similarity index 100%
rename from core/half.h
rename to cpp/core/half.h
diff --git a/core/header.cpp b/cpp/core/header.cpp
similarity index 100%
rename from core/header.cpp
rename to cpp/core/header.cpp
diff --git a/core/header.h b/cpp/core/header.h
similarity index 100%
rename from core/header.h
rename to cpp/core/header.h
diff --git a/core/image.cpp b/cpp/core/image.cpp
similarity index 100%
rename from core/image.cpp
rename to cpp/core/image.cpp
diff --git a/core/image.h b/cpp/core/image.h
similarity index 100%
rename from core/image.h
rename to cpp/core/image.h
diff --git a/core/image_diff.h b/cpp/core/image_diff.h
similarity index 100%
rename from core/image_diff.h
rename to cpp/core/image_diff.h
diff --git a/core/image_helpers.h b/cpp/core/image_helpers.h
similarity index 100%
rename from core/image_helpers.h
rename to cpp/core/image_helpers.h
diff --git a/core/image_io/base.cpp b/cpp/core/image_io/base.cpp
similarity index 100%
rename from core/image_io/base.cpp
rename to cpp/core/image_io/base.cpp
diff --git a/core/image_io/base.h b/cpp/core/image_io/base.h
similarity index 100%
rename from core/image_io/base.h
rename to cpp/core/image_io/base.h
diff --git a/core/image_io/default.cpp b/cpp/core/image_io/default.cpp
similarity index 100%
rename from core/image_io/default.cpp
rename to cpp/core/image_io/default.cpp
diff --git a/core/image_io/default.h b/cpp/core/image_io/default.h
similarity index 100%
rename from core/image_io/default.h
rename to cpp/core/image_io/default.h
diff --git a/core/image_io/gz.cpp b/cpp/core/image_io/gz.cpp
similarity index 100%
rename from core/image_io/gz.cpp
rename to cpp/core/image_io/gz.cpp
diff --git a/core/image_io/gz.h b/cpp/core/image_io/gz.h
similarity index 100%
rename from core/image_io/gz.h
rename to cpp/core/image_io/gz.h
diff --git a/core/image_io/mosaic.cpp b/cpp/core/image_io/mosaic.cpp
similarity index 100%
rename from core/image_io/mosaic.cpp
rename to cpp/core/image_io/mosaic.cpp
diff --git a/core/image_io/mosaic.h b/cpp/core/image_io/mosaic.h
similarity index 100%
rename from core/image_io/mosaic.h
rename to cpp/core/image_io/mosaic.h
diff --git a/core/image_io/pipe.cpp b/cpp/core/image_io/pipe.cpp
similarity index 100%
rename from core/image_io/pipe.cpp
rename to cpp/core/image_io/pipe.cpp
diff --git a/core/image_io/pipe.h b/cpp/core/image_io/pipe.h
similarity index 100%
rename from core/image_io/pipe.h
rename to cpp/core/image_io/pipe.h
diff --git a/core/image_io/png.cpp b/cpp/core/image_io/png.cpp
similarity index 100%
rename from core/image_io/png.cpp
rename to cpp/core/image_io/png.cpp
diff --git a/core/image_io/png.h b/cpp/core/image_io/png.h
similarity index 100%
rename from core/image_io/png.h
rename to cpp/core/image_io/png.h
diff --git a/core/image_io/ram.cpp b/cpp/core/image_io/ram.cpp
similarity index 100%
rename from core/image_io/ram.cpp
rename to cpp/core/image_io/ram.cpp
diff --git a/core/image_io/ram.h b/cpp/core/image_io/ram.h
similarity index 100%
rename from core/image_io/ram.h
rename to cpp/core/image_io/ram.h
diff --git a/core/image_io/scratch.cpp b/cpp/core/image_io/scratch.cpp
similarity index 100%
rename from core/image_io/scratch.cpp
rename to cpp/core/image_io/scratch.cpp
diff --git a/core/image_io/scratch.h b/cpp/core/image_io/scratch.h
similarity index 100%
rename from core/image_io/scratch.h
rename to cpp/core/image_io/scratch.h
diff --git a/core/image_io/sparse.cpp b/cpp/core/image_io/sparse.cpp
similarity index 100%
rename from core/image_io/sparse.cpp
rename to cpp/core/image_io/sparse.cpp
diff --git a/core/image_io/sparse.h b/cpp/core/image_io/sparse.h
similarity index 100%
rename from core/image_io/sparse.h
rename to cpp/core/image_io/sparse.h
diff --git a/core/image_io/variable_scaling.cpp b/cpp/core/image_io/variable_scaling.cpp
similarity index 100%
rename from core/image_io/variable_scaling.cpp
rename to cpp/core/image_io/variable_scaling.cpp
diff --git a/core/image_io/variable_scaling.h b/cpp/core/image_io/variable_scaling.h
similarity index 100%
rename from core/image_io/variable_scaling.h
rename to cpp/core/image_io/variable_scaling.h
diff --git a/core/interp/base.h b/cpp/core/interp/base.h
similarity index 100%
rename from core/interp/base.h
rename to cpp/core/interp/base.h
diff --git a/core/interp/cubic.h b/cpp/core/interp/cubic.h
similarity index 100%
rename from core/interp/cubic.h
rename to cpp/core/interp/cubic.h
diff --git a/core/interp/linear.h b/cpp/core/interp/linear.h
similarity index 100%
rename from core/interp/linear.h
rename to cpp/core/interp/linear.h
diff --git a/core/interp/masked.h b/cpp/core/interp/masked.h
similarity index 100%
rename from core/interp/masked.h
rename to cpp/core/interp/masked.h
diff --git a/core/interp/nearest.h b/cpp/core/interp/nearest.h
similarity index 100%
rename from core/interp/nearest.h
rename to cpp/core/interp/nearest.h
diff --git a/core/interp/sinc.h b/cpp/core/interp/sinc.h
similarity index 100%
rename from core/interp/sinc.h
rename to cpp/core/interp/sinc.h
diff --git a/core/math/SH.cpp b/cpp/core/math/SH.cpp
similarity index 97%
rename from core/math/SH.cpp
rename to cpp/core/math/SH.cpp
index 616c6eff14..053c1de7ea 100644
--- a/core/math/SH.cpp
+++ b/cpp/core/math/SH.cpp
@@ -15,7 +15,7 @@
  */
 
 #include "math/SH.h"
-#include "version.h"
+#include "mrtrix_version.h"
 
 namespace MR::Math::SH {
 
diff --git a/core/math/SH.h b/cpp/core/math/SH.h
similarity index 100%
rename from core/math/SH.h
rename to cpp/core/math/SH.h
diff --git a/core/math/Sn_scale_estimator.h b/cpp/core/math/Sn_scale_estimator.h
similarity index 100%
rename from core/math/Sn_scale_estimator.h
rename to cpp/core/math/Sn_scale_estimator.h
diff --git a/core/math/ZSH.h b/cpp/core/math/ZSH.h
similarity index 100%
rename from core/math/ZSH.h
rename to cpp/core/math/ZSH.h
diff --git a/core/math/average_space.cpp b/cpp/core/math/average_space.cpp
similarity index 100%
rename from core/math/average_space.cpp
rename to cpp/core/math/average_space.cpp
diff --git a/core/math/average_space.h b/cpp/core/math/average_space.h
similarity index 100%
rename from core/math/average_space.h
rename to cpp/core/math/average_space.h
diff --git a/core/math/bessel.cpp b/cpp/core/math/bessel.cpp
similarity index 100%
rename from core/math/bessel.cpp
rename to cpp/core/math/bessel.cpp
diff --git a/core/math/bessel.h b/cpp/core/math/bessel.h
similarity index 100%
rename from core/math/bessel.h
rename to cpp/core/math/bessel.h
diff --git a/core/math/betainc.cpp b/cpp/core/math/betainc.cpp
similarity index 100%
rename from core/math/betainc.cpp
rename to cpp/core/math/betainc.cpp
diff --git a/core/math/betainc.h b/cpp/core/math/betainc.h
similarity index 100%
rename from core/math/betainc.h
rename to cpp/core/math/betainc.h
diff --git a/core/math/cauchy.h b/cpp/core/math/cauchy.h
similarity index 100%
rename from core/math/cauchy.h
rename to cpp/core/math/cauchy.h
diff --git a/core/math/chebyshev.h b/cpp/core/math/chebyshev.h
similarity index 100%
rename from core/math/chebyshev.h
rename to cpp/core/math/chebyshev.h
diff --git a/core/math/check_gradient.h b/cpp/core/math/check_gradient.h
similarity index 100%
rename from core/math/check_gradient.h
rename to cpp/core/math/check_gradient.h
diff --git a/core/math/condition_number.cpp b/cpp/core/math/condition_number.cpp
similarity index 100%
rename from core/math/condition_number.cpp
rename to cpp/core/math/condition_number.cpp
diff --git a/core/math/condition_number.h b/cpp/core/math/condition_number.h
similarity index 100%
rename from core/math/condition_number.h
rename to cpp/core/math/condition_number.h
diff --git a/core/math/constrained_least_squares.h b/cpp/core/math/constrained_least_squares.h
similarity index 100%
rename from core/math/constrained_least_squares.h
rename to cpp/core/math/constrained_least_squares.h
diff --git a/core/math/cubic_spline.h b/cpp/core/math/cubic_spline.h
similarity index 100%
rename from core/math/cubic_spline.h
rename to cpp/core/math/cubic_spline.h
diff --git a/core/math/erfinv.cpp b/cpp/core/math/erfinv.cpp
similarity index 100%
rename from core/math/erfinv.cpp
rename to cpp/core/math/erfinv.cpp
diff --git a/core/math/erfinv.h b/cpp/core/math/erfinv.h
similarity index 100%
rename from core/math/erfinv.h
rename to cpp/core/math/erfinv.h
diff --git a/core/math/factorial.h b/cpp/core/math/factorial.h
similarity index 100%
rename from core/math/factorial.h
rename to cpp/core/math/factorial.h
diff --git a/core/math/fft.h b/cpp/core/math/fft.h
similarity index 100%
rename from core/math/fft.h
rename to cpp/core/math/fft.h
diff --git a/core/math/gaussian.h b/cpp/core/math/gaussian.h
similarity index 100%
rename from core/math/gaussian.h
rename to cpp/core/math/gaussian.h
diff --git a/core/math/golden_section_search.h b/cpp/core/math/golden_section_search.h
similarity index 100%
rename from core/math/golden_section_search.h
rename to cpp/core/math/golden_section_search.h
diff --git a/core/math/gradient_descent.h b/cpp/core/math/gradient_descent.h
similarity index 100%
rename from core/math/gradient_descent.h
rename to cpp/core/math/gradient_descent.h
diff --git a/core/math/gradient_descent_bb.h b/cpp/core/math/gradient_descent_bb.h
similarity index 100%
rename from core/math/gradient_descent_bb.h
rename to cpp/core/math/gradient_descent_bb.h
diff --git a/core/math/hermite.h b/cpp/core/math/hermite.h
similarity index 100%
rename from core/math/hermite.h
rename to cpp/core/math/hermite.h
diff --git a/core/math/least_squares.h b/cpp/core/math/least_squares.h
similarity index 100%
rename from core/math/least_squares.h
rename to cpp/core/math/least_squares.h
diff --git a/core/math/legendre.h b/cpp/core/math/legendre.h
similarity index 100%
rename from core/math/legendre.h
rename to cpp/core/math/legendre.h
diff --git a/core/math/math.h b/cpp/core/math/math.h
similarity index 100%
rename from core/math/math.h
rename to cpp/core/math/math.h
diff --git a/core/math/median.h b/cpp/core/math/median.h
similarity index 100%
rename from core/math/median.h
rename to cpp/core/math/median.h
diff --git a/core/math/polynomial.h b/cpp/core/math/polynomial.h
similarity index 100%
rename from core/math/polynomial.h
rename to cpp/core/math/polynomial.h
diff --git a/core/math/quadratic_line_search.h b/cpp/core/math/quadratic_line_search.h
similarity index 100%
rename from core/math/quadratic_line_search.h
rename to cpp/core/math/quadratic_line_search.h
diff --git a/core/math/rician.h b/cpp/core/math/rician.h
similarity index 100%
rename from core/math/rician.h
rename to cpp/core/math/rician.h
diff --git a/core/math/rng.h b/cpp/core/math/rng.h
similarity index 100%
rename from core/math/rng.h
rename to cpp/core/math/rng.h
diff --git a/core/math/sech.h b/cpp/core/math/sech.h
similarity index 100%
rename from core/math/sech.h
rename to cpp/core/math/sech.h
diff --git a/core/math/sinc.h b/cpp/core/math/sinc.h
similarity index 100%
rename from core/math/sinc.h
rename to cpp/core/math/sinc.h
diff --git a/core/math/sphere.h b/cpp/core/math/sphere.h
similarity index 100%
rename from core/math/sphere.h
rename to cpp/core/math/sphere.h
diff --git a/core/math/stats/fwe.cpp b/cpp/core/math/stats/fwe.cpp
similarity index 100%
rename from core/math/stats/fwe.cpp
rename to cpp/core/math/stats/fwe.cpp
diff --git a/core/math/stats/fwe.h b/cpp/core/math/stats/fwe.h
similarity index 100%
rename from core/math/stats/fwe.h
rename to cpp/core/math/stats/fwe.h
diff --git a/core/math/stats/glm.cpp b/cpp/core/math/stats/glm.cpp
similarity index 100%
rename from core/math/stats/glm.cpp
rename to cpp/core/math/stats/glm.cpp
diff --git a/core/math/stats/glm.h b/cpp/core/math/stats/glm.h
similarity index 100%
rename from core/math/stats/glm.h
rename to cpp/core/math/stats/glm.h
diff --git a/core/math/stats/import.cpp b/cpp/core/math/stats/import.cpp
similarity index 100%
rename from core/math/stats/import.cpp
rename to cpp/core/math/stats/import.cpp
diff --git a/core/math/stats/import.h b/cpp/core/math/stats/import.h
similarity index 100%
rename from core/math/stats/import.h
rename to cpp/core/math/stats/import.h
diff --git a/core/math/stats/shuffle.cpp b/cpp/core/math/stats/shuffle.cpp
similarity index 100%
rename from core/math/stats/shuffle.cpp
rename to cpp/core/math/stats/shuffle.cpp
diff --git a/core/math/stats/shuffle.h b/cpp/core/math/stats/shuffle.h
similarity index 100%
rename from core/math/stats/shuffle.h
rename to cpp/core/math/stats/shuffle.h
diff --git a/core/math/stats/typedefs.h b/cpp/core/math/stats/typedefs.h
similarity index 100%
rename from core/math/stats/typedefs.h
rename to cpp/core/math/stats/typedefs.h
diff --git a/core/math/welch_satterthwaite.h b/cpp/core/math/welch_satterthwaite.h
similarity index 100%
rename from core/math/welch_satterthwaite.h
rename to cpp/core/math/welch_satterthwaite.h
diff --git a/core/math/zstatistic.cpp b/cpp/core/math/zstatistic.cpp
similarity index 100%
rename from core/math/zstatistic.cpp
rename to cpp/core/math/zstatistic.cpp
diff --git a/core/math/zstatistic.h b/cpp/core/math/zstatistic.h
similarity index 100%
rename from core/math/zstatistic.h
rename to cpp/core/math/zstatistic.h
diff --git a/core/memory.h b/cpp/core/memory.h
similarity index 100%
rename from core/memory.h
rename to cpp/core/memory.h
diff --git a/src/min_mem_array.h b/cpp/core/min_mem_array.h
similarity index 100%
rename from src/min_mem_array.h
rename to cpp/core/min_mem_array.h
diff --git a/core/misc/bitset.cpp b/cpp/core/misc/bitset.cpp
similarity index 100%
rename from core/misc/bitset.cpp
rename to cpp/core/misc/bitset.cpp
diff --git a/core/misc/bitset.h b/cpp/core/misc/bitset.h
similarity index 100%
rename from core/misc/bitset.h
rename to cpp/core/misc/bitset.h
diff --git a/core/misc/voxel2vector.h b/cpp/core/misc/voxel2vector.h
similarity index 100%
rename from core/misc/voxel2vector.h
rename to cpp/core/misc/voxel2vector.h
diff --git a/core/mrtrix.cpp b/cpp/core/mrtrix.cpp
similarity index 100%
rename from core/mrtrix.cpp
rename to cpp/core/mrtrix.cpp
diff --git a/core/mrtrix.h b/cpp/core/mrtrix.h
similarity index 100%
rename from core/mrtrix.h
rename to cpp/core/mrtrix.h
diff --git a/cpp/core/mrtrix_version.cpp.in b/cpp/core/mrtrix_version.cpp.in
new file mode 100644
index 0000000000..87d2935f92
--- /dev/null
+++ b/cpp/core/mrtrix_version.cpp.in
@@ -0,0 +1,7 @@
+#include "mrtrix_version.h"
+#include <string>
+
+namespace MR::App {
+const std::string mrtrix_version = "@MRTRIX_VERSION@";
+const std::string build_date = __DATE__;
+}
diff --git a/cpp/core/mrtrix_version.h b/cpp/core/mrtrix_version.h
new file mode 100644
index 0000000000..c765871502
--- /dev/null
+++ b/cpp/core/mrtrix_version.h
@@ -0,0 +1,23 @@
+/* Copyright (c) 2008-2024 the MRtrix3 contributors.
+ *
+ * This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ *
+ * Covered Software is provided under this License on an "as is"
+ * basis, without warranty of any kind, either expressed, implied, or
+ * statutory, including, without limitation, warranties that the
+ * Covered Software is free of defects, merchantable, fit for a
+ * particular purpose or non-infringing.
+ * See the Mozilla Public License v. 2.0 for more details.
+ *
+ * For more details, see http://www.mrtrix.org/.
+ */
+
+#pragma once
+#include <string>
+
+namespace MR::App {
+extern const std::string mrtrix_version;
+extern const std::string build_date;
+} // namespace MR::App
diff --git a/core/mutexprotected.h b/cpp/core/mutexprotected.h
similarity index 100%
rename from core/mutexprotected.h
rename to cpp/core/mutexprotected.h
diff --git a/core/ordered_thread_queue.h b/cpp/core/ordered_thread_queue.h
similarity index 100%
rename from core/ordered_thread_queue.h
rename to cpp/core/ordered_thread_queue.h
diff --git a/core/phase_encoding.cpp b/cpp/core/phase_encoding.cpp
similarity index 100%
rename from core/phase_encoding.cpp
rename to cpp/core/phase_encoding.cpp
diff --git a/core/phase_encoding.h b/cpp/core/phase_encoding.h
similarity index 100%
rename from core/phase_encoding.h
rename to cpp/core/phase_encoding.h
diff --git a/core/progressbar.cpp b/cpp/core/progressbar.cpp
similarity index 100%
rename from core/progressbar.cpp
rename to cpp/core/progressbar.cpp
diff --git a/core/progressbar.h b/cpp/core/progressbar.h
similarity index 100%
rename from core/progressbar.h
rename to cpp/core/progressbar.h
diff --git a/core/raw.h b/cpp/core/raw.h
similarity index 100%
rename from core/raw.h
rename to cpp/core/raw.h
diff --git a/src/registration/linear.cpp b/cpp/core/registration/linear.cpp
similarity index 100%
rename from src/registration/linear.cpp
rename to cpp/core/registration/linear.cpp
diff --git a/src/registration/linear.h b/cpp/core/registration/linear.h
similarity index 100%
rename from src/registration/linear.h
rename to cpp/core/registration/linear.h
diff --git a/src/registration/metric/cc_helper.h b/cpp/core/registration/metric/cc_helper.h
similarity index 100%
rename from src/registration/metric/cc_helper.h
rename to cpp/core/registration/metric/cc_helper.h
diff --git a/src/registration/metric/cross_correlation.h b/cpp/core/registration/metric/cross_correlation.h
similarity index 100%
rename from src/registration/metric/cross_correlation.h
rename to cpp/core/registration/metric/cross_correlation.h
diff --git a/src/registration/metric/demons.h b/cpp/core/registration/metric/demons.h
similarity index 100%
rename from src/registration/metric/demons.h
rename to cpp/core/registration/metric/demons.h
diff --git a/src/registration/metric/demons4D.h b/cpp/core/registration/metric/demons4D.h
similarity index 100%
rename from src/registration/metric/demons4D.h
rename to cpp/core/registration/metric/demons4D.h
diff --git a/src/registration/metric/demons_cc.h b/cpp/core/registration/metric/demons_cc.h
similarity index 100%
rename from src/registration/metric/demons_cc.h
rename to cpp/core/registration/metric/demons_cc.h
diff --git a/src/registration/metric/difference_robust.h b/cpp/core/registration/metric/difference_robust.h
similarity index 100%
rename from src/registration/metric/difference_robust.h
rename to cpp/core/registration/metric/difference_robust.h
diff --git a/src/registration/metric/evaluate.h b/cpp/core/registration/metric/evaluate.h
similarity index 100%
rename from src/registration/metric/evaluate.h
rename to cpp/core/registration/metric/evaluate.h
diff --git a/src/registration/metric/linear_base.h b/cpp/core/registration/metric/linear_base.h
similarity index 100%
rename from src/registration/metric/linear_base.h
rename to cpp/core/registration/metric/linear_base.h
diff --git a/src/registration/metric/local_cross_correlation.h b/cpp/core/registration/metric/local_cross_correlation.h
similarity index 100%
rename from src/registration/metric/local_cross_correlation.h
rename to cpp/core/registration/metric/local_cross_correlation.h
diff --git a/src/registration/metric/mean_squared.h b/cpp/core/registration/metric/mean_squared.h
similarity index 100%
rename from src/registration/metric/mean_squared.h
rename to cpp/core/registration/metric/mean_squared.h
diff --git a/src/registration/metric/params.h b/cpp/core/registration/metric/params.h
similarity index 100%
rename from src/registration/metric/params.h
rename to cpp/core/registration/metric/params.h
diff --git a/src/registration/metric/robust_estimators.h b/cpp/core/registration/metric/robust_estimators.h
similarity index 100%
rename from src/registration/metric/robust_estimators.h
rename to cpp/core/registration/metric/robust_estimators.h
diff --git a/src/registration/metric/thread_kernel.h b/cpp/core/registration/metric/thread_kernel.h
similarity index 100%
rename from src/registration/metric/thread_kernel.h
rename to cpp/core/registration/metric/thread_kernel.h
diff --git a/src/registration/multi_contrast.cpp b/cpp/core/registration/multi_contrast.cpp
similarity index 100%
rename from src/registration/multi_contrast.cpp
rename to cpp/core/registration/multi_contrast.cpp
diff --git a/src/registration/multi_contrast.h b/cpp/core/registration/multi_contrast.h
similarity index 100%
rename from src/registration/multi_contrast.h
rename to cpp/core/registration/multi_contrast.h
diff --git a/src/registration/multi_resolution_lmax.h b/cpp/core/registration/multi_resolution_lmax.h
similarity index 100%
rename from src/registration/multi_resolution_lmax.h
rename to cpp/core/registration/multi_resolution_lmax.h
diff --git a/src/registration/nonlinear.cpp b/cpp/core/registration/nonlinear.cpp
similarity index 100%
rename from src/registration/nonlinear.cpp
rename to cpp/core/registration/nonlinear.cpp
diff --git a/src/registration/nonlinear.h b/cpp/core/registration/nonlinear.h
similarity index 100%
rename from src/registration/nonlinear.h
rename to cpp/core/registration/nonlinear.h
diff --git a/src/registration/shared.h b/cpp/core/registration/shared.h
similarity index 100%
rename from src/registration/shared.h
rename to cpp/core/registration/shared.h
diff --git a/src/registration/transform/affine.cpp b/cpp/core/registration/transform/affine.cpp
similarity index 100%
rename from src/registration/transform/affine.cpp
rename to cpp/core/registration/transform/affine.cpp
diff --git a/src/registration/transform/affine.h b/cpp/core/registration/transform/affine.h
similarity index 100%
rename from src/registration/transform/affine.h
rename to cpp/core/registration/transform/affine.h
diff --git a/src/registration/transform/base.cpp b/cpp/core/registration/transform/base.cpp
similarity index 100%
rename from src/registration/transform/base.cpp
rename to cpp/core/registration/transform/base.cpp
diff --git a/src/registration/transform/base.h b/cpp/core/registration/transform/base.h
similarity index 100%
rename from src/registration/transform/base.h
rename to cpp/core/registration/transform/base.h
diff --git a/src/registration/transform/convergence_check.cpp b/cpp/core/registration/transform/convergence_check.cpp
similarity index 100%
rename from src/registration/transform/convergence_check.cpp
rename to cpp/core/registration/transform/convergence_check.cpp
diff --git a/src/registration/transform/convergence_check.h b/cpp/core/registration/transform/convergence_check.h
similarity index 100%
rename from src/registration/transform/convergence_check.h
rename to cpp/core/registration/transform/convergence_check.h
diff --git a/src/registration/transform/initialiser.cpp b/cpp/core/registration/transform/initialiser.cpp
similarity index 100%
rename from src/registration/transform/initialiser.cpp
rename to cpp/core/registration/transform/initialiser.cpp
diff --git a/src/registration/transform/initialiser.h b/cpp/core/registration/transform/initialiser.h
similarity index 100%
rename from src/registration/transform/initialiser.h
rename to cpp/core/registration/transform/initialiser.h
diff --git a/src/registration/transform/initialiser_helpers.cpp b/cpp/core/registration/transform/initialiser_helpers.cpp
similarity index 100%
rename from src/registration/transform/initialiser_helpers.cpp
rename to cpp/core/registration/transform/initialiser_helpers.cpp
diff --git a/src/registration/transform/initialiser_helpers.h b/cpp/core/registration/transform/initialiser_helpers.h
similarity index 100%
rename from src/registration/transform/initialiser_helpers.h
rename to cpp/core/registration/transform/initialiser_helpers.h
diff --git a/src/registration/transform/reorient.cpp b/cpp/core/registration/transform/reorient.cpp
similarity index 100%
rename from src/registration/transform/reorient.cpp
rename to cpp/core/registration/transform/reorient.cpp
diff --git a/src/registration/transform/reorient.h b/cpp/core/registration/transform/reorient.h
similarity index 100%
rename from src/registration/transform/reorient.h
rename to cpp/core/registration/transform/reorient.h
diff --git a/src/registration/transform/rigid.cpp b/cpp/core/registration/transform/rigid.cpp
similarity index 100%
rename from src/registration/transform/rigid.cpp
rename to cpp/core/registration/transform/rigid.cpp
diff --git a/src/registration/transform/rigid.h b/cpp/core/registration/transform/rigid.h
similarity index 100%
rename from src/registration/transform/rigid.h
rename to cpp/core/registration/transform/rigid.h
diff --git a/src/registration/transform/search.h b/cpp/core/registration/transform/search.h
similarity index 100%
rename from src/registration/transform/search.h
rename to cpp/core/registration/transform/search.h
diff --git a/src/registration/warp/compose.h b/cpp/core/registration/warp/compose.h
similarity index 100%
rename from src/registration/warp/compose.h
rename to cpp/core/registration/warp/compose.h
diff --git a/src/registration/warp/convert.h b/cpp/core/registration/warp/convert.h
similarity index 100%
rename from src/registration/warp/convert.h
rename to cpp/core/registration/warp/convert.h
diff --git a/src/registration/warp/helpers.h b/cpp/core/registration/warp/helpers.h
similarity index 100%
rename from src/registration/warp/helpers.h
rename to cpp/core/registration/warp/helpers.h
diff --git a/src/registration/warp/invert.h b/cpp/core/registration/warp/invert.h
similarity index 100%
rename from src/registration/warp/invert.h
rename to cpp/core/registration/warp/invert.h
diff --git a/core/signal_handler.cpp b/cpp/core/signal_handler.cpp
similarity index 100%
rename from core/signal_handler.cpp
rename to cpp/core/signal_handler.cpp
diff --git a/core/signal_handler.h b/cpp/core/signal_handler.h
similarity index 100%
rename from core/signal_handler.h
rename to cpp/core/signal_handler.h
diff --git a/core/signals.h b/cpp/core/signals.h
similarity index 100%
rename from core/signals.h
rename to cpp/core/signals.h
diff --git a/core/stats.cpp b/cpp/core/stats.cpp
similarity index 100%
rename from core/stats.cpp
rename to cpp/core/stats.cpp
diff --git a/core/stats.h b/cpp/core/stats.h
similarity index 100%
rename from core/stats.h
rename to cpp/core/stats.h
diff --git a/src/stats/cfe.cpp b/cpp/core/stats/cfe.cpp
similarity index 100%
rename from src/stats/cfe.cpp
rename to cpp/core/stats/cfe.cpp
diff --git a/src/stats/cfe.h b/cpp/core/stats/cfe.h
similarity index 100%
rename from src/stats/cfe.h
rename to cpp/core/stats/cfe.h
diff --git a/src/stats/cluster.cpp b/cpp/core/stats/cluster.cpp
similarity index 100%
rename from src/stats/cluster.cpp
rename to cpp/core/stats/cluster.cpp
diff --git a/src/stats/cluster.h b/cpp/core/stats/cluster.h
similarity index 100%
rename from src/stats/cluster.h
rename to cpp/core/stats/cluster.h
diff --git a/src/stats/enhance.h b/cpp/core/stats/enhance.h
similarity index 100%
rename from src/stats/enhance.h
rename to cpp/core/stats/enhance.h
diff --git a/src/stats/permtest.cpp b/cpp/core/stats/permtest.cpp
similarity index 100%
rename from src/stats/permtest.cpp
rename to cpp/core/stats/permtest.cpp
diff --git a/src/stats/permtest.h b/cpp/core/stats/permtest.h
similarity index 100%
rename from src/stats/permtest.h
rename to cpp/core/stats/permtest.h
diff --git a/src/stats/tfce.cpp b/cpp/core/stats/tfce.cpp
similarity index 100%
rename from src/stats/tfce.cpp
rename to cpp/core/stats/tfce.cpp
diff --git a/src/stats/tfce.h b/cpp/core/stats/tfce.h
similarity index 100%
rename from src/stats/tfce.h
rename to cpp/core/stats/tfce.h
diff --git a/core/stride.cpp b/cpp/core/stride.cpp
similarity index 100%
rename from core/stride.cpp
rename to cpp/core/stride.cpp
diff --git a/core/stride.h b/cpp/core/stride.h
similarity index 100%
rename from core/stride.h
rename to cpp/core/stride.h
diff --git a/src/surface/algo/image2mesh.h b/cpp/core/surface/algo/image2mesh.h
similarity index 100%
rename from src/surface/algo/image2mesh.h
rename to cpp/core/surface/algo/image2mesh.h
diff --git a/src/surface/algo/mesh2image.cpp b/cpp/core/surface/algo/mesh2image.cpp
similarity index 100%
rename from src/surface/algo/mesh2image.cpp
rename to cpp/core/surface/algo/mesh2image.cpp
diff --git a/src/surface/algo/mesh2image.h b/cpp/core/surface/algo/mesh2image.h
similarity index 100%
rename from src/surface/algo/mesh2image.h
rename to cpp/core/surface/algo/mesh2image.h
diff --git a/src/surface/filter/base.cpp b/cpp/core/surface/filter/base.cpp
similarity index 100%
rename from src/surface/filter/base.cpp
rename to cpp/core/surface/filter/base.cpp
diff --git a/src/surface/filter/base.h b/cpp/core/surface/filter/base.h
similarity index 100%
rename from src/surface/filter/base.h
rename to cpp/core/surface/filter/base.h
diff --git a/src/surface/filter/smooth.cpp b/cpp/core/surface/filter/smooth.cpp
similarity index 100%
rename from src/surface/filter/smooth.cpp
rename to cpp/core/surface/filter/smooth.cpp
diff --git a/src/surface/filter/smooth.h b/cpp/core/surface/filter/smooth.h
similarity index 100%
rename from src/surface/filter/smooth.h
rename to cpp/core/surface/filter/smooth.h
diff --git a/src/surface/filter/vertex_transform.cpp b/cpp/core/surface/filter/vertex_transform.cpp
similarity index 100%
rename from src/surface/filter/vertex_transform.cpp
rename to cpp/core/surface/filter/vertex_transform.cpp
diff --git a/src/surface/filter/vertex_transform.h b/cpp/core/surface/filter/vertex_transform.h
similarity index 100%
rename from src/surface/filter/vertex_transform.h
rename to cpp/core/surface/filter/vertex_transform.h
diff --git a/src/surface/freesurfer.cpp b/cpp/core/surface/freesurfer.cpp
similarity index 100%
rename from src/surface/freesurfer.cpp
rename to cpp/core/surface/freesurfer.cpp
diff --git a/src/surface/freesurfer.h b/cpp/core/surface/freesurfer.h
similarity index 100%
rename from src/surface/freesurfer.h
rename to cpp/core/surface/freesurfer.h
diff --git a/src/surface/mesh.cpp b/cpp/core/surface/mesh.cpp
similarity index 100%
rename from src/surface/mesh.cpp
rename to cpp/core/surface/mesh.cpp
diff --git a/src/surface/mesh.h b/cpp/core/surface/mesh.h
similarity index 100%
rename from src/surface/mesh.h
rename to cpp/core/surface/mesh.h
diff --git a/src/surface/mesh_multi.cpp b/cpp/core/surface/mesh_multi.cpp
similarity index 100%
rename from src/surface/mesh_multi.cpp
rename to cpp/core/surface/mesh_multi.cpp
diff --git a/src/surface/mesh_multi.h b/cpp/core/surface/mesh_multi.h
similarity index 100%
rename from src/surface/mesh_multi.h
rename to cpp/core/surface/mesh_multi.h
diff --git a/src/surface/polygon.cpp b/cpp/core/surface/polygon.cpp
similarity index 100%
rename from src/surface/polygon.cpp
rename to cpp/core/surface/polygon.cpp
diff --git a/src/surface/polygon.h b/cpp/core/surface/polygon.h
similarity index 100%
rename from src/surface/polygon.h
rename to cpp/core/surface/polygon.h
diff --git a/src/surface/scalar.cpp b/cpp/core/surface/scalar.cpp
similarity index 100%
rename from src/surface/scalar.cpp
rename to cpp/core/surface/scalar.cpp
diff --git a/src/surface/scalar.h b/cpp/core/surface/scalar.h
similarity index 100%
rename from src/surface/scalar.h
rename to cpp/core/surface/scalar.h
diff --git a/src/surface/types.h b/cpp/core/surface/types.h
similarity index 100%
rename from src/surface/types.h
rename to cpp/core/surface/types.h
diff --git a/src/surface/utils.h b/cpp/core/surface/utils.h
similarity index 100%
rename from src/surface/utils.h
rename to cpp/core/surface/utils.h
diff --git a/core/thread.cpp b/cpp/core/thread.cpp
similarity index 100%
rename from core/thread.cpp
rename to cpp/core/thread.cpp
diff --git a/core/thread.h b/cpp/core/thread.h
similarity index 100%
rename from core/thread.h
rename to cpp/core/thread.h
diff --git a/core/thread_queue.h b/cpp/core/thread_queue.h
similarity index 100%
rename from core/thread_queue.h
rename to cpp/core/thread_queue.h
diff --git a/core/timer.h b/cpp/core/timer.h
similarity index 100%
rename from core/timer.h
rename to cpp/core/timer.h
diff --git a/core/transform.h b/cpp/core/transform.h
similarity index 100%
rename from core/transform.h
rename to cpp/core/transform.h
diff --git a/core/types.h b/cpp/core/types.h
similarity index 100%
rename from core/types.h
rename to cpp/core/types.h
diff --git a/src/wrap_r.h b/cpp/core/wrap_r.h
similarity index 100%
rename from src/wrap_r.h
rename to cpp/core/wrap_r.h
diff --git a/cpp/gui/CMakeLists.txt b/cpp/gui/CMakeLists.txt
new file mode 100644
index 0000000000..f613d23f8a
--- /dev/null
+++ b/cpp/gui/CMakeLists.txt
@@ -0,0 +1,55 @@
+if(MRTRIX_USE_QT5)
+    find_package(Qt5 COMPONENTS Core Gui Widgets OpenGL Network REQUIRED)
+    qt5_add_resources(RCC_SOURCES ${PROJECT_SOURCE_DIR}/icons/icons.qrc)
+else()
+    find_package(Qt6 COMPONENTS Core Gui Widgets OpenGL Network OpenGLWidgets REQUIRED)
+    qt6_add_resources(RCC_SOURCES ${PROJECT_SOURCE_DIR}/icons/icons.qrc)
+endif()
+# Explicitly log Qt's location since it's not done automatically by the FindQt module
+message(STATUS "Qt${QT_MAJOR_VERSION}_DIR is set to: ${Qt${QT_MAJOR_VERSION}_DIR}")
+
+find_package(OpenGL REQUIRED)
+find_package(Threads REQUIRED)
+
+file(GLOB_RECURSE GUI_SOURCES *.h *.cpp)
+
+add_library(mrtrix-gui ${MRTRIX_LIBRARY_TYPE} ${GUI_SOURCES} ${RCC_SOURCES})
+add_library(mrtrix::gui ALIAS mrtrix-gui)
+
+set_target_properties(mrtrix-gui PROPERTIES
+    AUTOMOC ON
+    AUTOUIC ON
+    LINK_DEPENDS_NO_SHARED ON
+)
+
+if(MRTRIX_USE_PCH)
+    target_precompile_headers(mrtrix-gui PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/gui_pch.h)
+endif()
+
+target_include_directories(mrtrix-gui PUBLIC
+    ${CMAKE_CURRENT_SOURCE_DIR}
+)
+
+target_link_libraries(mrtrix-gui PUBLIC
+    mrtrix::core
+    Qt${QT_MAJOR_VERSION}::Core
+    Qt${QT_MAJOR_VERSION}::Gui
+    Qt${QT_MAJOR_VERSION}::Widgets
+    Qt${QT_MAJOR_VERSION}::OpenGL
+    Qt${QT_MAJOR_VERSION}::Network
+    Threads::Threads
+    ${OPENGL_LIBRARIES}
+)
+
+if(NOT MRTRIX_USE_QT5)
+    target_link_libraries(mrtrix-gui PUBLIC Qt6::OpenGLWidgets)
+endif()
+
+set_target_properties(mrtrix-gui PROPERTIES
+    RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/bin
+)
+
+install(TARGETS mrtrix-gui
+    RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+)
\ No newline at end of file
diff --git a/src/gui/color_button.cpp b/cpp/gui/color_button.cpp
similarity index 98%
rename from src/gui/color_button.cpp
rename to cpp/gui/color_button.cpp
index b47d9e19ba..20d4a08614 100644
--- a/src/gui/color_button.cpp
+++ b/cpp/gui/color_button.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/color_button.h"
+#include "color_button.h"
 
 QColorButton::QColorButton(QWidget *parent, const char *name) : QPushButton(name, parent) {
   connect(this, SIGNAL(clicked()), this, SLOT(chooseColor()));
diff --git a/src/gui/color_button.h b/cpp/gui/color_button.h
similarity index 97%
rename from src/gui/color_button.h
rename to cpp/gui/color_button.h
index c51ed4cb8c..2aa8062f2f 100644
--- a/src/gui/color_button.h
+++ b/cpp/gui/color_button.h
@@ -16,7 +16,7 @@
 
 #pragma once
 
-#include "gui/opengl/gl.h"
+#include "opengl/glutils.h"
 
 class QColorButton : public QPushButton {
   Q_OBJECT
diff --git a/src/gui/crosshair.cpp b/cpp/gui/crosshair.cpp
similarity index 97%
rename from src/gui/crosshair.cpp
rename to cpp/gui/crosshair.cpp
index fb0f6b00a7..4019a81e6f 100644
--- a/src/gui/crosshair.cpp
+++ b/cpp/gui/crosshair.cpp
@@ -14,9 +14,9 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/crosshair.h"
+#include "crosshair.h"
 
-#include "gui/projection.h"
+#include "projection.h"
 
 namespace MR::GUI {
 
diff --git a/src/gui/crosshair.h b/cpp/gui/crosshair.h
similarity index 94%
rename from src/gui/crosshair.h
rename to cpp/gui/crosshair.h
index 6c3582e487..c6dac8865d 100644
--- a/src/gui/crosshair.h
+++ b/cpp/gui/crosshair.h
@@ -18,8 +18,8 @@
 
 #include "types.h"
 
-#include "gui/opengl/gl.h"
-#include "gui/opengl/shader.h"
+#include "opengl/glutils.h"
+#include "opengl/shader.h"
 
 namespace MR::GUI {
 
diff --git a/src/gui/cursor.cpp b/cpp/gui/cursor.cpp
similarity index 98%
rename from src/gui/cursor.cpp
rename to cpp/gui/cursor.cpp
index 45b7fa0dd3..ee3e4b9b16 100644
--- a/src/gui/cursor.cpp
+++ b/cpp/gui/cursor.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/cursor.h"
+#include "cursor.h"
 
 namespace MR::GUI {
 
diff --git a/src/gui/cursor.h b/cpp/gui/cursor.h
similarity index 97%
rename from src/gui/cursor.h
rename to cpp/gui/cursor.h
index 897ff8e91c..822a9ac327 100644
--- a/src/gui/cursor.h
+++ b/cpp/gui/cursor.h
@@ -16,7 +16,7 @@
 
 #pragma once
 
-#include "gui/opengl/gl.h"
+#include "opengl/glutils.h"
 
 namespace MR::GUI {
 class Cursor {
diff --git a/src/gui/dialog/dialog.cpp b/cpp/gui/dialog/dialog.cpp
similarity index 88%
rename from src/gui/dialog/dialog.cpp
rename to cpp/gui/dialog/dialog.cpp
index cc4b21b773..5874caed88 100644
--- a/src/gui/dialog/dialog.cpp
+++ b/cpp/gui/dialog/dialog.cpp
@@ -14,17 +14,17 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/dialog/dialog.h"
+#include "dialog/dialog.h"
 
 #include "app.h"
 #include "exception.h"
 #include "file/dicom/tree.h"
 #include "progressbar.h"
 
-#include "gui/dialog/dicom.h"
-#include "gui/dialog/file.h"
-#include "gui/dialog/progress.h"
-#include "gui/dialog/report_exception.h"
+#include "dialog/dicom.h"
+#include "dialog/file.h"
+#include "dialog/progress.h"
+#include "dialog/report_exception.h"
 
 namespace MR::GUI::Dialog {
 
diff --git a/src/gui/dialog/dialog.h b/cpp/gui/dialog/dialog.h
similarity index 100%
rename from src/gui/dialog/dialog.h
rename to cpp/gui/dialog/dialog.h
diff --git a/src/gui/dialog/dicom.cpp b/cpp/gui/dialog/dicom.cpp
similarity index 98%
rename from src/gui/dialog/dicom.cpp
rename to cpp/gui/dialog/dicom.cpp
index 083ef2ca5d..55272c8425 100644
--- a/src/gui/dialog/dicom.cpp
+++ b/cpp/gui/dialog/dicom.cpp
@@ -14,10 +14,10 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/dialog/dicom.h"
+#include "dialog/dicom.h"
+#include "dialog/list.h"
 #include "file/dicom/tree.h"
-#include "gui/dialog/list.h"
-#include "gui/gui.h"
+#include "gui.h"
 
 namespace MR::GUI::Dialog {
 
diff --git a/src/gui/dialog/dicom.h b/cpp/gui/dialog/dicom.h
similarity index 96%
rename from src/gui/dialog/dicom.h
rename to cpp/gui/dialog/dicom.h
index 1a4e762cf2..1645919608 100644
--- a/src/gui/dialog/dicom.h
+++ b/cpp/gui/dialog/dicom.h
@@ -17,7 +17,7 @@
 #pragma once
 
 #include "file/dicom/tree.h"
-#include "gui/opengl/gl.h"
+#include "opengl/glutils.h"
 
 namespace MR::GUI::Dialog {
 
diff --git a/src/gui/dialog/file.cpp b/cpp/gui/dialog/file.cpp
similarity index 98%
rename from src/gui/dialog/file.cpp
rename to cpp/gui/dialog/file.cpp
index fa4572c2a3..628a1ea97f 100644
--- a/src/gui/dialog/file.cpp
+++ b/cpp/gui/dialog/file.cpp
@@ -17,9 +17,9 @@
 #include <QMessageBox>
 
 #include "app.h"
+#include "dialog/file.h"
 #include "formats/list.h"
-#include "gui/dialog/file.h"
-#include "gui/gui.h"
+#include "gui.h"
 
 #ifdef MRTRIX_MACOSX
 #define FILE_DIALOG_OPTIONS QFileDialog::DontUseNativeDialog
diff --git a/src/gui/dialog/file.h b/cpp/gui/dialog/file.h
similarity index 98%
rename from src/gui/dialog/file.h
rename to cpp/gui/dialog/file.h
index d26862699f..ec0bfd42eb 100644
--- a/src/gui/dialog/file.h
+++ b/cpp/gui/dialog/file.h
@@ -17,7 +17,7 @@
 #pragma once
 
 #include "file/path.h"
-#include "gui/opengl/gl.h"
+#include "opengl/glutils.h"
 
 namespace MR::GUI::Dialog::File {
 
diff --git a/src/gui/dialog/image_properties.cpp b/cpp/gui/dialog/image_properties.cpp
similarity index 98%
rename from src/gui/dialog/image_properties.cpp
rename to cpp/gui/dialog/image_properties.cpp
index 1f6634ec62..60905f938c 100644
--- a/src/gui/dialog/image_properties.cpp
+++ b/cpp/gui/dialog/image_properties.cpp
@@ -14,11 +14,11 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/dialog/image_properties.h"
+#include "dialog/image_properties.h"
+#include "dialog/file.h"
+#include "dialog/list.h"
 #include "dwi/gradient.h"
 #include "file/matrix.h"
-#include "gui/dialog/file.h"
-#include "gui/dialog/list.h"
 #include "header.h"
 #include "stride.h"
 
diff --git a/src/gui/dialog/image_properties.h b/cpp/gui/dialog/image_properties.h
similarity index 97%
rename from src/gui/dialog/image_properties.h
rename to cpp/gui/dialog/image_properties.h
index ef9cfb59f0..b4c0b06f87 100644
--- a/src/gui/dialog/image_properties.h
+++ b/cpp/gui/dialog/image_properties.h
@@ -16,8 +16,8 @@
 
 #pragma once
 
-#include "gui/opengl/gl.h"
 #include "header.h"
+#include "opengl/glutils.h"
 
 namespace MR {
 class Header;
diff --git a/src/gui/dialog/list.cpp b/cpp/gui/dialog/list.cpp
similarity index 98%
rename from src/gui/dialog/list.cpp
rename to cpp/gui/dialog/list.cpp
index 4044b1b1b0..8f56dbfd84 100644
--- a/src/gui/dialog/list.cpp
+++ b/cpp/gui/dialog/list.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/dialog/list.h"
+#include "dialog/list.h"
 
 namespace MR::GUI::Dialog {
 
diff --git a/src/gui/dialog/list.h b/cpp/gui/dialog/list.h
similarity index 97%
rename from src/gui/dialog/list.h
rename to cpp/gui/dialog/list.h
index 03da171263..9cb7b5eb76 100644
--- a/src/gui/dialog/list.h
+++ b/cpp/gui/dialog/list.h
@@ -16,8 +16,8 @@
 
 #pragma once
 
-#include "gui/gui.h"
-#include "gui/opengl/gl.h"
+#include "gui.h"
+#include "opengl/glutils.h"
 
 namespace MR::GUI::Dialog {
 
diff --git a/src/gui/dialog/opengl.cpp b/cpp/gui/dialog/opengl.cpp
similarity index 97%
rename from src/gui/dialog/opengl.cpp
rename to cpp/gui/dialog/opengl.cpp
index 2175040e23..735df1aab0 100644
--- a/src/gui/dialog/opengl.cpp
+++ b/cpp/gui/dialog/opengl.cpp
@@ -14,9 +14,9 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/dialog/opengl.h"
-#include "gui/dialog/list.h"
-#include "gui/opengl/gl.h"
+#include "dialog/opengl.h"
+#include "dialog/list.h"
+#include "opengl/glutils.h"
 
 namespace MR::GUI::Dialog {
 
diff --git a/src/gui/dialog/opengl.h b/cpp/gui/dialog/opengl.h
similarity index 96%
rename from src/gui/dialog/opengl.h
rename to cpp/gui/dialog/opengl.h
index 4280825193..e39942e607 100644
--- a/src/gui/dialog/opengl.h
+++ b/cpp/gui/dialog/opengl.h
@@ -16,7 +16,7 @@
 
 #pragma once
 
-#include "gui/opengl/gl.h"
+#include "opengl/glutils.h"
 
 namespace MR::GUI::Dialog {
 
diff --git a/src/gui/dialog/progress.cpp b/cpp/gui/dialog/progress.cpp
similarity index 97%
rename from src/gui/dialog/progress.cpp
rename to cpp/gui/dialog/progress.cpp
index 4ae877aae4..d967cbca92 100644
--- a/src/gui/dialog/progress.cpp
+++ b/cpp/gui/dialog/progress.cpp
@@ -14,8 +14,8 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/dialog/progress.h"
-#include "gui/gui.h"
+#include "dialog/progress.h"
+#include "gui.h"
 #include <cassert>
 
 namespace MR::GUI::Dialog::ProgressBar {
diff --git a/src/gui/dialog/progress.h b/cpp/gui/dialog/progress.h
similarity index 96%
rename from src/gui/dialog/progress.h
rename to cpp/gui/dialog/progress.h
index 84c04ebd9d..80232d1ef2 100644
--- a/src/gui/dialog/progress.h
+++ b/cpp/gui/dialog/progress.h
@@ -16,7 +16,7 @@
 
 #pragma once
 
-#include "gui/opengl/gl.h"
+#include "opengl/glutils.h"
 #include "progressbar.h"
 
 namespace MR::GUI::Dialog::ProgressBar {
diff --git a/src/gui/dialog/report_exception.cpp b/cpp/gui/dialog/report_exception.cpp
similarity index 95%
rename from src/gui/dialog/report_exception.cpp
rename to cpp/gui/dialog/report_exception.cpp
index e69f7b500c..d215781115 100644
--- a/src/gui/dialog/report_exception.cpp
+++ b/cpp/gui/dialog/report_exception.cpp
@@ -14,8 +14,8 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/dialog/report_exception.h"
-#include "gui/gui.h"
+#include "dialog/report_exception.h"
+#include "gui.h"
 
 namespace MR::GUI::Dialog {
 
diff --git a/src/gui/dialog/report_exception.h b/cpp/gui/dialog/report_exception.h
similarity index 96%
rename from src/gui/dialog/report_exception.h
rename to cpp/gui/dialog/report_exception.h
index 896fe314bf..8367765cb3 100644
--- a/src/gui/dialog/report_exception.h
+++ b/cpp/gui/dialog/report_exception.h
@@ -17,7 +17,7 @@
 #pragma once
 
 #include "exception.h"
-#include "gui/opengl/gl.h"
+#include "opengl/glutils.h"
 
 namespace MR::GUI::Dialog {
 
diff --git a/src/gui/dwi/render_frame.cpp b/cpp/gui/dwi/render_frame.cpp
similarity index 99%
rename from src/gui/dwi/render_frame.cpp
rename to cpp/gui/dwi/render_frame.cpp
index 1e5cde3fc5..ecc4bcf761 100644
--- a/src/gui/dwi/render_frame.cpp
+++ b/cpp/gui/dwi/render_frame.cpp
@@ -19,7 +19,7 @@
 #include <QOpenGLWidget>
 
 #include "app.h"
-#include "gui/dwi/render_frame.h"
+#include "dwi/render_frame.h"
 
 namespace MR::GUI::DWI {
 
diff --git a/src/gui/dwi/render_frame.h b/cpp/gui/dwi/render_frame.h
similarity index 95%
rename from src/gui/dwi/render_frame.h
rename to cpp/gui/dwi/render_frame.h
index 523548de60..ec2d77891a 100644
--- a/src/gui/dwi/render_frame.h
+++ b/cpp/gui/dwi/render_frame.h
@@ -17,13 +17,13 @@
 #pragma once
 
 #include "dwi/directions/set.h"
-#include "gui/dwi/renderer.h"
-#include "gui/opengl/font.h"
-#include "gui/opengl/gl.h"
-#include "gui/opengl/lighting.h"
-#include "gui/opengl/transformation.h"
-#include "gui/projection.h"
+#include "dwi/renderer.h"
 #include "memory.h"
+#include "opengl/font.h"
+#include "opengl/glutils.h"
+#include "opengl/lighting.h"
+#include "opengl/transformation.h"
+#include "projection.h"
 #include "types.h"
 
 #define MAX_LOD 8
diff --git a/src/gui/dwi/renderer.cpp b/cpp/gui/dwi/renderer.cpp
similarity index 99%
rename from src/gui/dwi/renderer.cpp
rename to cpp/gui/dwi/renderer.cpp
index 725d1c8f85..2df422925e 100644
--- a/src/gui/dwi/renderer.cpp
+++ b/cpp/gui/dwi/renderer.cpp
@@ -16,11 +16,11 @@
 
 #include <map>
 
-#include "gui/dwi/renderer.h"
-#include "gui/gui.h"
-#include "gui/opengl/lighting.h"
-#include "gui/projection.h"
+#include "dwi/renderer.h"
+#include "gui.h"
 #include "math/legendre.h"
+#include "opengl/lighting.h"
+#include "projection.h"
 
 namespace MR::GUI::DWI {
 
diff --git a/src/gui/dwi/renderer.h b/cpp/gui/dwi/renderer.h
similarity index 98%
rename from src/gui/dwi/renderer.h
rename to cpp/gui/dwi/renderer.h
index 9fb1fe4abd..44cba7204c 100644
--- a/src/gui/dwi/renderer.h
+++ b/cpp/gui/dwi/renderer.h
@@ -20,11 +20,11 @@
 #include <QOpenGLWidget>
 
 #include "dwi/directions/set.h"
-#include "gui/gui.h"
-#include "gui/opengl/gl.h"
-#include "gui/opengl/shader.h"
-#include "gui/shapes/halfsphere.h"
+#include "gui.h"
 #include "math/SH.h"
+#include "opengl/glutils.h"
+#include "opengl/shader.h"
+#include "shapes/halfsphere.h"
 
 namespace MR::GUI {
 
diff --git a/src/gui/gui.cpp b/cpp/gui/gui.cpp
similarity index 96%
rename from src/gui/gui.cpp
rename to cpp/gui/gui.cpp
index 68185fc72f..09a888ca80 100644
--- a/src/gui/gui.cpp
+++ b/cpp/gui/gui.cpp
@@ -14,8 +14,8 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/gui.h"
-#include "gui/opengl/gl.h"
+#include "gui.h"
+#include "opengl/glutils.h"
 #include <clocale>
 #include <locale>
 
diff --git a/src/gui/gui.h b/cpp/gui/gui.h
similarity index 98%
rename from src/gui/gui.h
rename to cpp/gui/gui.h
index 63dc5928cd..599662a81f 100644
--- a/src/gui/gui.h
+++ b/cpp/gui/gui.h
@@ -24,7 +24,7 @@
 
 #include "app.h"
 #include "file/config.h"
-#include "gui/opengl/gl.h"
+#include "opengl/glutils.h"
 
 #include <functional>
 
diff --git a/src/gui/gui_pch.h b/cpp/gui/gui_pch.h
similarity index 96%
rename from src/gui/gui_pch.h
rename to cpp/gui/gui_pch.h
index 7227f6795f..e9f7d69347 100644
--- a/src/gui/gui_pch.h
+++ b/cpp/gui/gui_pch.h
@@ -16,4 +16,4 @@
 #ifdef __APPLE__
 #define GL_SILENCE_DEPRECATION
 #endif
-#include "gui/opengl/gl.h"
+#include "opengl/glutils.h"
diff --git a/src/gui/lighting_dock.cpp b/cpp/gui/lighting_dock.cpp
similarity index 98%
rename from src/gui/lighting_dock.cpp
rename to cpp/gui/lighting_dock.cpp
index 05380efd56..e285f9da51 100644
--- a/src/gui/lighting_dock.cpp
+++ b/cpp/gui/lighting_dock.cpp
@@ -14,10 +14,10 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/lighting_dock.h"
+#include "lighting_dock.h"
+#include "color_button.h"
 #include "file/config.h"
-#include "gui/color_button.h"
-#include "gui/gui.h"
+#include "gui.h"
 #include "math/math.h"
 
 namespace MR::GUI {
diff --git a/src/gui/lighting_dock.h b/cpp/gui/lighting_dock.h
similarity index 97%
rename from src/gui/lighting_dock.h
rename to cpp/gui/lighting_dock.h
index 3d06a5b297..a13f830e2a 100644
--- a/src/gui/lighting_dock.h
+++ b/cpp/gui/lighting_dock.h
@@ -16,7 +16,7 @@
 
 #pragma once
 
-#include "gui/opengl/lighting.h"
+#include "opengl/lighting.h"
 
 namespace MR::GUI {
 class LightingSettings : public QFrame {
diff --git a/src/gui/mrview/adjust_button.cpp b/cpp/gui/mrview/adjust_button.cpp
similarity index 98%
rename from src/gui/mrview/adjust_button.cpp
rename to cpp/gui/mrview/adjust_button.cpp
index 208c90ecef..71dac9cd1b 100644
--- a/src/gui/mrview/adjust_button.cpp
+++ b/cpp/gui/mrview/adjust_button.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/adjust_button.h"
+#include "mrview/adjust_button.h"
 #include "math/math.h"
 
 namespace MR::GUI::MRView {
diff --git a/src/gui/mrview/adjust_button.h b/cpp/gui/mrview/adjust_button.h
similarity index 98%
rename from src/gui/mrview/adjust_button.h
rename to cpp/gui/mrview/adjust_button.h
index b8ecc4c6a2..25b97baa01 100644
--- a/src/gui/mrview/adjust_button.h
+++ b/cpp/gui/mrview/adjust_button.h
@@ -16,8 +16,8 @@
 
 #pragma once
 
-#include "gui/opengl/gl.h"
 #include "mrtrix.h"
+#include "opengl/glutils.h"
 
 #define ADJUST_BUTTON_DEADZONE_SIZE 8
 
diff --git a/src/gui/mrview/colourbars.cpp b/cpp/gui/mrview/colourbars.cpp
similarity index 98%
rename from src/gui/mrview/colourbars.cpp
rename to cpp/gui/mrview/colourbars.cpp
index c73a0614be..f3d9f43125 100644
--- a/src/gui/mrview/colourbars.cpp
+++ b/cpp/gui/mrview/colourbars.cpp
@@ -14,11 +14,11 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/colourbars.h"
+#include "mrview/colourbars.h"
 #include "file/config.h"
-#include "gui/mrview/displayable.h"
-#include "gui/opengl/font.h"
-#include "gui/projection.h"
+#include "mrview/displayable.h"
+#include "opengl/font.h"
+#include "projection.h"
 
 namespace MR::GUI::MRView {
 // CONF option: MRViewMaxNumColourBarRows
diff --git a/src/gui/mrview/colourbars.h b/cpp/gui/mrview/colourbars.h
similarity index 97%
rename from src/gui/mrview/colourbars.h
rename to cpp/gui/mrview/colourbars.h
index 2194a81ce3..fdff4713eb 100644
--- a/src/gui/mrview/colourbars.h
+++ b/cpp/gui/mrview/colourbars.h
@@ -17,8 +17,8 @@
 #pragma once
 
 #include "colourmap.h"
-#include "gui/opengl/gl.h"
-#include "gui/opengl/shader.h"
+#include "opengl/glutils.h"
+#include "opengl/shader.h"
 
 namespace MR::GUI {
 class Projection;
diff --git a/src/gui/mrview/colourmap_button.cpp b/cpp/gui/mrview/colourmap_button.cpp
similarity index 99%
rename from src/gui/mrview/colourmap_button.cpp
rename to cpp/gui/mrview/colourmap_button.cpp
index b6d331c349..3c21f05285 100644
--- a/src/gui/mrview/colourmap_button.cpp
+++ b/cpp/gui/mrview/colourmap_button.cpp
@@ -14,8 +14,8 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/colourmap_button.h"
-#include "gui/gui.h"
+#include "mrview/colourmap_button.h"
+#include "gui.h"
 #include "math/rng.h"
 
 namespace MR::GUI::MRView {
diff --git a/src/gui/mrview/colourmap_button.h b/cpp/gui/mrview/colourmap_button.h
similarity index 98%
rename from src/gui/mrview/colourmap_button.h
rename to cpp/gui/mrview/colourmap_button.h
index 66087d7fc9..69eee748f6 100644
--- a/src/gui/mrview/colourmap_button.h
+++ b/cpp/gui/mrview/colourmap_button.h
@@ -19,7 +19,7 @@
 #include "mrtrix.h"
 
 #include "colourmap.h"
-#include "gui/opengl/gl.h"
+#include "opengl/glutils.h"
 
 namespace MR::GUI::MRView {
 
diff --git a/src/gui/mrview/combo_box_error.cpp b/cpp/gui/mrview/combo_box_error.cpp
similarity index 97%
rename from src/gui/mrview/combo_box_error.cpp
rename to cpp/gui/mrview/combo_box_error.cpp
index f2666b2278..1b89f76463 100644
--- a/src/gui/mrview/combo_box_error.cpp
+++ b/cpp/gui/mrview/combo_box_error.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/combo_box_error.h"
+#include "mrview/combo_box_error.h"
 #include "math/math.h"
 
 namespace MR::GUI::MRView {
diff --git a/src/gui/mrview/combo_box_error.h b/cpp/gui/mrview/combo_box_error.h
similarity index 97%
rename from src/gui/mrview/combo_box_error.h
rename to cpp/gui/mrview/combo_box_error.h
index ffdb8c09d4..b1b458cf46 100644
--- a/src/gui/mrview/combo_box_error.h
+++ b/cpp/gui/mrview/combo_box_error.h
@@ -16,8 +16,8 @@
 
 #pragma once
 
-#include "gui/opengl/gl.h"
 #include "mrtrix.h"
+#include "opengl/glutils.h"
 
 namespace MR::GUI::MRView {
 
diff --git a/src/gui/mrview/displayable.cpp b/cpp/gui/mrview/displayable.cpp
similarity index 97%
rename from src/gui/mrview/displayable.cpp
rename to cpp/gui/mrview/displayable.cpp
index f6f4edadf0..a5d7d2d078 100644
--- a/src/gui/mrview/displayable.cpp
+++ b/cpp/gui/mrview/displayable.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/displayable.h"
+#include "mrview/displayable.h"
 
 namespace MR::GUI::MRView {
 
diff --git a/src/gui/mrview/displayable.h b/cpp/gui/mrview/displayable.h
similarity index 99%
rename from src/gui/mrview/displayable.h
rename to cpp/gui/mrview/displayable.h
index 35ad64ba3a..c7112bc36c 100644
--- a/src/gui/mrview/displayable.h
+++ b/cpp/gui/mrview/displayable.h
@@ -19,9 +19,9 @@
 #include "math/math.h"
 
 #include "colourmap.h"
-#include "gui/opengl/gl.h"
-#include "gui/opengl/shader.h"
-#include "gui/projection.h"
+#include "opengl/glutils.h"
+#include "opengl/shader.h"
+#include "projection.h"
 
 namespace MR {
 class ProgressBar;
diff --git a/src/gui/mrview/gui_image.cpp b/cpp/gui/mrview/gui_image.cpp
similarity index 99%
rename from src/gui/mrview/gui_image.cpp
rename to cpp/gui/mrview/gui_image.cpp
index 4673c3953f..a5a99f7a32 100644
--- a/src/gui/mrview/gui_image.cpp
+++ b/cpp/gui/mrview/gui_image.cpp
@@ -14,12 +14,12 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/gui_image.h"
+#include "mrview/gui_image.h"
 
-#include "gui/mrview/window.h"
-#include "gui/projection.h"
 #include "header.h"
+#include "mrview/window.h"
 #include "progressbar.h"
+#include "projection.h"
 
 namespace MR::GUI::MRView {
 
diff --git a/src/gui/mrview/gui_image.h b/cpp/gui/mrview/gui_image.h
similarity index 97%
rename from src/gui/mrview/gui_image.h
rename to cpp/gui/mrview/gui_image.h
index 2f9b2df0ba..af71e32e77 100644
--- a/src/gui/mrview/gui_image.h
+++ b/cpp/gui/mrview/gui_image.h
@@ -16,11 +16,11 @@
 
 #pragma once
 
-#include "gui/mrview/volume.h"
-#include "gui/opengl/gl.h"
 #include "image.h"
 #include "interp/linear.h"
 #include "interp/nearest.h"
+#include "mrview/volume.h"
+#include "opengl/glutils.h"
 #include "types.h"
 #include <unordered_map>
 
diff --git a/src/gui/mrview/icons.h b/cpp/gui/mrview/icons.h
similarity index 100%
rename from src/gui/mrview/icons.h
rename to cpp/gui/mrview/icons.h
diff --git a/src/gui/mrview/mode/base.cpp b/cpp/gui/mrview/mode/base.cpp
similarity index 99%
rename from src/gui/mrview/mode/base.cpp
rename to cpp/gui/mrview/mode/base.cpp
index ef0a3eecf1..1005379a3b 100644
--- a/src/gui/mrview/mode/base.cpp
+++ b/cpp/gui/mrview/mode/base.cpp
@@ -14,9 +14,9 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/mode/base.h"
+#include "mrview/mode/base.h"
 #include "file/config.h"
-#include "gui/opengl/gl.h"
+#include "opengl/glutils.h"
 
 namespace MR::GUI::MRView::Mode {
 
diff --git a/src/gui/mrview/mode/base.h b/cpp/gui/mrview/mode/base.h
similarity index 97%
rename from src/gui/mrview/mode/base.h
rename to cpp/gui/mrview/mode/base.h
index 9fff55f35f..badd693aca 100644
--- a/src/gui/mrview/mode/base.h
+++ b/cpp/gui/mrview/mode/base.h
@@ -16,11 +16,11 @@
 
 #pragma once
 
-#include "gui/mrview/tool/base.h"
-#include "gui/mrview/window.h"
-#include "gui/opengl/gl.h"
-#include "gui/opengl/transformation.h"
-#include "gui/projection.h"
+#include "mrview/tool/base.h"
+#include "mrview/window.h"
+#include "opengl/glutils.h"
+#include "opengl/transformation.h"
+#include "projection.h"
 
 #define ROTATION_INC 0.002
 #define MOVE_IN_OUT_FOV_MULTIPLIER 1.0e-3f
diff --git a/src/gui/mrview/mode/lightbox.cpp b/cpp/gui/mrview/mode/lightbox.cpp
similarity index 99%
rename from src/gui/mrview/mode/lightbox.cpp
rename to cpp/gui/mrview/mode/lightbox.cpp
index ac53cb6088..08622067a7 100644
--- a/src/gui/mrview/mode/lightbox.cpp
+++ b/cpp/gui/mrview/mode/lightbox.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/mode/lightbox.h"
+#include "mrview/mode/lightbox.h"
 
 namespace MR::GUI::MRView::Mode {
 
diff --git a/src/gui/mrview/mode/lightbox.h b/cpp/gui/mrview/mode/lightbox.h
similarity index 98%
rename from src/gui/mrview/mode/lightbox.h
rename to cpp/gui/mrview/mode/lightbox.h
index 11a996b41b..c37e6147df 100644
--- a/src/gui/mrview/mode/lightbox.h
+++ b/cpp/gui/mrview/mode/lightbox.h
@@ -16,7 +16,7 @@
 
 #pragma once
 
-#include "gui/mrview/mode/slice.h"
+#include "mrview/mode/slice.h"
 
 namespace MR::GUI::MRView::Mode {
 class LightBox : public Slice {
diff --git a/src/gui/mrview/mode/lightbox_gui.h b/cpp/gui/mrview/mode/lightbox_gui.h
similarity index 97%
rename from src/gui/mrview/mode/lightbox_gui.h
rename to cpp/gui/mrview/mode/lightbox_gui.h
index d81a04e9c1..aff1317931 100644
--- a/src/gui/mrview/mode/lightbox_gui.h
+++ b/cpp/gui/mrview/mode/lightbox_gui.h
@@ -16,7 +16,7 @@
 
 #pragma once
 
-#include "gui/mrview/spin_box.h"
+#include "mrview/spin_box.h"
 
 namespace MR::GUI::MRView::Mode::LightBoxViewControls {
 class LightBoxEditButton : public SpinBox {
diff --git a/src/gui/mrview/mode/list.h b/cpp/gui/mrview/mode/list.h
similarity index 90%
rename from src/gui/mrview/mode/list.h
rename to cpp/gui/mrview/mode/list.h
index 272e783837..e947a798a5 100644
--- a/src/gui/mrview/mode/list.h
+++ b/cpp/gui/mrview/mode/list.h
@@ -17,10 +17,10 @@
 #ifndef MODE
 
 // place #include files in here:
-#include "gui/mrview/mode/lightbox.h"
-#include "gui/mrview/mode/ortho.h"
-#include "gui/mrview/mode/slice.h"
-#include "gui/mrview/mode/volume.h"
+#include "mrview/mode/lightbox.h"
+#include "mrview/mode/ortho.h"
+#include "mrview/mode/slice.h"
+#include "mrview/mode/volume.h"
 
 #else
 
diff --git a/src/gui/mrview/mode/ortho.cpp b/cpp/gui/mrview/mode/ortho.cpp
similarity index 98%
rename from src/gui/mrview/mode/ortho.cpp
rename to cpp/gui/mrview/mode/ortho.cpp
index de4583756d..67d095a1de 100644
--- a/src/gui/mrview/mode/ortho.cpp
+++ b/cpp/gui/mrview/mode/ortho.cpp
@@ -14,9 +14,9 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/mode/ortho.h"
+#include "mrview/mode/ortho.h"
 
-#include "gui/cursor.h"
+#include "cursor.h"
 #include "mrtrix.h"
 
 namespace MR::GUI::MRView::Mode {
diff --git a/src/gui/mrview/mode/ortho.h b/cpp/gui/mrview/mode/ortho.h
similarity index 97%
rename from src/gui/mrview/mode/ortho.h
rename to cpp/gui/mrview/mode/ortho.h
index e65cfc3351..6ae0787064 100644
--- a/src/gui/mrview/mode/ortho.h
+++ b/cpp/gui/mrview/mode/ortho.h
@@ -17,7 +17,7 @@
 #pragma once
 
 #include "app.h"
-#include "gui/mrview/mode/slice.h"
+#include "mrview/mode/slice.h"
 
 namespace MR::GUI::MRView::Mode {
 
diff --git a/src/gui/mrview/mode/slice.cpp b/cpp/gui/mrview/mode/slice.cpp
similarity index 98%
rename from src/gui/mrview/mode/slice.cpp
rename to cpp/gui/mrview/mode/slice.cpp
index 4477a7a280..21dc8d7959 100644
--- a/src/gui/mrview/mode/slice.cpp
+++ b/cpp/gui/mrview/mode/slice.cpp
@@ -14,9 +14,9 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/mode/slice.h"
+#include "mrview/mode/slice.h"
 
-#include "gui/opengl/transformation.h"
+#include "opengl/transformation.h"
 
 namespace MR::GUI::MRView::Mode {
 
diff --git a/src/gui/mrview/mode/slice.h b/cpp/gui/mrview/mode/slice.h
similarity index 97%
rename from src/gui/mrview/mode/slice.h
rename to cpp/gui/mrview/mode/slice.h
index b763613d89..b11d0241ed 100644
--- a/src/gui/mrview/mode/slice.h
+++ b/cpp/gui/mrview/mode/slice.h
@@ -17,7 +17,7 @@
 #pragma once
 
 #include "app.h"
-#include "gui/mrview/mode/base.h"
+#include "mrview/mode/base.h"
 
 namespace MR::GUI::MRView::Mode {
 
diff --git a/src/gui/mrview/mode/volume.cpp b/cpp/gui/mrview/mode/volume.cpp
similarity index 99%
rename from src/gui/mrview/mode/volume.cpp
rename to cpp/gui/mrview/mode/volume.cpp
index 7d47f2a54b..38ea4a8d60 100644
--- a/src/gui/mrview/mode/volume.cpp
+++ b/cpp/gui/mrview/mode/volume.cpp
@@ -14,12 +14,12 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/mode/volume.h"
+#include "mrview/mode/volume.h"
 #include "file/config.h"
-#include "gui/mrview/adjust_button.h"
-#include "gui/mrview/tool/base.h"
-#include "gui/mrview/tool/view.h"
-#include "gui/opengl/lighting.h"
+#include "mrview/adjust_button.h"
+#include "mrview/tool/base.h"
+#include "mrview/tool/view.h"
+#include "opengl/lighting.h"
 
 namespace MR::GUI::MRView::Mode {
 
diff --git a/src/gui/mrview/mode/volume.h b/cpp/gui/mrview/mode/volume.h
similarity index 96%
rename from src/gui/mrview/mode/volume.h
rename to cpp/gui/mrview/mode/volume.h
index a2a5d9ec01..850336e12c 100644
--- a/src/gui/mrview/mode/volume.h
+++ b/cpp/gui/mrview/mode/volume.h
@@ -17,8 +17,8 @@
 #pragma once
 
 #include "app.h"
-#include "gui/mrview/mode/base.h"
-#include "gui/opengl/transformation.h"
+#include "mrview/mode/base.h"
+#include "opengl/transformation.h"
 
 namespace MR::GUI::MRView {
 namespace Tool {
diff --git a/src/gui/mrview/qthelpers.cpp b/cpp/gui/mrview/qthelpers.cpp
similarity index 96%
rename from src/gui/mrview/qthelpers.cpp
rename to cpp/gui/mrview/qthelpers.cpp
index aa4627e82c..4bff14af57 100644
--- a/src/gui/mrview/qthelpers.cpp
+++ b/cpp/gui/mrview/qthelpers.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/qthelpers.h"
+#include "mrview/qthelpers.h"
 
 #include <QString>
 #include <QUrl>
diff --git a/src/gui/mrview/qthelpers.h b/cpp/gui/mrview/qthelpers.h
similarity index 100%
rename from src/gui/mrview/qthelpers.h
rename to cpp/gui/mrview/qthelpers.h
diff --git a/src/gui/mrview/spin_box.h b/cpp/gui/mrview/spin_box.h
similarity index 97%
rename from src/gui/mrview/spin_box.h
rename to cpp/gui/mrview/spin_box.h
index 1f4bb58a2a..d01f439d93 100644
--- a/src/gui/mrview/spin_box.h
+++ b/cpp/gui/mrview/spin_box.h
@@ -16,8 +16,8 @@
 
 #pragma once
 
-#include "gui/opengl/gl.h"
 #include "mrtrix.h"
+#include "opengl/glutils.h"
 
 namespace MR::GUI {
 
diff --git a/src/gui/mrview/sync/client.cpp b/cpp/gui/mrview/sync/client.cpp
similarity index 98%
rename from src/gui/mrview/sync/client.cpp
rename to cpp/gui/mrview/sync/client.cpp
index eb78c892d6..28877b903d 100644
--- a/src/gui/mrview/sync/client.cpp
+++ b/cpp/gui/mrview/sync/client.cpp
@@ -15,7 +15,7 @@
  */
 #include <QtNetwork>
 
-#include "gui/mrview/sync/client.h"
+#include "mrview/sync/client.h"
 #include <iostream>
 
 namespace MR::GUI::MRView::Sync {
diff --git a/src/gui/mrview/sync/client.h b/cpp/gui/mrview/sync/client.h
similarity index 100%
rename from src/gui/mrview/sync/client.h
rename to cpp/gui/mrview/sync/client.h
diff --git a/src/gui/mrview/sync/enums.h b/cpp/gui/mrview/sync/enums.h
similarity index 100%
rename from src/gui/mrview/sync/enums.h
rename to cpp/gui/mrview/sync/enums.h
diff --git a/src/gui/mrview/sync/interprocesscommunicator.cpp b/cpp/gui/mrview/sync/interprocesscommunicator.cpp
similarity index 98%
rename from src/gui/mrview/sync/interprocesscommunicator.cpp
rename to cpp/gui/mrview/sync/interprocesscommunicator.cpp
index fc49e3be45..408cad1eed 100644
--- a/src/gui/mrview/sync/interprocesscommunicator.cpp
+++ b/cpp/gui/mrview/sync/interprocesscommunicator.cpp
@@ -19,9 +19,9 @@
 #include <thread>
 
 #include "exception.h"
-#include "gui/mrview/sync/enums.h"
-#include "gui/mrview/sync/interprocesscommunicator.h"
-#include "gui/mrview/sync/processlock.h"
+#include "mrview/sync/enums.h"
+#include "mrview/sync/interprocesscommunicator.h"
+#include "mrview/sync/processlock.h"
 
 namespace MR::GUI::MRView::Sync {
 InterprocessCommunicator::InterprocessCommunicator() : QObject(0) {
diff --git a/src/gui/mrview/sync/interprocesscommunicator.h b/cpp/gui/mrview/sync/interprocesscommunicator.h
similarity index 96%
rename from src/gui/mrview/sync/interprocesscommunicator.h
rename to cpp/gui/mrview/sync/interprocesscommunicator.h
index bbcc125d7f..ea88d4577a 100644
--- a/src/gui/mrview/sync/interprocesscommunicator.h
+++ b/cpp/gui/mrview/sync/interprocesscommunicator.h
@@ -17,8 +17,8 @@
 
 #include <qlocalsocket.h>
 
-#include "gui/mrview/sync/client.h"
-#include "gui/mrview/sync/localsocketreader.h"
+#include "mrview/sync/client.h"
+#include "mrview/sync/localsocketreader.h"
 
 // maximum number of inter process syncers that are allowed. This can be
 // raised, but may reduce performance when new IPS are created.
diff --git a/src/gui/mrview/sync/localsocketreader.cpp b/cpp/gui/mrview/sync/localsocketreader.cpp
similarity index 98%
rename from src/gui/mrview/sync/localsocketreader.cpp
rename to cpp/gui/mrview/sync/localsocketreader.cpp
index 551e6f1a98..d185570cf1 100644
--- a/src/gui/mrview/sync/localsocketreader.cpp
+++ b/cpp/gui/mrview/sync/localsocketreader.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/sync/localsocketreader.h"
+#include "mrview/sync/localsocketreader.h"
 #include "exception.h"
 
 namespace MR::GUI::MRView::Sync {
diff --git a/src/gui/mrview/sync/localsocketreader.h b/cpp/gui/mrview/sync/localsocketreader.h
similarity index 100%
rename from src/gui/mrview/sync/localsocketreader.h
rename to cpp/gui/mrview/sync/localsocketreader.h
diff --git a/src/gui/mrview/sync/processlock.cpp b/cpp/gui/mrview/sync/processlock.cpp
similarity index 98%
rename from src/gui/mrview/sync/processlock.cpp
rename to cpp/gui/mrview/sync/processlock.cpp
index e1b881f819..80fc9cc3ca 100644
--- a/src/gui/mrview/sync/processlock.cpp
+++ b/cpp/gui/mrview/sync/processlock.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/sync/processlock.h"
+#include "mrview/sync/processlock.h"
 #include <QCryptographicHash>
 
 namespace MR::GUI::MRView::Sync {
diff --git a/src/gui/mrview/sync/processlock.h b/cpp/gui/mrview/sync/processlock.h
similarity index 100%
rename from src/gui/mrview/sync/processlock.h
rename to cpp/gui/mrview/sync/processlock.h
diff --git a/src/gui/mrview/sync/syncmanager.cpp b/cpp/gui/mrview/sync/syncmanager.cpp
similarity index 98%
rename from src/gui/mrview/sync/syncmanager.cpp
rename to cpp/gui/mrview/sync/syncmanager.cpp
index 8a74c011f6..07b82bf85a 100644
--- a/src/gui/mrview/sync/syncmanager.cpp
+++ b/cpp/gui/mrview/sync/syncmanager.cpp
@@ -14,8 +14,8 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/sync/syncmanager.h"
-#include "gui/mrview/window.h"
+#include "mrview/sync/syncmanager.h"
+#include "mrview/window.h"
 
 namespace MR::GUI::MRView::Sync {
 SyncManager::SyncManager() : QObject(0) {
diff --git a/src/gui/mrview/sync/syncmanager.h b/cpp/gui/mrview/sync/syncmanager.h
similarity index 95%
rename from src/gui/mrview/sync/syncmanager.h
rename to cpp/gui/mrview/sync/syncmanager.h
index 0c5d941863..ebf2f4411b 100644
--- a/src/gui/mrview/sync/syncmanager.h
+++ b/cpp/gui/mrview/sync/syncmanager.h
@@ -15,8 +15,8 @@
  */
 #pragma once
 
-#include "gui/mrview/sync/enums.h"
-#include "gui/mrview/sync/interprocesscommunicator.h"
+#include "mrview/sync/enums.h"
+#include "mrview/sync/interprocesscommunicator.h"
 
 namespace MR::GUI::MRView::Sync {
 /**
diff --git a/src/gui/mrview/tool/base.cpp b/cpp/gui/mrview/tool/base.cpp
similarity index 98%
rename from src/gui/mrview/tool/base.cpp
rename to cpp/gui/mrview/tool/base.cpp
index 61df483771..e0cd88ee43 100644
--- a/src/gui/mrview/tool/base.cpp
+++ b/cpp/gui/mrview/tool/base.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/base.h"
+#include "mrview/tool/base.h"
 #include "app.h"
 
 namespace MR::GUI::MRView::Tool {
diff --git a/src/gui/mrview/tool/base.h b/cpp/gui/mrview/tool/base.h
similarity index 98%
rename from src/gui/mrview/tool/base.h
rename to cpp/gui/mrview/tool/base.h
index 8866264c13..19744a0a3c 100644
--- a/src/gui/mrview/tool/base.h
+++ b/cpp/gui/mrview/tool/base.h
@@ -18,8 +18,8 @@
 
 #include "file/config.h"
 
-#include "gui/mrview/window.h"
-#include "gui/projection.h"
+#include "mrview/window.h"
+#include "projection.h"
 
 #define LAYOUT_SPACING 3
 
diff --git a/src/gui/mrview/tool/connectome/colourmap_observers.cpp b/cpp/gui/mrview/tool/connectome/colourmap_observers.cpp
similarity index 96%
rename from src/gui/mrview/tool/connectome/colourmap_observers.cpp
rename to cpp/gui/mrview/tool/connectome/colourmap_observers.cpp
index 5766bf212a..a71da5c2b1 100644
--- a/src/gui/mrview/tool/connectome/colourmap_observers.cpp
+++ b/cpp/gui/mrview/tool/connectome/colourmap_observers.cpp
@@ -14,9 +14,9 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/connectome/colourmap_observers.h"
+#include "mrview/tool/connectome/colourmap_observers.h"
 
-#include "gui/mrview/tool/connectome/connectome.h"
+#include "mrview/tool/connectome/connectome.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/connectome/colourmap_observers.h b/cpp/gui/mrview/tool/connectome/colourmap_observers.h
similarity index 96%
rename from src/gui/mrview/tool/connectome/colourmap_observers.h
rename to cpp/gui/mrview/tool/connectome/colourmap_observers.h
index c3e912e002..5edf3d8308 100644
--- a/src/gui/mrview/tool/connectome/colourmap_observers.h
+++ b/cpp/gui/mrview/tool/connectome/colourmap_observers.h
@@ -16,8 +16,8 @@
 
 #pragma once
 
-#include "gui/mrview/colourmap_button.h"
-#include "gui/opengl/gl.h"
+#include "mrview/colourmap_button.h"
+#include "opengl/glutils.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/connectome/connectome.cpp b/cpp/gui/mrview/tool/connectome/connectome.cpp
similarity index 99%
rename from src/gui/mrview/tool/connectome/connectome.cpp
rename to cpp/gui/mrview/tool/connectome/connectome.cpp
index d0a8341f81..d9750b738b 100644
--- a/src/gui/mrview/tool/connectome/connectome.cpp
+++ b/cpp/gui/mrview/tool/connectome/connectome.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/connectome/connectome.h"
+#include "mrview/tool/connectome/connectome.h"
 
 #include "header.h"
 #include "transform.h"
@@ -22,8 +22,8 @@
 #include "adapter/subset.h"
 #include "algo/loop.h"
 #include "algo/threaded_loop.h"
+#include "dialog/file.h"
 #include "file/path.h"
-#include "gui/dialog/file.h"
 #include "math/math.h"
 #include "math/rng.h"
 
diff --git a/src/gui/mrview/tool/connectome/connectome.h b/cpp/gui/mrview/tool/connectome/connectome.h
similarity index 92%
rename from src/gui/mrview/tool/connectome/connectome.h
rename to cpp/gui/mrview/tool/connectome/connectome.h
index 288d71ec8b..e4ee520fcc 100644
--- a/src/gui/mrview/tool/connectome/connectome.h
+++ b/cpp/gui/mrview/tool/connectome/connectome.h
@@ -24,34 +24,34 @@
 #include "misc/bitset.h"
 #include "surface/mesh.h"
 
-#include "gui/color_button.h"
-#include "gui/lighting_dock.h"
-#include "gui/mrview/adjust_button.h"
-#include "gui/mrview/colourmap_button.h"
-#include "gui/mrview/mode/base.h"
-#include "gui/mrview/spin_box.h"
-#include "gui/mrview/tool/base.h"
-#include "gui/opengl/gl.h"
-#include "gui/opengl/lighting.h"
-#include "gui/opengl/shader.h"
-#include "gui/projection.h"
-#include "gui/shapes/cube.h"
-#include "gui/shapes/cylinder.h"
-#include "gui/shapes/sphere.h"
+#include "color_button.h"
+#include "lighting_dock.h"
+#include "mrview/adjust_button.h"
+#include "mrview/colourmap_button.h"
+#include "mrview/mode/base.h"
+#include "mrview/spin_box.h"
+#include "mrview/tool/base.h"
+#include "opengl/glutils.h"
+#include "opengl/lighting.h"
+#include "opengl/shader.h"
+#include "projection.h"
+#include "shapes/cube.h"
+#include "shapes/cylinder.h"
+#include "shapes/sphere.h"
 
 #include "connectome/lut.h"
 #include "connectome/mat2vec.h"
 
-#include "gui/mrview/tool/connectome/colourmap_observers.h"
-#include "gui/mrview/tool/connectome/edge.h"
-#include "gui/mrview/tool/connectome/file_data_vector.h"
-#include "gui/mrview/tool/connectome/matrix_list.h"
-#include "gui/mrview/tool/connectome/node.h"
-#include "gui/mrview/tool/connectome/node_list.h"
-#include "gui/mrview/tool/connectome/node_overlay.h"
-#include "gui/mrview/tool/connectome/selection.h"
-#include "gui/mrview/tool/connectome/shaders.h"
-#include "gui/mrview/tool/connectome/types.h"
+#include "mrview/tool/connectome/colourmap_observers.h"
+#include "mrview/tool/connectome/edge.h"
+#include "mrview/tool/connectome/file_data_vector.h"
+#include "mrview/tool/connectome/matrix_list.h"
+#include "mrview/tool/connectome/node.h"
+#include "mrview/tool/connectome/node_list.h"
+#include "mrview/tool/connectome/node_overlay.h"
+#include "mrview/tool/connectome/selection.h"
+#include "mrview/tool/connectome/shaders.h"
+#include "mrview/tool/connectome/types.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/connectome/edge.cpp b/cpp/gui/mrview/tool/connectome/edge.cpp
similarity index 99%
rename from src/gui/mrview/tool/connectome/edge.cpp
rename to cpp/gui/mrview/tool/connectome/edge.cpp
index 240b496601..f876dc8c5b 100644
--- a/src/gui/mrview/tool/connectome/edge.cpp
+++ b/cpp/gui/mrview/tool/connectome/edge.cpp
@@ -14,14 +14,14 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/connectome/edge.h"
+#include "mrview/tool/connectome/edge.h"
 
 #include "math/rng.h"
 
 #include "dwi/tractography/file.h"
 #include "dwi/tractography/properties.h"
 #include "dwi/tractography/streamline.h"
-#include "gui/mrview/tool/connectome/connectome.h"
+#include "mrview/tool/connectome/connectome.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/connectome/edge.h b/cpp/gui/mrview/tool/connectome/edge.h
similarity index 99%
rename from src/gui/mrview/tool/connectome/edge.h
rename to cpp/gui/mrview/tool/connectome/edge.h
index 3f55c60a16..1caf6225e7 100644
--- a/src/gui/mrview/tool/connectome/edge.h
+++ b/cpp/gui/mrview/tool/connectome/edge.h
@@ -20,8 +20,8 @@
 
 #include "connectome/connectome.h"
 #include "dwi/tractography/streamline.h"
-#include "gui/opengl/gl.h"
 #include "math/math.h"
+#include "opengl/glutils.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/connectome/file_data_vector.cpp b/cpp/gui/mrview/tool/connectome/file_data_vector.cpp
similarity index 97%
rename from src/gui/mrview/tool/connectome/file_data_vector.cpp
rename to cpp/gui/mrview/tool/connectome/file_data_vector.cpp
index 91195a8a2e..ba4831c9bf 100644
--- a/src/gui/mrview/tool/connectome/file_data_vector.cpp
+++ b/cpp/gui/mrview/tool/connectome/file_data_vector.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/connectome/file_data_vector.h"
+#include "mrview/tool/connectome/file_data_vector.h"
 
 #include <limits>
 
diff --git a/src/gui/mrview/tool/connectome/file_data_vector.h b/cpp/gui/mrview/tool/connectome/file_data_vector.h
similarity index 98%
rename from src/gui/mrview/tool/connectome/file_data_vector.h
rename to cpp/gui/mrview/tool/connectome/file_data_vector.h
index c4f78a96a1..39afb40c8b 100644
--- a/src/gui/mrview/tool/connectome/file_data_vector.h
+++ b/cpp/gui/mrview/tool/connectome/file_data_vector.h
@@ -18,7 +18,7 @@
 
 #include <QString>
 
-#include "gui/gui.h"
+#include "gui.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/connectome/matrix_list.cpp b/cpp/gui/mrview/tool/connectome/matrix_list.cpp
similarity index 91%
rename from src/gui/mrview/tool/connectome/matrix_list.cpp
rename to cpp/gui/mrview/tool/connectome/matrix_list.cpp
index cc5dc10763..a451e9bbf6 100644
--- a/src/gui/mrview/tool/connectome/matrix_list.cpp
+++ b/cpp/gui/mrview/tool/connectome/matrix_list.cpp
@@ -14,9 +14,9 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/connectome/matrix_list.h"
+#include "mrview/tool/connectome/matrix_list.h"
 
-#include "gui/mrview/tool/connectome/connectome.h"
+#include "mrview/tool/connectome/connectome.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/connectome/matrix_list.h b/cpp/gui/mrview/tool/connectome/matrix_list.h
similarity index 97%
rename from src/gui/mrview/tool/connectome/matrix_list.h
rename to cpp/gui/mrview/tool/connectome/matrix_list.h
index 4802c5ea53..5c825ba4f6 100644
--- a/src/gui/mrview/tool/connectome/matrix_list.h
+++ b/cpp/gui/mrview/tool/connectome/matrix_list.h
@@ -20,8 +20,8 @@
 
 #include <QAbstractItemModel>
 
-#include "gui/mrview/tool/connectome/file_data_vector.h"
 #include "mrtrix.h"
+#include "mrview/tool/connectome/file_data_vector.h"
 
 namespace MR::GUI::MRView {
 
diff --git a/src/gui/mrview/tool/connectome/node.cpp b/cpp/gui/mrview/tool/connectome/node.cpp
similarity index 97%
rename from src/gui/mrview/tool/connectome/node.cpp
rename to cpp/gui/mrview/tool/connectome/node.cpp
index f0876ec3ce..14cdff2c85 100644
--- a/src/gui/mrview/tool/connectome/node.cpp
+++ b/cpp/gui/mrview/tool/connectome/node.cpp
@@ -14,11 +14,11 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/connectome/node.h"
-#include "gui/mrview/window.h"
+#include "mrview/tool/connectome/node.h"
+#include "mrview/window.h"
 
 #include "exception.h"
-#include "gui/mrview/window.h"
+#include "mrview/window.h"
 #include "types.h"
 
 namespace MR::GUI::MRView::Tool {
diff --git a/src/gui/mrview/tool/connectome/node.h b/cpp/gui/mrview/tool/connectome/node.h
similarity index 99%
rename from src/gui/mrview/tool/connectome/node.h
rename to cpp/gui/mrview/tool/connectome/node.h
index c24fafadef..8744e4853b 100644
--- a/src/gui/mrview/tool/connectome/node.h
+++ b/cpp/gui/mrview/tool/connectome/node.h
@@ -18,7 +18,7 @@
 
 #include "image.h"
 
-#include "gui/opengl/gl.h"
+#include "opengl/glutils.h"
 #include "surface/mesh.h"
 
 namespace MR::GUI::MRView::Tool {
diff --git a/src/gui/mrview/tool/connectome/node_list.cpp b/cpp/gui/mrview/tool/connectome/node_list.cpp
similarity index 97%
rename from src/gui/mrview/tool/connectome/node_list.cpp
rename to cpp/gui/mrview/tool/connectome/node_list.cpp
index ffeddc2f95..95671d394f 100644
--- a/src/gui/mrview/tool/connectome/node_list.cpp
+++ b/cpp/gui/mrview/tool/connectome/node_list.cpp
@@ -14,12 +14,12 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/connectome/node_list.h"
+#include "mrview/tool/connectome/node_list.h"
 
 #include <QVector>
 
-#include "gui/mrview/tool/base.h"
-#include "gui/mrview/tool/connectome/connectome.h"
+#include "mrview/tool/base.h"
+#include "mrview/tool/connectome/connectome.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/connectome/node_list.h b/cpp/gui/mrview/tool/connectome/node_list.h
similarity index 97%
rename from src/gui/mrview/tool/connectome/node_list.h
rename to cpp/gui/mrview/tool/connectome/node_list.h
index 5f16e67a46..73a937a518 100644
--- a/src/gui/mrview/tool/connectome/node_list.h
+++ b/cpp/gui/mrview/tool/connectome/node_list.h
@@ -18,8 +18,8 @@
 
 #include <memory>
 
-#include "gui/mrview/tool/base.h"
-#include "gui/mrview/tool/connectome/selection.h"
+#include "mrview/tool/base.h"
+#include "mrview/tool/connectome/selection.h"
 
 #include <QAbstractItemModel>
 #include <QTableView>
diff --git a/src/gui/mrview/tool/connectome/node_overlay.cpp b/cpp/gui/mrview/tool/connectome/node_overlay.cpp
similarity index 98%
rename from src/gui/mrview/tool/connectome/node_overlay.cpp
rename to cpp/gui/mrview/tool/connectome/node_overlay.cpp
index af3c44d7f8..3509221e0e 100644
--- a/src/gui/mrview/tool/connectome/node_overlay.cpp
+++ b/cpp/gui/mrview/tool/connectome/node_overlay.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/connectome/node_overlay.h"
+#include "mrview/tool/connectome/node_overlay.h"
 
 #include <limits>
 
diff --git a/src/gui/mrview/tool/connectome/node_overlay.h b/cpp/gui/mrview/tool/connectome/node_overlay.h
similarity index 94%
rename from src/gui/mrview/tool/connectome/node_overlay.h
rename to cpp/gui/mrview/tool/connectome/node_overlay.h
index 0e36bedaab..76cb7ffed9 100644
--- a/src/gui/mrview/tool/connectome/node_overlay.h
+++ b/cpp/gui/mrview/tool/connectome/node_overlay.h
@@ -19,8 +19,8 @@
 #include "header.h"
 #include "types.h"
 
-#include "gui/mrview/displayable.h"
-#include "gui/mrview/gui_image.h"
+#include "mrview/displayable.h"
+#include "mrview/gui_image.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/connectome/selection.cpp b/cpp/gui/mrview/tool/connectome/selection.cpp
similarity index 99%
rename from src/gui/mrview/tool/connectome/selection.cpp
rename to cpp/gui/mrview/tool/connectome/selection.cpp
index bd83c9b58f..5ca1f8b9b1 100644
--- a/src/gui/mrview/tool/connectome/selection.cpp
+++ b/cpp/gui/mrview/tool/connectome/selection.cpp
@@ -14,9 +14,9 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/connectome/selection.h"
+#include "mrview/tool/connectome/selection.h"
 
-#include "gui/mrview/tool/base.h"
+#include "mrview/tool/base.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/connectome/selection.h b/cpp/gui/mrview/tool/connectome/selection.h
similarity index 99%
rename from src/gui/mrview/tool/connectome/selection.h
rename to cpp/gui/mrview/tool/connectome/selection.h
index f06182cdbb..ed82c46574 100644
--- a/src/gui/mrview/tool/connectome/selection.h
+++ b/cpp/gui/mrview/tool/connectome/selection.h
@@ -18,8 +18,8 @@
 
 #include "mrtrix.h"
 
-#include "gui/color_button.h"
-#include "gui/mrview/adjust_button.h"
+#include "color_button.h"
+#include "mrview/adjust_button.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/connectome/shaders.cpp b/cpp/gui/mrview/tool/connectome/shaders.cpp
similarity index 99%
rename from src/gui/mrview/tool/connectome/shaders.cpp
rename to cpp/gui/mrview/tool/connectome/shaders.cpp
index 9cd343d48b..7fefd933d0 100644
--- a/src/gui/mrview/tool/connectome/shaders.cpp
+++ b/cpp/gui/mrview/tool/connectome/shaders.cpp
@@ -14,10 +14,10 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/connectome/shaders.h"
-#include "gui/mrview/window.h"
+#include "mrview/tool/connectome/shaders.h"
+#include "mrview/window.h"
 
-#include "gui/mrview/tool/connectome/connectome.h"
+#include "mrview/tool/connectome/connectome.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/connectome/shaders.h b/cpp/gui/mrview/tool/connectome/shaders.h
similarity index 96%
rename from src/gui/mrview/tool/connectome/shaders.h
rename to cpp/gui/mrview/tool/connectome/shaders.h
index a87f5fdf68..bf7d1ceb41 100644
--- a/src/gui/mrview/tool/connectome/shaders.h
+++ b/cpp/gui/mrview/tool/connectome/shaders.h
@@ -16,9 +16,9 @@
 
 #pragma once
 
-#include "gui/opengl/shader.h"
+#include "opengl/shader.h"
 
-#include "gui/mrview/tool/connectome/types.h"
+#include "mrview/tool/connectome/types.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/connectome/types.h b/cpp/gui/mrview/tool/connectome/types.h
similarity index 100%
rename from src/gui/mrview/tool/connectome/types.h
rename to cpp/gui/mrview/tool/connectome/types.h
diff --git a/src/gui/mrview/tool/fixel/base_fixel.cpp b/cpp/gui/mrview/tool/fixel/base_fixel.cpp
similarity index 99%
rename from src/gui/mrview/tool/fixel/base_fixel.cpp
rename to cpp/gui/mrview/tool/fixel/base_fixel.cpp
index 463d0d6c98..0068827b1d 100644
--- a/src/gui/mrview/tool/fixel/base_fixel.cpp
+++ b/cpp/gui/mrview/tool/fixel/base_fixel.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/fixel/base_fixel.h"
+#include "mrview/tool/fixel/base_fixel.h"
 
 namespace MR::GUI::MRView::Tool {
 BaseFixel::BaseFixel(const std::string &filename, Fixel &fixel_tool)
diff --git a/src/gui/mrview/tool/fixel/base_fixel.h b/cpp/gui/mrview/tool/fixel/base_fixel.h
similarity index 98%
rename from src/gui/mrview/tool/fixel/base_fixel.h
rename to cpp/gui/mrview/tool/fixel/base_fixel.h
index fa78f92eff..5c1cfa95ca 100644
--- a/src/gui/mrview/tool/fixel/base_fixel.h
+++ b/cpp/gui/mrview/tool/fixel/base_fixel.h
@@ -27,9 +27,9 @@
 #include "fixel/legacy/fixel_metric.h"
 #include "fixel/legacy/image.h"
 
-#include "gui/mrview/displayable.h"
-#include "gui/mrview/tool/fixel/fixel.h"
-#include "gui/mrview/tool/fixel/vector_structs.h"
+#include "mrview/displayable.h"
+#include "mrview/tool/fixel/fixel.h"
+#include "mrview/tool/fixel/vector_structs.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/fixel/directory.cpp b/cpp/gui/mrview/tool/fixel/directory.cpp
similarity index 98%
rename from src/gui/mrview/tool/fixel/directory.cpp
rename to cpp/gui/mrview/tool/fixel/directory.cpp
index a58a0fc33e..8819b16fec 100644
--- a/src/gui/mrview/tool/fixel/directory.cpp
+++ b/cpp/gui/mrview/tool/fixel/directory.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/fixel/directory.h"
+#include "mrview/tool/fixel/directory.h"
 
 namespace MR::GUI::MRView::Tool {
 void Directory::load_image_buffer() {
diff --git a/src/gui/mrview/tool/fixel/directory.h b/cpp/gui/mrview/tool/fixel/directory.h
similarity index 96%
rename from src/gui/mrview/tool/fixel/directory.h
rename to cpp/gui/mrview/tool/fixel/directory.h
index 7df06b4ebf..2417a8ed04 100644
--- a/src/gui/mrview/tool/fixel/directory.h
+++ b/cpp/gui/mrview/tool/fixel/directory.h
@@ -16,7 +16,7 @@
 
 #pragma once
 
-#include "gui/mrview/tool/fixel/base_fixel.h"
+#include "mrview/tool/fixel/base_fixel.h"
 
 namespace MR::GUI::MRView::Tool {
 class Directory : public FixelType<FixelIndexImageType> {
diff --git a/src/gui/mrview/tool/fixel/fixel.cpp b/cpp/gui/mrview/tool/fixel/fixel.cpp
similarity index 98%
rename from src/gui/mrview/tool/fixel/fixel.cpp
rename to cpp/gui/mrview/tool/fixel/fixel.cpp
index d8a749a253..17b7ef6685 100644
--- a/src/gui/mrview/tool/fixel/fixel.cpp
+++ b/cpp/gui/mrview/tool/fixel/fixel.cpp
@@ -14,18 +14,18 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/fixel/fixel.h"
-
-#include "gui/dialog/file.h"
-#include "gui/mrview/qthelpers.h"
-#include "gui/mrview/tool/fixel/base_fixel.h"
-#include "gui/mrview/tool/fixel/directory.h"
-#include "gui/mrview/tool/fixel/image4D.h"
-#include "gui/mrview/tool/fixel/legacy.h"
-#include "gui/mrview/tool/list_model_base.h"
-#include "gui/mrview/window.h"
+#include "mrview/tool/fixel/fixel.h"
+
+#include "dialog/file.h"
 #include "math/rng.h"
 #include "mrtrix.h"
+#include "mrview/qthelpers.h"
+#include "mrview/tool/fixel/base_fixel.h"
+#include "mrview/tool/fixel/directory.h"
+#include "mrview/tool/fixel/image4D.h"
+#include "mrview/tool/fixel/legacy.h"
+#include "mrview/tool/list_model_base.h"
+#include "mrview/window.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/fixel/fixel.h b/cpp/gui/mrview/tool/fixel/fixel.h
similarity index 95%
rename from src/gui/mrview/tool/fixel/fixel.h
rename to cpp/gui/mrview/tool/fixel/fixel.h
index 528b88d1b4..dd496e1267 100644
--- a/src/gui/mrview/tool/fixel/fixel.h
+++ b/cpp/gui/mrview/tool/fixel/fixel.h
@@ -16,11 +16,11 @@
 
 #pragma once
 
-#include "gui/mrview/adjust_button.h"
-#include "gui/mrview/colourmap_button.h"
-#include "gui/mrview/combo_box_error.h"
-#include "gui/mrview/tool/base.h"
-#include "gui/projection.h"
+#include "mrview/adjust_button.h"
+#include "mrview/colourmap_button.h"
+#include "mrview/combo_box_error.h"
+#include "mrview/tool/base.h"
+#include "projection.h"
 
 namespace MR::GUI::MRView::Tool {
 class Fixel : public Base, public ColourMapButtonObserver, public DisplayableVisitor {
diff --git a/src/gui/mrview/tool/fixel/image4D.cpp b/cpp/gui/mrview/tool/fixel/image4D.cpp
similarity index 98%
rename from src/gui/mrview/tool/fixel/image4D.cpp
rename to cpp/gui/mrview/tool/fixel/image4D.cpp
index 1ba73a9d5c..c44adf1187 100644
--- a/src/gui/mrview/tool/fixel/image4D.cpp
+++ b/cpp/gui/mrview/tool/fixel/image4D.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/fixel/image4D.h"
+#include "mrview/tool/fixel/image4D.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/fixel/image4D.h b/cpp/gui/mrview/tool/fixel/image4D.h
similarity index 96%
rename from src/gui/mrview/tool/fixel/image4D.h
rename to cpp/gui/mrview/tool/fixel/image4D.h
index 2ce2241b46..dab9e0c219 100644
--- a/src/gui/mrview/tool/fixel/image4D.h
+++ b/cpp/gui/mrview/tool/fixel/image4D.h
@@ -16,7 +16,7 @@
 
 #pragma once
 
-#include "gui/mrview/tool/fixel/base_fixel.h"
+#include "mrview/tool/fixel/base_fixel.h"
 
 namespace MR::GUI::MRView::Tool {
 class Image4D : public FixelType<FixelImage4DType> {
diff --git a/src/gui/mrview/tool/fixel/legacy.cpp b/cpp/gui/mrview/tool/fixel/legacy.cpp
similarity index 98%
rename from src/gui/mrview/tool/fixel/legacy.cpp
rename to cpp/gui/mrview/tool/fixel/legacy.cpp
index 579e81307e..27bff99e1f 100644
--- a/src/gui/mrview/tool/fixel/legacy.cpp
+++ b/cpp/gui/mrview/tool/fixel/legacy.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/fixel/legacy.h"
+#include "mrview/tool/fixel/legacy.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/fixel/legacy.h b/cpp/gui/mrview/tool/fixel/legacy.h
similarity index 96%
rename from src/gui/mrview/tool/fixel/legacy.h
rename to cpp/gui/mrview/tool/fixel/legacy.h
index 6f56a15393..8d8f6ce427 100644
--- a/src/gui/mrview/tool/fixel/legacy.h
+++ b/cpp/gui/mrview/tool/fixel/legacy.h
@@ -16,7 +16,7 @@
 
 #pragma once
 
-#include "gui/mrview/tool/fixel/base_fixel.h"
+#include "mrview/tool/fixel/base_fixel.h"
 
 namespace MR::GUI::MRView::Tool {
 class Legacy : public FixelType<FixelLegacyType> {
diff --git a/src/gui/mrview/tool/fixel/vector_structs.h b/cpp/gui/mrview/tool/fixel/vector_structs.h
similarity index 100%
rename from src/gui/mrview/tool/fixel/vector_structs.h
rename to cpp/gui/mrview/tool/fixel/vector_structs.h
diff --git a/src/gui/mrview/tool/list.h b/cpp/gui/mrview/tool/list.h
similarity index 80%
rename from src/gui/mrview/tool/list.h
rename to cpp/gui/mrview/tool/list.h
index 701288ddb4..58ea938bd9 100644
--- a/src/gui/mrview/tool/list.h
+++ b/cpp/gui/mrview/tool/list.h
@@ -17,15 +17,15 @@
 #ifndef TOOL
 
 // place #include files in here:
-#include "gui/mrview/tool/connectome/connectome.h"
-#include "gui/mrview/tool/fixel/fixel.h"
-#include "gui/mrview/tool/odf/odf.h"
-#include "gui/mrview/tool/overlay.h"
-#include "gui/mrview/tool/roi_editor/roi.h"
-#include "gui/mrview/tool/screen_capture.h"
-#include "gui/mrview/tool/tractography/tractography.h"
-#include "gui/mrview/tool/transform.h"
-#include "gui/mrview/tool/view.h"
+#include "mrview/tool/connectome/connectome.h"
+#include "mrview/tool/fixel/fixel.h"
+#include "mrview/tool/odf/odf.h"
+#include "mrview/tool/overlay.h"
+#include "mrview/tool/roi_editor/roi.h"
+#include "mrview/tool/screen_capture.h"
+#include "mrview/tool/tractography/tractography.h"
+#include "mrview/tool/transform.h"
+#include "mrview/tool/view.h"
 
 #else
 
diff --git a/src/gui/mrview/tool/list_model_base.h b/cpp/gui/mrview/tool/list_model_base.h
similarity index 99%
rename from src/gui/mrview/tool/list_model_base.h
rename to cpp/gui/mrview/tool/list_model_base.h
index 739f720618..8893878ade 100644
--- a/src/gui/mrview/tool/list_model_base.h
+++ b/cpp/gui/mrview/tool/list_model_base.h
@@ -16,7 +16,7 @@
 
 #pragma once
 
-#include "gui/mrview/displayable.h"
+#include "mrview/displayable.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/odf/item.cpp b/cpp/gui/mrview/tool/odf/item.cpp
similarity index 99%
rename from src/gui/mrview/tool/odf/item.cpp
rename to cpp/gui/mrview/tool/odf/item.cpp
index 7e7e85ca3a..b9d415d477 100644
--- a/src/gui/mrview/tool/odf/item.cpp
+++ b/cpp/gui/mrview/tool/odf/item.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/odf/item.h"
+#include "mrview/tool/odf/item.h"
 
 #include "dwi/gradient.h"
 #include "header.h"
diff --git a/src/gui/mrview/tool/odf/item.h b/cpp/gui/mrview/tool/odf/item.h
similarity index 95%
rename from src/gui/mrview/tool/odf/item.h
rename to cpp/gui/mrview/tool/odf/item.h
index d1b9384ded..4912864646 100644
--- a/src/gui/mrview/tool/odf/item.h
+++ b/cpp/gui/mrview/tool/odf/item.h
@@ -21,9 +21,9 @@
 #include "dwi/shells.h"
 
 #include "dwi/directions/set.h"
-#include "gui/dwi/renderer.h"
-#include "gui/mrview/gui_image.h"
-#include "gui/mrview/tool/odf/type.h"
+#include "dwi/renderer.h"
+#include "mrview/gui_image.h"
+#include "mrview/tool/odf/type.h"
 
 namespace MR {
 
diff --git a/src/gui/mrview/tool/odf/model.cpp b/cpp/gui/mrview/tool/odf/model.cpp
similarity index 98%
rename from src/gui/mrview/tool/odf/model.cpp
rename to cpp/gui/mrview/tool/odf/model.cpp
index a694d97614..55e4851528 100644
--- a/src/gui/mrview/tool/odf/model.cpp
+++ b/cpp/gui/mrview/tool/odf/model.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/odf/model.h"
+#include "mrview/tool/odf/model.h"
 
 #include "header.h"
 
diff --git a/src/gui/mrview/tool/odf/model.h b/cpp/gui/mrview/tool/odf/model.h
similarity index 97%
rename from src/gui/mrview/tool/odf/model.h
rename to cpp/gui/mrview/tool/odf/model.h
index 439cf739ae..2ff95353cf 100644
--- a/src/gui/mrview/tool/odf/model.h
+++ b/cpp/gui/mrview/tool/odf/model.h
@@ -21,8 +21,8 @@
 
 #include "types.h"
 
-#include "gui/mrview/tool/odf/item.h"
-#include "gui/mrview/tool/odf/type.h"
+#include "mrview/tool/odf/item.h"
+#include "mrview/tool/odf/type.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/odf/odf.cpp b/cpp/gui/mrview/tool/odf/odf.cpp
similarity index 98%
rename from src/gui/mrview/tool/odf/odf.cpp
rename to cpp/gui/mrview/tool/odf/odf.cpp
index 849db14e37..1229ca4132 100644
--- a/src/gui/mrview/tool/odf/odf.cpp
+++ b/cpp/gui/mrview/tool/odf/odf.cpp
@@ -18,16 +18,16 @@
 #include "dwi/shells.h"
 #include "mrtrix.h"
 
+#include "dialog/file.h"
 #include "dwi/directions/set.h"
-#include "gui/dialog/file.h"
-#include "gui/dwi/render_frame.h"
-#include "gui/lighting_dock.h"
-#include "gui/mrview/mode/base.h"
-#include "gui/mrview/tool/odf/item.h"
-#include "gui/mrview/tool/odf/model.h"
-#include "gui/mrview/tool/odf/odf.h"
-#include "gui/mrview/tool/odf/preview.h"
-#include "gui/mrview/window.h"
+#include "dwi/render_frame.h"
+#include "lighting_dock.h"
+#include "mrview/mode/base.h"
+#include "mrview/tool/odf/item.h"
+#include "mrview/tool/odf/model.h"
+#include "mrview/tool/odf/odf.h"
+#include "mrview/tool/odf/preview.h"
+#include "mrview/window.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/odf/odf.h b/cpp/gui/mrview/tool/odf/odf.h
similarity index 94%
rename from src/gui/mrview/tool/odf/odf.h
rename to cpp/gui/mrview/tool/odf/odf.h
index 1e586faf2c..9f83c6a413 100644
--- a/src/gui/mrview/tool/odf/odf.h
+++ b/cpp/gui/mrview/tool/odf/odf.h
@@ -16,11 +16,11 @@
 
 #pragma once
 
-#include "gui/color_button.h"
-#include "gui/mrview/adjust_button.h"
-#include "gui/mrview/spin_box.h"
-#include "gui/mrview/tool/base.h"
-#include "gui/mrview/tool/odf/type.h"
+#include "color_button.h"
+#include "mrview/adjust_button.h"
+#include "mrview/spin_box.h"
+#include "mrview/tool/base.h"
+#include "mrview/tool/odf/type.h"
 
 namespace MR::GUI {
 namespace DWI {
diff --git a/src/gui/mrview/tool/odf/preview.cpp b/cpp/gui/mrview/tool/odf/preview.cpp
similarity index 95%
rename from src/gui/mrview/tool/odf/preview.cpp
rename to cpp/gui/mrview/tool/odf/preview.cpp
index 87a3be4987..938dff622f 100644
--- a/src/gui/mrview/tool/odf/preview.cpp
+++ b/cpp/gui/mrview/tool/odf/preview.cpp
@@ -14,11 +14,11 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/odf/preview.h"
-#include "gui/dwi/render_frame.h"
-#include "gui/mrview/mode/base.h"
-#include "gui/mrview/tool/odf/odf.h"
-#include "gui/mrview/window.h"
+#include "mrview/tool/odf/preview.h"
+#include "dwi/render_frame.h"
+#include "mrview/mode/base.h"
+#include "mrview/tool/odf/odf.h"
+#include "mrview/window.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/odf/preview.h b/cpp/gui/mrview/tool/odf/preview.h
similarity index 92%
rename from src/gui/mrview/tool/odf/preview.h
rename to cpp/gui/mrview/tool/odf/preview.h
index ad12d4e62c..9fa48f65e8 100644
--- a/src/gui/mrview/tool/odf/preview.h
+++ b/cpp/gui/mrview/tool/odf/preview.h
@@ -16,11 +16,11 @@
 
 #pragma once
 
-#include "gui/dwi/render_frame.h"
+#include "dwi/render_frame.h"
 
-#include "gui/mrview/spin_box.h"
-#include "gui/mrview/tool/odf/odf.h"
-#include "gui/mrview/window.h"
+#include "mrview/spin_box.h"
+#include "mrview/tool/odf/odf.h"
+#include "mrview/window.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/odf/type.h b/cpp/gui/mrview/tool/odf/type.h
similarity index 96%
rename from src/gui/mrview/tool/odf/type.h
rename to cpp/gui/mrview/tool/odf/type.h
index e67ab16c26..d6a9ad1627 100644
--- a/src/gui/mrview/tool/odf/type.h
+++ b/cpp/gui/mrview/tool/odf/type.h
@@ -16,7 +16,7 @@
 
 #pragma once
 
-#include "gui/dwi/renderer.h"
+#include "dwi/renderer.h"
 
 namespace MR {
 
diff --git a/src/gui/mrview/tool/overlay.cpp b/cpp/gui/mrview/tool/overlay.cpp
similarity index 99%
rename from src/gui/mrview/tool/overlay.cpp
rename to cpp/gui/mrview/tool/overlay.cpp
index c9613cd12e..602e29339b 100644
--- a/src/gui/mrview/tool/overlay.cpp
+++ b/cpp/gui/mrview/tool/overlay.cpp
@@ -14,15 +14,15 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/overlay.h"
-
-#include "gui/dialog/file.h"
-#include "gui/mrview/gui_image.h"
-#include "gui/mrview/mode/slice.h"
-#include "gui/mrview/qthelpers.h"
-#include "gui/mrview/tool/list_model_base.h"
-#include "gui/mrview/window.h"
+#include "mrview/tool/overlay.h"
+
+#include "dialog/file.h"
 #include "mrtrix.h"
+#include "mrview/gui_image.h"
+#include "mrview/mode/slice.h"
+#include "mrview/qthelpers.h"
+#include "mrview/tool/list_model_base.h"
+#include "mrview/window.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/overlay.h b/cpp/gui/mrview/tool/overlay.h
similarity index 95%
rename from src/gui/mrview/tool/overlay.h
rename to cpp/gui/mrview/tool/overlay.h
index b16a037021..58bf052c7d 100644
--- a/src/gui/mrview/tool/overlay.h
+++ b/cpp/gui/mrview/tool/overlay.h
@@ -16,11 +16,11 @@
 
 #pragma once
 
-#include "gui/mrview/adjust_button.h"
-#include "gui/mrview/colourmap_button.h"
-#include "gui/mrview/mode/base.h"
-#include "gui/mrview/spin_box.h"
-#include "gui/mrview/tool/base.h"
+#include "mrview/adjust_button.h"
+#include "mrview/colourmap_button.h"
+#include "mrview/mode/base.h"
+#include "mrview/spin_box.h"
+#include "mrview/tool/base.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/roi_editor/item.cpp b/cpp/gui/mrview/tool/roi_editor/item.cpp
similarity index 97%
rename from src/gui/mrview/tool/roi_editor/item.cpp
rename to cpp/gui/mrview/tool/roi_editor/item.cpp
index e62d235a56..c4c6152c1a 100644
--- a/src/gui/mrview/tool/roi_editor/item.cpp
+++ b/cpp/gui/mrview/tool/roi_editor/item.cpp
@@ -17,14 +17,14 @@
 #include <iomanip>
 #include <string>
 
-#include "gui/mrview/tool/roi_editor/item.h"
+#include "mrview/tool/roi_editor/item.h"
 
 #include "algo/loop.h"
 #include "file/config.h"
 #include "progressbar.h"
 
-#include "gui/dialog/file.h"
-#include "gui/mrview/window.h"
+#include "dialog/file.h"
+#include "mrview/window.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/roi_editor/item.h b/cpp/gui/mrview/tool/roi_editor/item.h
similarity index 96%
rename from src/gui/mrview/tool/roi_editor/item.h
rename to cpp/gui/mrview/tool/roi_editor/item.h
index df1d163f46..824b689ec4 100644
--- a/src/gui/mrview/tool/roi_editor/item.h
+++ b/cpp/gui/mrview/tool/roi_editor/item.h
@@ -19,9 +19,9 @@
 #include <array>
 
 #include "algo/loop.h"
-#include "gui/mrview/tool/roi_editor/undoentry.h"
-#include "gui/mrview/volume.h"
 #include "header.h"
+#include "mrview/tool/roi_editor/undoentry.h"
+#include "mrview/volume.h"
 #include "types.h"
 
 namespace MR::GUI::MRView::Tool {
diff --git a/src/gui/mrview/tool/roi_editor/model.cpp b/cpp/gui/mrview/tool/roi_editor/model.cpp
similarity index 94%
rename from src/gui/mrview/tool/roi_editor/model.cpp
rename to cpp/gui/mrview/tool/roi_editor/model.cpp
index 617d1bb5d5..26d068e5c4 100644
--- a/src/gui/mrview/tool/roi_editor/model.cpp
+++ b/cpp/gui/mrview/tool/roi_editor/model.cpp
@@ -14,8 +14,8 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/roi_editor/model.h"
-#include "gui/mrview/window.h"
+#include "mrview/tool/roi_editor/model.h"
+#include "mrview/window.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/roi_editor/model.h b/cpp/gui/mrview/tool/roi_editor/model.h
similarity index 92%
rename from src/gui/mrview/tool/roi_editor/model.h
rename to cpp/gui/mrview/tool/roi_editor/model.h
index 2e5bd5579b..d3340ade6b 100644
--- a/src/gui/mrview/tool/roi_editor/model.h
+++ b/cpp/gui/mrview/tool/roi_editor/model.h
@@ -16,10 +16,10 @@
 
 #pragma once
 
-#include "gui/mrview/tool/list_model_base.h"
-#include "gui/mrview/tool/roi_editor/item.h"
 #include "header.h"
 #include "memory.h"
+#include "mrview/tool/list_model_base.h"
+#include "mrview/tool/roi_editor/item.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/roi_editor/roi.cpp b/cpp/gui/mrview/tool/roi_editor/roi.cpp
similarity index 99%
rename from src/gui/mrview/tool/roi_editor/roi.cpp
rename to cpp/gui/mrview/tool/roi_editor/roi.cpp
index df5adfb7ea..ba77bd2dec 100644
--- a/src/gui/mrview/tool/roi_editor/roi.cpp
+++ b/cpp/gui/mrview/tool/roi_editor/roi.cpp
@@ -16,13 +16,13 @@
 
 #include <string>
 
-#include "gui/mrview/qthelpers.h"
-#include "gui/mrview/tool/roi_editor/roi.h"
+#include "mrview/qthelpers.h"
+#include "mrview/tool/roi_editor/roi.h"
 
-#include "gui/cursor.h"
-#include "gui/dialog/file.h"
-#include "gui/projection.h"
+#include "cursor.h"
+#include "dialog/file.h"
 #include "header.h"
+#include "projection.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/roi_editor/roi.h b/cpp/gui/mrview/tool/roi_editor/roi.h
similarity index 89%
rename from src/gui/mrview/tool/roi_editor/roi.h
rename to cpp/gui/mrview/tool/roi_editor/roi.h
index 5625d91ca1..fa7b42867e 100644
--- a/src/gui/mrview/tool/roi_editor/roi.h
+++ b/cpp/gui/mrview/tool/roi_editor/roi.h
@@ -20,15 +20,15 @@
 #include "transform.h"
 #include "types.h"
 
-#include "gui/color_button.h"
-#include "gui/mrview/adjust_button.h"
-#include "gui/mrview/mode/base.h"
-#include "gui/mrview/mode/slice.h"
-#include "gui/mrview/tool/base.h"
-
-#include "gui/mrview/tool/roi_editor/item.h"
-#include "gui/mrview/tool/roi_editor/model.h"
-#include "gui/mrview/tool/roi_editor/undoentry.h"
+#include "color_button.h"
+#include "mrview/adjust_button.h"
+#include "mrview/mode/base.h"
+#include "mrview/mode/slice.h"
+#include "mrview/tool/base.h"
+
+#include "mrview/tool/roi_editor/item.h"
+#include "mrview/tool/roi_editor/model.h"
+#include "mrview/tool/roi_editor/undoentry.h"
 
 namespace MR {
 
diff --git a/src/gui/mrview/tool/roi_editor/undoentry.cpp b/cpp/gui/mrview/tool/roi_editor/undoentry.cpp
similarity index 99%
rename from src/gui/mrview/tool/roi_editor/undoentry.cpp
rename to cpp/gui/mrview/tool/roi_editor/undoentry.cpp
index 6c25deccea..5b4037ee3a 100644
--- a/src/gui/mrview/tool/roi_editor/undoentry.cpp
+++ b/cpp/gui/mrview/tool/roi_editor/undoentry.cpp
@@ -16,9 +16,9 @@
 
 #include <limits>
 
-#include "gui/mrview/tool/roi_editor/item.h"
-#include "gui/mrview/tool/roi_editor/undoentry.h"
-#include "gui/mrview/window.h"
+#include "mrview/tool/roi_editor/item.h"
+#include "mrview/tool/roi_editor/undoentry.h"
+#include "mrview/window.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/roi_editor/undoentry.h b/cpp/gui/mrview/tool/roi_editor/undoentry.h
similarity index 97%
rename from src/gui/mrview/tool/roi_editor/undoentry.h
rename to cpp/gui/mrview/tool/roi_editor/undoentry.h
index 3afa217fc5..a4293976dc 100644
--- a/src/gui/mrview/tool/roi_editor/undoentry.h
+++ b/cpp/gui/mrview/tool/roi_editor/undoentry.h
@@ -21,8 +21,8 @@
 
 #include "types.h"
 
-#include "gui/opengl/gl.h"
-#include "gui/opengl/shader.h"
+#include "opengl/glutils.h"
+#include "opengl/shader.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/screen_capture.cpp b/cpp/gui/mrview/tool/screen_capture.cpp
similarity index 98%
rename from src/gui/mrview/tool/screen_capture.cpp
rename to cpp/gui/mrview/tool/screen_capture.cpp
index 8c0e800fee..cc978d74b8 100644
--- a/src/gui/mrview/tool/screen_capture.cpp
+++ b/cpp/gui/mrview/tool/screen_capture.cpp
@@ -16,13 +16,13 @@
 
 #include <Eigen/Geometry>
 
+#include "dialog/file.h"
 #include "file/path.h"
-#include "gui/dialog/file.h"
-#include "gui/mrview/mode/base.h"
-#include "gui/mrview/tool/screen_capture.h"
-#include "gui/mrview/window.h"
-#include "gui/opengl/transformation.h"
 #include "mrtrix.h"
+#include "mrview/mode/base.h"
+#include "mrview/tool/screen_capture.h"
+#include "mrview/window.h"
+#include "opengl/transformation.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/screen_capture.h b/cpp/gui/mrview/tool/screen_capture.h
similarity index 96%
rename from src/gui/mrview/tool/screen_capture.h
rename to cpp/gui/mrview/tool/screen_capture.h
index 54cef10694..8abcedcbc4 100644
--- a/src/gui/mrview/tool/screen_capture.h
+++ b/cpp/gui/mrview/tool/screen_capture.h
@@ -18,9 +18,9 @@
 
 #include <deque>
 
-#include "gui/mrview/adjust_button.h"
-#include "gui/mrview/spin_box.h"
-#include "gui/mrview/tool/base.h"
+#include "mrview/adjust_button.h"
+#include "mrview/spin_box.h"
+#include "mrview/tool/base.h"
 
 namespace MR::GUI::MRView {
 class AdjustButton;
diff --git a/src/gui/mrview/tool/tractography/track_scalar_file.cpp b/cpp/gui/mrview/tool/tractography/track_scalar_file.cpp
similarity index 98%
rename from src/gui/mrview/tool/tractography/track_scalar_file.cpp
rename to cpp/gui/mrview/tool/tractography/track_scalar_file.cpp
index 5a77745b04..b8a48422cb 100644
--- a/src/gui/mrview/tool/tractography/track_scalar_file.cpp
+++ b/cpp/gui/mrview/tool/tractography/track_scalar_file.cpp
@@ -14,10 +14,10 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/tractography/track_scalar_file.h"
+#include "mrview/tool/tractography/track_scalar_file.h"
 
-#include "gui/dialog/file.h"
-#include "gui/mrview/tool/tractography/tractogram.h"
+#include "dialog/file.h"
+#include "mrview/tool/tractography/tractogram.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/tractography/track_scalar_file.h b/cpp/gui/mrview/tool/tractography/track_scalar_file.h
similarity index 92%
rename from src/gui/mrview/tool/tractography/track_scalar_file.h
rename to cpp/gui/mrview/tool/tractography/track_scalar_file.h
index feb5a17e36..9d3abd757f 100644
--- a/src/gui/mrview/tool/tractography/track_scalar_file.h
+++ b/cpp/gui/mrview/tool/tractography/track_scalar_file.h
@@ -16,11 +16,11 @@
 
 #pragma once
 
-#include "gui/mrview/adjust_button.h"
-#include "gui/mrview/colourmap_button.h"
-#include "gui/mrview/displayable.h"
-#include "gui/mrview/tool/base.h"
-#include "gui/mrview/tool/tractography/tractogram_enums.h"
+#include "mrview/adjust_button.h"
+#include "mrview/colourmap_button.h"
+#include "mrview/displayable.h"
+#include "mrview/tool/base.h"
+#include "mrview/tool/tractography/tractogram_enums.h"
 
 namespace MR::GUI::MRView::Tool {
 class Tractogram;
diff --git a/src/gui/mrview/tool/tractography/tractogram.cpp b/cpp/gui/mrview/tool/tractography/tractogram.cpp
similarity index 99%
rename from src/gui/mrview/tool/tractography/tractogram.cpp
rename to cpp/gui/mrview/tool/tractography/tractogram.cpp
index 61d68a016c..5293e88db3 100644
--- a/src/gui/mrview/tool/tractography/tractogram.cpp
+++ b/cpp/gui/mrview/tool/tractography/tractogram.cpp
@@ -14,16 +14,16 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/tractography/tractogram.h"
+#include "mrview/tool/tractography/tractogram.h"
 #include "dwi/tractography/file.h"
 #include "dwi/tractography/properties.h"
 #include "dwi/tractography/scalar_file.h"
 #include "file/matrix.h"
-#include "gui/mrview/mode/base.h"
-#include "gui/mrview/window.h"
-#include "gui/opengl/lighting.h"
-#include "gui/projection.h"
+#include "mrview/mode/base.h"
+#include "mrview/window.h"
+#include "opengl/lighting.h"
 #include "progressbar.h"
+#include "projection.h"
 
 const size_t MAX_BUFFER_SIZE = 2796200; // number of points to fill 32MB
 
diff --git a/src/gui/mrview/tool/tractography/tractogram.h b/cpp/gui/mrview/tool/tractography/tractogram.h
similarity index 98%
rename from src/gui/mrview/tool/tractography/tractogram.h
rename to cpp/gui/mrview/tool/tractography/tractogram.h
index 20c3b26615..41f0e46d6e 100644
--- a/src/gui/mrview/tool/tractography/tractogram.h
+++ b/cpp/gui/mrview/tool/tractography/tractogram.h
@@ -17,8 +17,8 @@
 #pragma once
 
 #include "dwi/tractography/properties.h"
-#include "gui/mrview/displayable.h"
-#include "gui/mrview/tool/tractography/tractography.h"
+#include "mrview/displayable.h"
+#include "mrview/tool/tractography/tractography.h"
 
 namespace MR::GUI {
 class Projection;
diff --git a/src/gui/mrview/tool/tractography/tractogram_enums.h b/cpp/gui/mrview/tool/tractography/tractogram_enums.h
similarity index 100%
rename from src/gui/mrview/tool/tractography/tractogram_enums.h
rename to cpp/gui/mrview/tool/tractography/tractogram_enums.h
diff --git a/src/gui/mrview/tool/tractography/tractography.cpp b/cpp/gui/mrview/tool/tractography/tractography.cpp
similarity index 99%
rename from src/gui/mrview/tool/tractography/tractography.cpp
rename to cpp/gui/mrview/tool/tractography/tractography.cpp
index fb9e3aa7f0..aa4f9f3018 100644
--- a/src/gui/mrview/tool/tractography/tractography.cpp
+++ b/cpp/gui/mrview/tool/tractography/tractography.cpp
@@ -14,16 +14,16 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/tractography/tractography.h"
-#include "gui/dialog/file.h"
-#include "gui/lighting_dock.h"
-#include "gui/mrview/qthelpers.h"
-#include "gui/mrview/tool/list_model_base.h"
-#include "gui/mrview/tool/tractography/track_scalar_file.h"
-#include "gui/mrview/tool/tractography/tractogram.h"
-#include "gui/mrview/window.h"
-#include "gui/opengl/lighting.h"
+#include "mrview/tool/tractography/tractography.h"
+#include "dialog/file.h"
+#include "lighting_dock.h"
 #include "mrtrix.h"
+#include "mrview/qthelpers.h"
+#include "mrview/tool/list_model_base.h"
+#include "mrview/tool/tractography/track_scalar_file.h"
+#include "mrview/tool/tractography/tractogram.h"
+#include "mrview/window.h"
+#include "opengl/lighting.h"
 
 namespace MR::GUI::MRView::Tool {
 const std::vector<std::string> tractogram_geometry_types = {"pseudotubes", "lines", "points"};
diff --git a/src/gui/mrview/tool/tractography/tractography.h b/cpp/gui/mrview/tool/tractography/tractography.h
similarity index 93%
rename from src/gui/mrview/tool/tractography/tractography.h
rename to cpp/gui/mrview/tool/tractography/tractography.h
index 090ac53135..6853cdf7dd 100644
--- a/src/gui/mrview/tool/tractography/tractography.h
+++ b/cpp/gui/mrview/tool/tractography/tractography.h
@@ -16,12 +16,12 @@
 
 #pragma once
 
-#include "gui/color_button.h"
-#include "gui/mrview/adjust_button.h"
-#include "gui/mrview/combo_box_error.h"
-#include "gui/mrview/tool/base.h"
-#include "gui/mrview/tool/tractography/track_scalar_file.h"
-#include "gui/projection.h"
+#include "color_button.h"
+#include "mrview/adjust_button.h"
+#include "mrview/combo_box_error.h"
+#include "mrview/tool/base.h"
+#include "mrview/tool/tractography/track_scalar_file.h"
+#include "projection.h"
 
 namespace MR::GUI {
 namespace GL {
diff --git a/src/gui/mrview/tool/transform.cpp b/cpp/gui/mrview/tool/transform.cpp
similarity index 99%
rename from src/gui/mrview/tool/transform.cpp
rename to cpp/gui/mrview/tool/transform.cpp
index c87f81ecc2..8931ad2187 100644
--- a/src/gui/mrview/tool/transform.cpp
+++ b/cpp/gui/mrview/tool/transform.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/transform.h"
+#include "mrview/tool/transform.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/transform.h b/cpp/gui/mrview/tool/transform.h
similarity index 95%
rename from src/gui/mrview/tool/transform.h
rename to cpp/gui/mrview/tool/transform.h
index 438d63da93..0e6d5d8c44 100644
--- a/src/gui/mrview/tool/transform.h
+++ b/cpp/gui/mrview/tool/transform.h
@@ -16,8 +16,8 @@
 
 #pragma once
 
-#include "gui/mrview/mode/base.h"
-#include "gui/mrview/tool/base.h"
+#include "mrview/mode/base.h"
+#include "mrview/tool/base.h"
 
 namespace MR::GUI::MRView::Tool {
 
diff --git a/src/gui/mrview/tool/view.cpp b/cpp/gui/mrview/tool/view.cpp
similarity index 99%
rename from src/gui/mrview/tool/view.cpp
rename to cpp/gui/mrview/tool/view.cpp
index ac730c4c20..5cdd434273 100644
--- a/src/gui/mrview/tool/view.cpp
+++ b/cpp/gui/mrview/tool/view.cpp
@@ -14,16 +14,16 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/tool/view.h"
-
-#include "gui/mrview/adjust_button.h"
-#include "gui/mrview/mode/lightbox.h"
-#include "gui/mrview/mode/lightbox_gui.h"
-#include "gui/mrview/mode/ortho.h"
-#include "gui/mrview/mode/volume.h"
-#include "gui/mrview/window.h"
+#include "mrview/tool/view.h"
+
 #include "math/math.h"
 #include "mrtrix.h"
+#include "mrview/adjust_button.h"
+#include "mrview/mode/lightbox.h"
+#include "mrview/mode/lightbox_gui.h"
+#include "mrview/mode/ortho.h"
+#include "mrview/mode/volume.h"
+#include "mrview/window.h"
 
 #define FOV_RATE_MULTIPLIER 0.01f
 #define MRTRIX_MIN_ALPHA 1.0e-3f
diff --git a/src/gui/mrview/tool/view.h b/cpp/gui/mrview/tool/view.h
similarity index 97%
rename from src/gui/mrview/tool/view.h
rename to cpp/gui/mrview/tool/view.h
index ebb53c498a..68a5dc0a95 100644
--- a/src/gui/mrview/tool/view.h
+++ b/cpp/gui/mrview/tool/view.h
@@ -16,10 +16,10 @@
 
 #pragma once
 
-#include "gui/mrview/mode/base.h"
-#include "gui/mrview/spin_box.h"
-#include "gui/mrview/tool/base.h"
-#include "gui/opengl/transformation.h"
+#include "mrview/mode/base.h"
+#include "mrview/spin_box.h"
+#include "mrview/tool/base.h"
+#include "opengl/transformation.h"
 
 namespace MR::GUI::MRView {
 class AdjustButton;
diff --git a/src/gui/mrview/volume.cpp b/cpp/gui/mrview/volume.cpp
similarity index 96%
rename from src/gui/mrview/volume.cpp
rename to cpp/gui/mrview/volume.cpp
index 14d42eb834..cbcc179257 100644
--- a/src/gui/mrview/volume.cpp
+++ b/cpp/gui/mrview/volume.cpp
@@ -14,9 +14,9 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/mrview/volume.h"
+#include "mrview/volume.h"
 
-#include "gui/mrview/window.h"
+#include "mrview/window.h"
 
 namespace MR::GUI::MRView {
 
diff --git a/src/gui/mrview/volume.h b/cpp/gui/mrview/volume.h
similarity index 99%
rename from src/gui/mrview/volume.h
rename to cpp/gui/mrview/volume.h
index 8ed53270e4..38bd12f703 100644
--- a/src/gui/mrview/volume.h
+++ b/cpp/gui/mrview/volume.h
@@ -20,8 +20,8 @@
 #include "transform.h"
 
 #include "file/config.h"
-#include "gui/mrview/displayable.h"
-#include "gui/opengl/gl.h"
+#include "mrview/displayable.h"
+#include "opengl/glutils.h"
 
 namespace MR::GUI {
 class Projection;
diff --git a/src/gui/mrview/window.cpp b/cpp/gui/mrview/window.cpp
similarity index 99%
rename from src/gui/mrview/window.cpp
rename to cpp/gui/mrview/window.cpp
index d0e9ccdcbf..2b396dcafc 100644
--- a/src/gui/mrview/window.cpp
+++ b/cpp/gui/mrview/window.cpp
@@ -15,20 +15,20 @@
  */
 #include "algo/copy.h"
 #include "app.h"
+#include "dialog/dialog.h"
+#include "dialog/file.h"
+#include "dialog/image_properties.h"
+#include "dialog/opengl.h"
+#include "dialog/progress.h"
 #include "file/config.h"
-#include "gui/dialog/dialog.h"
-#include "gui/dialog/file.h"
-#include "gui/dialog/image_properties.h"
-#include "gui/dialog/opengl.h"
-#include "gui/dialog/progress.h"
-#include "gui/mrview/mode/base.h"
-#include "gui/mrview/mode/list.h"
-#include "gui/mrview/qthelpers.h"
-#include "gui/mrview/tool/base.h"
-#include "gui/mrview/tool/list.h"
-#include "gui/opengl/gl.h"
-#include "gui/opengl/lighting.h"
 #include "header.h"
+#include "mrview/mode/base.h"
+#include "mrview/mode/list.h"
+#include "mrview/qthelpers.h"
+#include "mrview/tool/base.h"
+#include "mrview/tool/list.h"
+#include "opengl/glutils.h"
+#include "opengl/lighting.h"
 #include "timer.h"
 #include <QDebug>
 
@@ -40,7 +40,7 @@ using namespace App;
 
       const OptionGroup Window::options = OptionGroup ("General options")
         + Option ("mode", "select initial display mode by its short ID. Valid mode IDs are: "
-#include "gui/mrview/mode/list.h"
+#include "mrview/mode/list.h"
             )
         + Argument ("name");
 #undef MODE
@@ -448,7 +448,7 @@ Window::Window()
 #define MODE_OPTION(classname, specifier, name, description) MODE(classname, specifier, name, description)
   {
     size_t n = 1;
-#include "gui/mrview/mode/list.h"
+#include "mrview/mode/list.h"
   }
 #undef MODE
 #undef MODE_OPTION
@@ -661,7 +661,7 @@ Window::Window()
   {
     using namespace Tool;
     size_t n = 1;
-#include "gui/mrview/tool/list.h"
+#include "mrview/tool/list.h"
   }
   for (int n = 0; n < tool_group->actions().size(); ++n)
     addAction(tool_group->actions()[n]);
@@ -1663,7 +1663,7 @@ void Window::process_commandline_option() {
     // see whether option is claimed by any tools:
     size_t tool_id = 0;
     std::string stub;
-#include "gui/mrview/tool/list.h"
+#include "mrview/tool/list.h"
 
     // process general options:
     if (opt.opt->is("mode")) {
diff --git a/src/gui/mrview/window.h b/cpp/gui/mrview/window.h
similarity index 98%
rename from src/gui/mrview/window.h
rename to cpp/gui/mrview/window.h
index 4a4ec26489..387c73f9d8 100644
--- a/src/gui/mrview/window.h
+++ b/cpp/gui/mrview/window.h
@@ -16,14 +16,14 @@
 
 #pragma once
 
-#include "gui/cursor.h"
-#include "gui/gui.h"
-#include "gui/mrview/colourbars.h"
-#include "gui/mrview/colourmap_button.h"
-#include "gui/mrview/gui_image.h"
-#include "gui/opengl/font.h"
+#include "cursor.h"
+#include "gui.h"
 #include "image.h"
 #include "memory.h"
+#include "mrview/colourbars.h"
+#include "mrview/colourmap_button.h"
+#include "mrview/gui_image.h"
+#include "opengl/font.h"
 
 namespace MR::GUI {
 namespace GL {
diff --git a/src/gui/opengl/font.cpp b/cpp/gui/opengl/font.cpp
similarity index 99%
rename from src/gui/opengl/font.cpp
rename to cpp/gui/opengl/font.cpp
index 86d01a9670..93791e75ca 100644
--- a/src/gui/opengl/font.cpp
+++ b/cpp/gui/opengl/font.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/opengl/font.h"
+#include "opengl/font.h"
 #include "debug.h"
 #include "math/math.h"
 
diff --git a/src/gui/opengl/font.h b/cpp/gui/opengl/font.h
similarity index 98%
rename from src/gui/opengl/font.h
rename to cpp/gui/opengl/font.h
index d8b9a356ef..b90ae5486b 100644
--- a/src/gui/opengl/font.h
+++ b/cpp/gui/opengl/font.h
@@ -16,7 +16,7 @@
 
 #pragma once
 
-#include "gui/opengl/shader.h"
+#include "opengl/shader.h"
 
 namespace MR::GUI::GL {
 
diff --git a/src/gui/opengl/gl_core_3_3.cpp b/cpp/gui/opengl/gl_core_3_3.cpp
similarity index 99%
rename from src/gui/opengl/gl_core_3_3.cpp
rename to cpp/gui/opengl/gl_core_3_3.cpp
index 884d7e702b..b01c5c2ca9 100644
--- a/src/gui/opengl/gl_core_3_3.cpp
+++ b/cpp/gui/opengl/gl_core_3_3.cpp
@@ -25,7 +25,7 @@
 #include <windows.h>
 #endif
 
-#include "gui/opengl/gl_core_3_3.h"
+#include "opengl/gl_core_3_3.h"
 #include <algorithm>
 #include <cstddef>
 #include <cstring>
diff --git a/src/gui/opengl/gl_core_3_3.h b/cpp/gui/opengl/gl_core_3_3.h
similarity index 100%
rename from src/gui/opengl/gl_core_3_3.h
rename to cpp/gui/opengl/gl_core_3_3.h
diff --git a/src/gui/opengl/gl.cpp b/cpp/gui/opengl/glutils.cpp
similarity index 99%
rename from src/gui/opengl/gl.cpp
rename to cpp/gui/opengl/glutils.cpp
index 6d8e68e019..ff27dfcacc 100644
--- a/src/gui/opengl/gl.cpp
+++ b/cpp/gui/opengl/glutils.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/opengl/gl.h"
+#include "opengl/glutils.h"
 #include "file/config.h"
 
 namespace MR::GUI::GL {
diff --git a/src/gui/opengl/gl.h b/cpp/gui/opengl/glutils.h
similarity index 99%
rename from src/gui/opengl/gl.h
rename to cpp/gui/opengl/glutils.h
index e579999fbc..bfcd69fcf6 100644
--- a/src/gui/opengl/gl.h
+++ b/cpp/gui/opengl/glutils.h
@@ -26,7 +26,7 @@
 #include <QOpenGLWidget>
 #include <QtGlobal>
 #include <QtWidgets>
-#include "gui/opengl/gl_core_3_3.h"
+#include "opengl/gl_core_3_3.h"
 // clang-format on
 
 #if QT_VERSION < QT_VERSION_CHECK(5, 5, 0)
diff --git a/src/gui/opengl/lighting.cpp b/cpp/gui/opengl/lighting.cpp
similarity index 98%
rename from src/gui/opengl/lighting.cpp
rename to cpp/gui/opengl/lighting.cpp
index 549ca22355..a95beb78bc 100644
--- a/src/gui/opengl/lighting.cpp
+++ b/cpp/gui/opengl/lighting.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/opengl/lighting.h"
+#include "opengl/lighting.h"
 #include "file/config.h"
 
 namespace MR::GUI::GL {
diff --git a/src/gui/opengl/lighting.h b/cpp/gui/opengl/lighting.h
similarity index 97%
rename from src/gui/opengl/lighting.h
rename to cpp/gui/opengl/lighting.h
index 8e5f89e85d..748ef652d7 100644
--- a/src/gui/opengl/lighting.h
+++ b/cpp/gui/opengl/lighting.h
@@ -16,7 +16,7 @@
 
 #pragma once
 
-#include "gui/opengl/gl.h"
+#include "opengl/glutils.h"
 
 namespace MR::GUI::GL {
 
diff --git a/src/gui/opengl/shader.cpp b/cpp/gui/opengl/shader.cpp
similarity index 97%
rename from src/gui/opengl/shader.cpp
rename to cpp/gui/opengl/shader.cpp
index ed7c3186fc..51a4e6b1e8 100644
--- a/src/gui/opengl/shader.cpp
+++ b/cpp/gui/opengl/shader.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/opengl/shader.h"
+#include "opengl/shader.h"
 
 namespace MR::GUI::GL::Shader {
 
diff --git a/src/gui/opengl/shader.h b/cpp/gui/opengl/shader.h
similarity index 99%
rename from src/gui/opengl/shader.h
rename to cpp/gui/opengl/shader.h
index 3497862730..9bc8ec6f1a 100644
--- a/src/gui/opengl/shader.h
+++ b/cpp/gui/opengl/shader.h
@@ -17,7 +17,7 @@
 #pragma once
 
 #include "app.h"
-#include "gui/opengl/gl.h"
+#include "opengl/glutils.h"
 
 namespace MR::GUI::GL::Shader {
 
diff --git a/src/gui/opengl/transformation.h b/cpp/gui/opengl/transformation.h
similarity index 99%
rename from src/gui/opengl/transformation.h
rename to cpp/gui/opengl/transformation.h
index 0d8ae8e946..517a5e8fe4 100644
--- a/src/gui/opengl/transformation.h
+++ b/cpp/gui/opengl/transformation.h
@@ -18,8 +18,8 @@
 
 #include <iostream>
 
-#include "gui/opengl/gl.h"
 #include "math/least_squares.h"
+#include "opengl/glutils.h"
 
 namespace MR::GUI::GL {
 
diff --git a/src/gui/projection.cpp b/cpp/gui/projection.cpp
similarity index 98%
rename from src/gui/projection.cpp
rename to cpp/gui/projection.cpp
index a83d314f54..8f7fa16c2f 100644
--- a/src/gui/projection.cpp
+++ b/cpp/gui/projection.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/projection.h"
+#include "projection.h"
 
 namespace MR::GUI {
 
diff --git a/src/gui/projection.h b/cpp/gui/projection.h
similarity index 98%
rename from src/gui/projection.h
rename to cpp/gui/projection.h
index c0ca984f9e..c6f66d5fa0 100644
--- a/src/gui/projection.h
+++ b/cpp/gui/projection.h
@@ -16,11 +16,11 @@
 
 #pragma once
 
-#include "gui/crosshair.h"
-#include "gui/gui.h"
-#include "gui/opengl/font.h"
-#include "gui/opengl/gl.h"
-#include "gui/opengl/transformation.h"
+#include "crosshair.h"
+#include "gui.h"
+#include "opengl/font.h"
+#include "opengl/glutils.h"
+#include "opengl/transformation.h"
 
 namespace MR::GUI {
 
diff --git a/src/gui/shapes/cube.cpp b/cpp/gui/shapes/cube.cpp
similarity index 99%
rename from src/gui/shapes/cube.cpp
rename to cpp/gui/shapes/cube.cpp
index 3d248d10ff..0c0ce96362 100644
--- a/src/gui/shapes/cube.cpp
+++ b/cpp/gui/shapes/cube.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/shapes/cube.h"
+#include "shapes/cube.h"
 
 namespace {
 
diff --git a/src/gui/shapes/cube.h b/cpp/gui/shapes/cube.h
similarity index 80%
rename from src/gui/shapes/cube.h
rename to cpp/gui/shapes/cube.h
index 94fe81cbef..31acf17ea0 100644
--- a/src/gui/shapes/cube.h
+++ b/cpp/gui/shapes/cube.h
@@ -16,8 +16,12 @@
 
 #pragma once
 
-#include "gui/opengl/gl.h"
-#include "gui/opengl/gl_core_3_3.h"
+// glutils.h must be included before gl_core_3_3.h since it include Qt OpenGL headers
+// which must be included before gl_core_3_3.h
+// clang-format off
+#include "opengl/glutils.h"
+#include "opengl/gl_core_3_3.h"
+// clang-format on
 
 namespace MR::GUI::Shapes {
 
diff --git a/src/gui/shapes/cylinder.cpp b/cpp/gui/shapes/cylinder.cpp
similarity index 99%
rename from src/gui/shapes/cylinder.cpp
rename to cpp/gui/shapes/cylinder.cpp
index bac8336892..4f018153ef 100644
--- a/src/gui/shapes/cylinder.cpp
+++ b/cpp/gui/shapes/cylinder.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/shapes/cylinder.h"
+#include "shapes/cylinder.h"
 
 #include "types.h"
 
diff --git a/src/gui/shapes/cylinder.h b/cpp/gui/shapes/cylinder.h
similarity index 80%
rename from src/gui/shapes/cylinder.h
rename to cpp/gui/shapes/cylinder.h
index 16d44687d5..064f4d9fda 100644
--- a/src/gui/shapes/cylinder.h
+++ b/cpp/gui/shapes/cylinder.h
@@ -16,8 +16,12 @@
 
 #pragma once
 
-#include "gui/opengl/gl.h"
-#include "gui/opengl/gl_core_3_3.h"
+// glutils.h must be included before gl_core_3_3.h since it include Qt OpenGL headers
+// which must be included before gl_core_3_3.h
+// clang-format off
+#include "opengl/glutils.h"
+#include "opengl/gl_core_3_3.h"
+// clang-format on
 
 namespace MR::GUI::Shapes {
 
diff --git a/src/gui/shapes/halfsphere.cpp b/cpp/gui/shapes/halfsphere.cpp
similarity index 99%
rename from src/gui/shapes/halfsphere.cpp
rename to cpp/gui/shapes/halfsphere.cpp
index ac797335b9..d1d00219d3 100644
--- a/src/gui/shapes/halfsphere.cpp
+++ b/cpp/gui/shapes/halfsphere.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/shapes/halfsphere.h"
+#include "shapes/halfsphere.h"
 
 #include <map>
 
diff --git a/src/gui/shapes/halfsphere.h b/cpp/gui/shapes/halfsphere.h
similarity index 88%
rename from src/gui/shapes/halfsphere.h
rename to cpp/gui/shapes/halfsphere.h
index 11be874b12..2781409a18 100644
--- a/src/gui/shapes/halfsphere.h
+++ b/cpp/gui/shapes/halfsphere.h
@@ -18,8 +18,12 @@
 
 #include "types.h"
 
-#include "gui/opengl/gl.h"
-#include "gui/opengl/gl_core_3_3.h"
+// glutils.h must be included before gl_core_3_3.h since it include Qt OpenGL headers
+// which must be included before gl_core_3_3.h
+// clang-format off
+#include "opengl/glutils.h"
+#include "opengl/gl_core_3_3.h"
+// clang-format on
 
 namespace MR::GUI::Shapes {
 
diff --git a/src/gui/shapes/sphere.cpp b/cpp/gui/shapes/sphere.cpp
similarity index 99%
rename from src/gui/shapes/sphere.cpp
rename to cpp/gui/shapes/sphere.cpp
index 721e09d429..a6a188f75c 100644
--- a/src/gui/shapes/sphere.cpp
+++ b/cpp/gui/shapes/sphere.cpp
@@ -14,7 +14,7 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/shapes/sphere.h"
+#include "shapes/sphere.h"
 
 #include <map>
 
diff --git a/src/gui/shapes/sphere.h b/cpp/gui/shapes/sphere.h
similarity index 88%
rename from src/gui/shapes/sphere.h
rename to cpp/gui/shapes/sphere.h
index 3e4a70d991..ddbca63f9b 100644
--- a/src/gui/shapes/sphere.h
+++ b/cpp/gui/shapes/sphere.h
@@ -18,8 +18,12 @@
 
 #include "types.h"
 
-#include "gui/opengl/gl.h"
-#include "gui/opengl/gl_core_3_3.h"
+// glutils.h must be included before gl_core_3_3.h since it include Qt OpenGL headers
+// which must be included before gl_core_3_3.h
+// clang-format off
+#include "opengl/glutils.h"
+#include "opengl/gl_core_3_3.h"
+// clang-format on
 
 namespace MR::GUI::Shapes {
 
diff --git a/src/gui/shview/icons.h b/cpp/gui/shview/icons.h
similarity index 100%
rename from src/gui/shview/icons.h
rename to cpp/gui/shview/icons.h
diff --git a/src/gui/shview/render_window.cpp b/cpp/gui/shview/render_window.cpp
similarity index 98%
rename from src/gui/shview/render_window.cpp
rename to cpp/gui/shview/render_window.cpp
index d956b4b9e9..71acb71afc 100644
--- a/src/gui/shview/render_window.cpp
+++ b/cpp/gui/shview/render_window.cpp
@@ -14,14 +14,14 @@
  * For more details, see http://www.mrtrix.org/.
  */
 
-#include "gui/shview/render_window.h"
+#include "shview/render_window.h"
 #include "app.h"
+#include "dialog/dialog.h"
+#include "dialog/file.h"
+#include "dwi/render_frame.h"
 #include "file/matrix.h"
 #include "file/path.h"
-#include "gui/dialog/dialog.h"
-#include "gui/dialog/file.h"
-#include "gui/dwi/render_frame.h"
-#include "gui/lighting_dock.h"
+#include "lighting_dock.h"
 #include "math/SH.h"
 #include "math/math.h"
 
diff --git a/src/gui/shview/render_window.h b/cpp/gui/shview/render_window.h
similarity index 97%
rename from src/gui/shview/render_window.h
rename to cpp/gui/shview/render_window.h
index cbada0332f..02234c7eef 100644
--- a/src/gui/shview/render_window.h
+++ b/cpp/gui/shview/render_window.h
@@ -16,8 +16,8 @@
 
 #pragma once
 
-#include "gui/dwi/render_frame.h"
-#include "gui/opengl/gl.h"
+#include "dwi/render_frame.h"
+#include "opengl/glutils.h"
 
 namespace MR::GUI {
 class LightingDock;
diff --git a/docs/generate_user_docs.sh b/docs/generate_user_docs.sh
index 3b76db5b36..2d71bd297f 100755
--- a/docs/generate_user_docs.sh
+++ b/docs/generate_user_docs.sh
@@ -79,7 +79,7 @@ echo "
 " > $table_file
 
 cmdlist=""
-for n in `find "${mrtrix_root}"/cmd/ -name "*.cpp"`; do
+for n in `find "${mrtrix_root}"/cpp/cmd/ -name "*.cpp"`; do
   cmdlist=$cmdlist$'\n'`basename $n`
 done
 for n in `ls "${mrtrix_root}"/python/mrtrix3/commands/ --ignore=__init__.py* --ignore=CMakeLists.txt`; do
diff --git a/packaging/mingw/PKGBUILD b/packaging/mingw/PKGBUILD
index 4ab03194cd..0753f7cbc5 100644
--- a/packaging/mingw/PKGBUILD
+++ b/packaging/mingw/PKGBUILD
@@ -39,7 +39,7 @@ pkgver() {
 
 build() {
   cd "${_realname}"
-  cmake -B build -G Ninja -DMRTRIX_BUILD_NON_CORE_STATIC=ON
+  cmake -B build -G Ninja
   cmake --build build
   cmake --install build --prefix=./install
 }
diff --git a/packaging/package-linux-tarball.sh b/packaging/package-linux-tarball.sh
index 29d980185a..18bbc848fa 100755
--- a/packaging/package-linux-tarball.sh
+++ b/packaging/package-linux-tarball.sh
@@ -66,9 +66,8 @@ cmake -B $build_dir -S $source_dir \
     -DCMAKE_BUILD_TYPE=Release \
     -DCMAKE_INSTALL_PREFIX=$install_dir \
     -DCMAKE_EXE_LINKER_FLAGS="-Wl,--as-needed" \
-    -DCMAKE_INTERPROCEDURAL_OPTIMIZATION=ON \
-    -DMRTRIX_BUILD_NON_CORE_STATIC=ON
-    
+    -DCMAKE_INTERPROCEDURAL_OPTIMIZATION=ON
+        
 cmake --build $build_dir
 cmake --install $build_dir
 
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
deleted file mode 100644
index 55c51f5ecd..0000000000
--- a/src/CMakeLists.txt
+++ /dev/null
@@ -1,124 +0,0 @@
-file(GLOB_RECURSE HEADLESS_SOURCES *.h *.cpp)
-list(FILTER HEADLESS_SOURCES EXCLUDE REGEX "gui/.*")
-
-file(GLOB_RECURSE GUI_SOURCES gui/*.h gui/*.cpp)
-
-if(MRTRIX_BUILD_GUI)
-    if(MRTRIX_USE_QT5)
-        find_package(Qt5 COMPONENTS Core Gui Widgets OpenGL Network REQUIRED)
-        qt5_add_resources(RCC_SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/../icons/icons.qrc)
-    else()
-        find_package(Qt6 COMPONENTS Core Gui Widgets OpenGL Network OpenGLWidgets REQUIRED)
-        qt6_add_resources(RCC_SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/../icons/icons.qrc)
-    endif()
-    # Explicitly log Qt's location since it's not done automatically by the FindQt module
-    message(STATUS "Qt${QT_MAJOR_VERSION}_DIR is set to: ${Qt${QT_MAJOR_VERSION}_DIR}")
-
-    find_package(OpenGL REQUIRED)
-    find_package(Threads REQUIRED)
-endif()
-
-find_package(Git QUIET)
-
-# Create version target and library
-set(EXEC_VERSION_CPP ${CMAKE_CURRENT_BINARY_DIR}/exec_version.cpp)
-
-add_custom_target(exec-version-target ALL
-    COMMAND ${CMAKE_COMMAND}
-        -D GIT_EXECUTABLE=${GIT_EXECUTABLE}
-        -D MRTRIX_BASE_VERSION=${MRTRIX_BASE_VERSION}
-        -D DST=${EXEC_VERSION_CPP}
-        -D SRC=${CMAKE_CURRENT_SOURCE_DIR}/exec_version.cpp.in
-        -P ${CMAKE_CURRENT_SOURCE_DIR}/../cmake/FindVersion.cmake
-    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-    COMMENT "Generating exec_version.cpp for executables"
-    BYPRODUCTS ${EXEC_VERSION_CPP}
-    VERBATIM
-)
-
-add_library(mrtrix-exec-version-lib STATIC ${EXEC_VERSION_CPP})
-add_library(mrtrix::exec-version-lib ALIAS mrtrix-exec-version-lib)
-add_dependencies(mrtrix-exec-version-lib exec-version-target)
-
-if(MRTRIX_BUILD_NON_CORE_STATIC)
-    set(MRTRIX_LIBRARY_TYPE STATIC)
-else()
-    set(MRTRIX_LIBRARY_TYPE SHARED)
-endif()
-
-add_library(mrtrix-headless ${MRTRIX_LIBRARY_TYPE} ${HEADLESS_SOURCES})
-add_library(mrtrix::headless ALIAS mrtrix-headless)
-
-
-target_include_directories(mrtrix-exec-version-lib PUBLIC
-    ${CMAKE_CURRENT_SOURCE_DIR}
-)
-
-target_include_directories(mrtrix-headless PUBLIC
-    ${CMAKE_CURRENT_SOURCE_DIR}
-)
-
-if(MRTRIX_USE_PCH)
-    target_precompile_headers(mrtrix-headless PRIVATE
-        [["exception.h"]]
-        <fstream>
-        <complex>
-    )
-endif()
-
-target_link_libraries(mrtrix-headless PUBLIC
-    mrtrix::core
-)
-
-if(MRTRIX_BUILD_GUI)
-    add_library(mrtrix-gui ${MRTRIX_LIBRARY_TYPE} ${GUI_SOURCES} ${RCC_SOURCES})
-    add_library(mrtrix::gui ALIAS mrtrix-gui)
-
-    set_target_properties(mrtrix-gui PROPERTIES
-        AUTOMOC ON
-        AUTOUIC ON
-        LINK_DEPENDS_NO_SHARED ON
-    )
-
-    if(MRTRIX_USE_PCH)
-        target_precompile_headers(mrtrix-gui PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/gui/gui_pch.h)
-    endif()
-
-    target_link_libraries(mrtrix-gui PUBLIC
-        mrtrix::headless
-        Qt${QT_MAJOR_VERSION}::Core
-        Qt${QT_MAJOR_VERSION}::Gui
-        Qt${QT_MAJOR_VERSION}::Widgets
-        Qt${QT_MAJOR_VERSION}::OpenGL
-        Qt${QT_MAJOR_VERSION}::Network
-        Threads::Threads
-        ${OPENGL_LIBRARIES}
-    )
-    if(NOT MRTRIX_USE_QT5)
-        target_link_libraries(mrtrix-gui PUBLIC Qt6::OpenGLWidgets)
-    endif()
-endif()
-
-# On Windows, the libraries need to be in the same directory as the executables
-if(WIN32)
-    set_target_properties(mrtrix-headless PROPERTIES
-        RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/bin
-    )
-    if(MRTRIX_BUILD_GUI)
-        set_target_properties(mrtrix-gui PROPERTIES
-            RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/bin
-        )
-    endif()
-endif()
-
-install(TARGETS mrtrix-headless
-    RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
-    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-)
-
-if(MRTRIX_BUILD_GUI)
-    install(TARGETS mrtrix-gui
-        RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
-        LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-    )
-endif()
diff --git a/src/exec_version.cpp.in b/src/exec_version.cpp.in
deleted file mode 100644
index a424de082d..0000000000
--- a/src/exec_version.cpp.in
+++ /dev/null
@@ -1,8 +0,0 @@
-#include "exec_version.h"
-
-namespace MR {
-  namespace App {
-    extern const char* executable_uses_mrtrix_version;
-    void set_executable_uses_mrtrix_version () { executable_uses_mrtrix_version = "@MRTRIX_VERSION@"; }
-  }
-}
\ No newline at end of file
diff --git a/testing/tools/CMakeLists.txt b/testing/tools/CMakeLists.txt
index 946b5f7370..7bc7cdfd10 100644
--- a/testing/tools/CMakeLists.txt
+++ b/testing/tools/CMakeLists.txt
@@ -31,8 +31,8 @@ function(add_cpp_tool TOOL_SRC)
     get_filename_component(TOOL_NAME ${TOOL_SRC} NAME_WE)
     add_executable(${TOOL_NAME} ${TOOL_SRC})
     target_link_libraries(${TOOL_NAME} PRIVATE
-        mrtrix::headless
-        mrtrix::exec-version-lib
+        mrtrix::core
+        mrtrix::executable-version
         mrtrix::tests-lib
     )
     set_target_properties(${TOOL_NAME} PROPERTIES LINK_DEPENDS_NO_SHARED true)
diff --git a/testing/unit_tests/CMakeLists.txt b/testing/unit_tests/CMakeLists.txt
index c161343f54..34d6b9d159 100644
--- a/testing/unit_tests/CMakeLists.txt
+++ b/testing/unit_tests/CMakeLists.txt
@@ -49,8 +49,8 @@ function(add_cpp_unit_test FILE_SRC)
     get_filename_component(NAME ${FILE_SRC} NAME_WE)
     add_executable(${NAME} ${FILE_SRC})
     target_link_libraries(${NAME} PRIVATE
-        mrtrix::headless
-        mrtrix::exec-version-lib
+        mrtrix::core
+        mrtrix::executable-version
         mrtrix::tests-lib
     )
     set_target_properties(${NAME} PROPERTIES
diff --git a/update_copyright b/update_copyright
index 9b34e52502..ff230e1e3e 100755
--- a/update_copyright
+++ b/update_copyright
@@ -43,20 +43,18 @@ SearchPath = namedtuple('SearchPath', 'dirname recursive need_shebang comment ex
 ProcessFile = namedtuple('ProcessFile', 'path keep_shebang comment')
 
 MRTRIX_ROOT = os.path.abspath(os.path.dirname(__file__))
-APP_CPP_PATH = os.path.join(MRTRIX_ROOT, 'core', 'app.cpp')
+APP_CPP_PATH = os.path.join(MRTRIX_ROOT, 'cpp', 'core', 'app.cpp')
 APP_CPP_STRING = 'std::string COPYRIGHT ='
 APP_PY_PATH = os.path.join(MRTRIX_ROOT, 'python', 'mrtrix3', 'app.py')
 APP_PY_STRING = '_DEFAULT_COPYRIGHT ='
 
 SEARCH_PATHS = [
     SearchPath('.', False, True, '#', [], ['mrtrix-mrview.desktop']),
-    SearchPath('cmd', False, False, '*', ['.cpp'], []),
-    SearchPath('core', True, False, '*', ['.cpp', '.h'], [os.path.join('file', 'json.h'), os.path.join('file', 'nifti1.h'), 'version.h']),
+    SearchPath(os.path.join('cpp'), True, False, '*', ['.cpp', '.h'], []),
     SearchPath('docs', False, True, '#', [], []),
     SearchPath('matlab', True, False, '%', ['.m'], []),
     SearchPath('python', True, False, '#', ['.py'], [os.path.join('mrtrix3', 'version.py.in'), os.path.join('mrtrix3', 'commands', '__init__.py.in')]),
     SearchPath(os.path.join('share', 'mrtrix3'), True, False, '#', ['.txt'], []),
-    SearchPath('src', True, False, '*', ['.cpp', '.h'], []),
     SearchPath(os.path.join('testing', 'tools'), False, False, '*', ['.cpp'], []),
     SearchPath(os.path.join('testing', 'unit_tests'), False, False, '*', ['.cpp'], []),
     SearchPath(os.path.join('testing', 'lib'), False, False, '*', ['.h'], []),