MRtrix3 · daljit46 · Nov 13, 2024 · Sep 24, 2024 · Sep 26, 2024 · Sep 26, 2024
diff --git 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
@@ -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
@@ -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
@@ -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
diff --git a/core/version.h b/core/version.h
diff --git a/cpp/CMakeLists.txt 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 → cpp/cmd/5tt2gmwmi.cpp b/cmd/5tt2gmwmi.cpp → cpp/cmd/5tt2gmwmi.cpp
diff --git a/cmd/5tt2vis.cpp → cpp/cmd/5tt2vis.cpp b/cmd/5tt2vis.cpp → cpp/cmd/5tt2vis.cpp
diff --git a/cmd/5ttcheck.cpp → cpp/cmd/5ttcheck.cpp b/cmd/5ttcheck.cpp → cpp/cmd/5ttcheck.cpp
diff --git a/cmd/5ttedit.cpp → cpp/cmd/5ttedit.cpp b/cmd/5ttedit.cpp → cpp/cmd/5ttedit.cpp
diff --git a/cmd/CMakeLists.txt → cpp/cmd/CMakeLists.txt b/cmd/CMakeLists.txt → 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 → cpp/cmd/afdconnectivity.cpp b/cmd/afdconnectivity.cpp → 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 → cpp/cmd/amp2response.cpp b/cmd/amp2response.cpp → cpp/cmd/amp2response.cpp
diff --git a/cmd/amp2sh.cpp → cpp/cmd/amp2sh.cpp b/cmd/amp2sh.cpp → cpp/cmd/amp2sh.cpp
diff --git a/cmd/connectome2tck.cpp → cpp/cmd/connectome2tck.cpp b/cmd/connectome2tck.cpp → cpp/cmd/connectome2tck.cpp
diff --git a/cmd/connectomeedit.cpp → cpp/cmd/connectomeedit.cpp b/cmd/connectomeedit.cpp → cpp/cmd/connectomeedit.cpp
diff --git a/cmd/connectomestats.cpp → cpp/cmd/connectomestats.cpp b/cmd/connectomestats.cpp → cpp/cmd/connectomestats.cpp
diff --git a/cmd/dcmedit.cpp → cpp/cmd/dcmedit.cpp b/cmd/dcmedit.cpp → cpp/cmd/dcmedit.cpp
diff --git a/cmd/dcminfo.cpp → cpp/cmd/dcminfo.cpp b/cmd/dcminfo.cpp → cpp/cmd/dcminfo.cpp
diff --git a/cmd/dirflip.cpp → cpp/cmd/dirflip.cpp b/cmd/dirflip.cpp → cpp/cmd/dirflip.cpp
diff --git a/cmd/dirgen.cpp → cpp/cmd/dirgen.cpp b/cmd/dirgen.cpp → cpp/cmd/dirgen.cpp
diff --git a/cmd/dirmerge.cpp → cpp/cmd/dirmerge.cpp b/cmd/dirmerge.cpp → cpp/cmd/dirmerge.cpp
diff --git a/cmd/dirorder.cpp → cpp/cmd/dirorder.cpp b/cmd/dirorder.cpp → cpp/cmd/dirorder.cpp
diff --git a/cmd/dirrotate.cpp → cpp/cmd/dirrotate.cpp b/cmd/dirrotate.cpp → cpp/cmd/dirrotate.cpp
diff --git a/cmd/dirsplit.cpp → cpp/cmd/dirsplit.cpp b/cmd/dirsplit.cpp → cpp/cmd/dirsplit.cpp
diff --git a/cmd/dirstat.cpp → cpp/cmd/dirstat.cpp b/cmd/dirstat.cpp → cpp/cmd/dirstat.cpp
diff --git a/cmd/dwi2adc.cpp → cpp/cmd/dwi2adc.cpp b/cmd/dwi2adc.cpp → cpp/cmd/dwi2adc.cpp
diff --git a/cmd/dwi2fod.cpp → cpp/cmd/dwi2fod.cpp b/cmd/dwi2fod.cpp → cpp/cmd/dwi2fod.cpp
diff --git a/cmd/dwi2tensor.cpp → cpp/cmd/dwi2tensor.cpp b/cmd/dwi2tensor.cpp → cpp/cmd/dwi2tensor.cpp
diff --git a/cmd/dwidenoise.cpp → cpp/cmd/dwidenoise.cpp b/cmd/dwidenoise.cpp → cpp/cmd/dwidenoise.cpp
diff --git a/cmd/dwiextract.cpp → cpp/cmd/dwiextract.cpp b/cmd/dwiextract.cpp → cpp/cmd/dwiextract.cpp
diff --git a/cmd/fixel2peaks.cpp → cpp/cmd/fixel2peaks.cpp b/cmd/fixel2peaks.cpp → cpp/cmd/fixel2peaks.cpp
diff --git a/cmd/fixel2sh.cpp → cpp/cmd/fixel2sh.cpp b/cmd/fixel2sh.cpp → cpp/cmd/fixel2sh.cpp
diff --git a/cmd/fixel2tsf.cpp → cpp/cmd/fixel2tsf.cpp b/cmd/fixel2tsf.cpp → cpp/cmd/fixel2tsf.cpp
diff --git a/cmd/fixel2voxel.cpp → cpp/cmd/fixel2voxel.cpp b/cmd/fixel2voxel.cpp → cpp/cmd/fixel2voxel.cpp
diff --git a/cmd/fixelcfestats.cpp → cpp/cmd/fixelcfestats.cpp b/cmd/fixelcfestats.cpp → cpp/cmd/fixelcfestats.cpp
diff --git a/cmd/fixelconnectivity.cpp → cpp/cmd/fixelconnectivity.cpp b/cmd/fixelconnectivity.cpp → cpp/cmd/fixelconnectivity.cpp
diff --git a/cmd/fixelconvert.cpp → cpp/cmd/fixelconvert.cpp b/cmd/fixelconvert.cpp → cpp/cmd/fixelconvert.cpp
diff --git a/cmd/fixelcorrespondence.cpp → cpp/cmd/fixelcorrespondence.cpp b/cmd/fixelcorrespondence.cpp → cpp/cmd/fixelcorrespondence.cpp
diff --git a/cmd/fixelcrop.cpp → cpp/cmd/fixelcrop.cpp b/cmd/fixelcrop.cpp → cpp/cmd/fixelcrop.cpp
diff --git a/cmd/fixelfilter.cpp → cpp/cmd/fixelfilter.cpp b/cmd/fixelfilter.cpp → cpp/cmd/fixelfilter.cpp
diff --git a/cmd/fixelreorient.cpp → cpp/cmd/fixelreorient.cpp b/cmd/fixelreorient.cpp → cpp/cmd/fixelreorient.cpp
diff --git a/cmd/fod2dec.cpp → cpp/cmd/fod2dec.cpp b/cmd/fod2dec.cpp → cpp/cmd/fod2dec.cpp
diff --git a/cmd/fod2fixel.cpp → cpp/cmd/fod2fixel.cpp b/cmd/fod2fixel.cpp → cpp/cmd/fod2fixel.cpp
diff --git a/cmd/label2colour.cpp → cpp/cmd/label2colour.cpp b/cmd/label2colour.cpp → cpp/cmd/label2colour.cpp
diff --git a/cmd/label2mesh.cpp → cpp/cmd/label2mesh.cpp b/cmd/label2mesh.cpp → cpp/cmd/label2mesh.cpp
diff --git a/cmd/labelconvert.cpp → cpp/cmd/labelconvert.cpp b/cmd/labelconvert.cpp → 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 → cpp/cmd/labelstats.cpp b/cmd/labelstats.cpp → cpp/cmd/labelstats.cpp
diff --git a/cmd/maskdump.cpp → cpp/cmd/maskdump.cpp b/cmd/maskdump.cpp → cpp/cmd/maskdump.cpp
diff --git a/cmd/maskfilter.cpp → cpp/cmd/maskfilter.cpp b/cmd/maskfilter.cpp → cpp/cmd/maskfilter.cpp
diff --git a/cmd/mesh2voxel.cpp → cpp/cmd/mesh2voxel.cpp b/cmd/mesh2voxel.cpp → cpp/cmd/mesh2voxel.cpp
diff --git a/cmd/meshconvert.cpp → cpp/cmd/meshconvert.cpp b/cmd/meshconvert.cpp → cpp/cmd/meshconvert.cpp
diff --git a/cmd/meshfilter.cpp → cpp/cmd/meshfilter.cpp b/cmd/meshfilter.cpp → cpp/cmd/meshfilter.cpp
diff --git a/cmd/mraverageheader.cpp → cpp/cmd/mraverageheader.cpp b/cmd/mraverageheader.cpp → cpp/cmd/mraverageheader.cpp
diff --git a/cmd/mrcalc.cpp → cpp/cmd/mrcalc.cpp b/cmd/mrcalc.cpp → cpp/cmd/mrcalc.cpp
diff --git a/cmd/mrcat.cpp → cpp/cmd/mrcat.cpp b/cmd/mrcat.cpp → cpp/cmd/mrcat.cpp
diff --git a/cmd/mrcentroid.cpp → cpp/cmd/mrcentroid.cpp b/cmd/mrcentroid.cpp → cpp/cmd/mrcentroid.cpp
diff --git a/cmd/mrcheckerboardmask.cpp → cpp/cmd/mrcheckerboardmask.cpp b/cmd/mrcheckerboardmask.cpp → cpp/cmd/mrcheckerboardmask.cpp
diff --git a/cmd/mrclusterstats.cpp → cpp/cmd/mrclusterstats.cpp b/cmd/mrclusterstats.cpp → cpp/cmd/mrclusterstats.cpp
diff --git a/cmd/mrcolour.cpp → cpp/cmd/mrcolour.cpp b/cmd/mrcolour.cpp → cpp/cmd/mrcolour.cpp
diff --git a/cmd/mrconvert.cpp → cpp/cmd/mrconvert.cpp b/cmd/mrconvert.cpp → cpp/cmd/mrconvert.cpp
diff --git a/cmd/mrdegibbs.cpp → cpp/cmd/mrdegibbs.cpp b/cmd/mrdegibbs.cpp → cpp/cmd/mrdegibbs.cpp
diff --git a/cmd/mrdump.cpp → cpp/cmd/mrdump.cpp b/cmd/mrdump.cpp → cpp/cmd/mrdump.cpp
diff --git a/cmd/mredit.cpp → cpp/cmd/mredit.cpp b/cmd/mredit.cpp → cpp/cmd/mredit.cpp
diff --git a/cmd/mrfilter.cpp → cpp/cmd/mrfilter.cpp b/cmd/mrfilter.cpp → cpp/cmd/mrfilter.cpp
diff --git a/cmd/mrgrid.cpp → cpp/cmd/mrgrid.cpp b/cmd/mrgrid.cpp → cpp/cmd/mrgrid.cpp
diff --git a/cmd/mrhistmatch.cpp → cpp/cmd/mrhistmatch.cpp b/cmd/mrhistmatch.cpp → cpp/cmd/mrhistmatch.cpp
diff --git a/cmd/mrhistogram.cpp → cpp/cmd/mrhistogram.cpp b/cmd/mrhistogram.cpp → cpp/cmd/mrhistogram.cpp
diff --git a/cmd/mrinfo.cpp → cpp/cmd/mrinfo.cpp b/cmd/mrinfo.cpp → cpp/cmd/mrinfo.cpp
diff --git a/cmd/mrmath.cpp → cpp/cmd/mrmath.cpp b/cmd/mrmath.cpp → cpp/cmd/mrmath.cpp
diff --git a/cmd/mrmetric.cpp → cpp/cmd/mrmetric.cpp b/cmd/mrmetric.cpp → cpp/cmd/mrmetric.cpp
diff --git a/cmd/mrregister.cpp → cpp/cmd/mrregister.cpp b/cmd/mrregister.cpp → cpp/cmd/mrregister.cpp
diff --git a/cmd/mrstats.cpp → cpp/cmd/mrstats.cpp b/cmd/mrstats.cpp → cpp/cmd/mrstats.cpp
diff --git a/cmd/mrthreshold.cpp → cpp/cmd/mrthreshold.cpp b/cmd/mrthreshold.cpp → cpp/cmd/mrthreshold.cpp
diff --git a/cmd/mrtransform.cpp → cpp/cmd/mrtransform.cpp b/cmd/mrtransform.cpp → cpp/cmd/mrtransform.cpp
diff --git a/cmd/mrview.cpp → cpp/cmd/mrview.cpp b/cmd/mrview.cpp → 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 → cpp/cmd/mtnormalise.cpp b/cmd/mtnormalise.cpp → cpp/cmd/mtnormalise.cpp
diff --git a/cmd/peaks2amp.cpp → cpp/cmd/peaks2amp.cpp b/cmd/peaks2amp.cpp → cpp/cmd/peaks2amp.cpp
diff --git a/cmd/peaks2fixel.cpp → cpp/cmd/peaks2fixel.cpp b/cmd/peaks2fixel.cpp → cpp/cmd/peaks2fixel.cpp
diff --git a/cmd/sh2amp.cpp → cpp/cmd/sh2amp.cpp b/cmd/sh2amp.cpp → cpp/cmd/sh2amp.cpp
diff --git a/cmd/sh2peaks.cpp → cpp/cmd/sh2peaks.cpp b/cmd/sh2peaks.cpp → cpp/cmd/sh2peaks.cpp
diff --git a/cmd/sh2power.cpp → cpp/cmd/sh2power.cpp b/cmd/sh2power.cpp → cpp/cmd/sh2power.cpp
diff --git a/cmd/sh2response.cpp → cpp/cmd/sh2response.cpp b/cmd/sh2response.cpp → cpp/cmd/sh2response.cpp
diff --git a/cmd/shbasis.cpp → cpp/cmd/shbasis.cpp b/cmd/shbasis.cpp → cpp/cmd/shbasis.cpp
diff --git a/cmd/shconv.cpp → cpp/cmd/shconv.cpp b/cmd/shconv.cpp → cpp/cmd/shconv.cpp
diff --git a/cmd/shview.cpp → cpp/cmd/shview.cpp b/cmd/shview.cpp → 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 → cpp/cmd/tck2connectome.cpp b/cmd/tck2connectome.cpp → cpp/cmd/tck2connectome.cpp
diff --git a/cmd/tck2fixel.cpp → cpp/cmd/tck2fixel.cpp b/cmd/tck2fixel.cpp → cpp/cmd/tck2fixel.cpp
diff --git a/cmd/tckconvert.cpp → cpp/cmd/tckconvert.cpp b/cmd/tckconvert.cpp → cpp/cmd/tckconvert.cpp
diff --git a/cmd/tckdfc.cpp → cpp/cmd/tckdfc.cpp b/cmd/tckdfc.cpp → cpp/cmd/tckdfc.cpp
diff --git a/cmd/tckedit.cpp → cpp/cmd/tckedit.cpp b/cmd/tckedit.cpp → cpp/cmd/tckedit.cpp
diff --git a/cmd/tckgen.cpp → cpp/cmd/tckgen.cpp b/cmd/tckgen.cpp → cpp/cmd/tckgen.cpp
diff --git a/cmd/tckglobal.cpp → cpp/cmd/tckglobal.cpp b/cmd/tckglobal.cpp → 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 → cpp/cmd/tckinfo.cpp b/cmd/tckinfo.cpp → cpp/cmd/tckinfo.cpp
diff --git a/cmd/tckmap.cpp → cpp/cmd/tckmap.cpp b/cmd/tckmap.cpp → cpp/cmd/tckmap.cpp
diff --git a/cmd/tckresample.cpp → cpp/cmd/tckresample.cpp b/cmd/tckresample.cpp → cpp/cmd/tckresample.cpp
diff --git a/cmd/tcksample.cpp → cpp/cmd/tcksample.cpp b/cmd/tcksample.cpp → cpp/cmd/tcksample.cpp
diff --git a/cmd/tcksift.cpp → cpp/cmd/tcksift.cpp b/cmd/tcksift.cpp → cpp/cmd/tcksift.cpp
diff --git a/cmd/tcksift2.cpp → cpp/cmd/tcksift2.cpp b/cmd/tcksift2.cpp → cpp/cmd/tcksift2.cpp
diff --git a/cmd/tckstats.cpp → cpp/cmd/tckstats.cpp b/cmd/tckstats.cpp → cpp/cmd/tckstats.cpp
diff --git a/cmd/tcktransform.cpp → cpp/cmd/tcktransform.cpp b/cmd/tcktransform.cpp → cpp/cmd/tcktransform.cpp
diff --git a/cmd/tensor2metric.cpp → cpp/cmd/tensor2metric.cpp b/cmd/tensor2metric.cpp → cpp/cmd/tensor2metric.cpp
diff --git a/cmd/transformcalc.cpp → cpp/cmd/transformcalc.cpp b/cmd/transformcalc.cpp → cpp/cmd/transformcalc.cpp
diff --git a/cmd/transformcompose.cpp → cpp/cmd/transformcompose.cpp b/cmd/transformcompose.cpp → cpp/cmd/transformcompose.cpp
diff --git a/cmd/transformconvert.cpp → cpp/cmd/transformconvert.cpp b/cmd/transformconvert.cpp → cpp/cmd/transformconvert.cpp
diff --git a/cmd/tsfdivide.cpp → cpp/cmd/tsfdivide.cpp b/cmd/tsfdivide.cpp → cpp/cmd/tsfdivide.cpp
diff --git a/cmd/tsfinfo.cpp → cpp/cmd/tsfinfo.cpp b/cmd/tsfinfo.cpp → cpp/cmd/tsfinfo.cpp
diff --git a/cmd/tsfmult.cpp → cpp/cmd/tsfmult.cpp b/cmd/tsfmult.cpp → cpp/cmd/tsfmult.cpp
diff --git a/cmd/tsfsmooth.cpp → cpp/cmd/tsfsmooth.cpp b/cmd/tsfsmooth.cpp → cpp/cmd/tsfsmooth.cpp
diff --git a/cmd/tsfthreshold.cpp → cpp/cmd/tsfthreshold.cpp b/cmd/tsfthreshold.cpp → cpp/cmd/tsfthreshold.cpp
diff --git a/cmd/tsfvalidate.cpp → cpp/cmd/tsfvalidate.cpp b/cmd/tsfvalidate.cpp → cpp/cmd/tsfvalidate.cpp
diff --git a/cmd/vectorstats.cpp → cpp/cmd/vectorstats.cpp b/cmd/vectorstats.cpp → cpp/cmd/vectorstats.cpp
diff --git a/cmd/voxel2fixel.cpp → cpp/cmd/voxel2fixel.cpp b/cmd/voxel2fixel.cpp → cpp/cmd/voxel2fixel.cpp
diff --git a/cmd/voxel2mesh.cpp → cpp/cmd/voxel2mesh.cpp b/cmd/voxel2mesh.cpp → cpp/cmd/voxel2mesh.cpp
diff --git a/cmd/warp2metric.cpp → cpp/cmd/warp2metric.cpp b/cmd/warp2metric.cpp → cpp/cmd/warp2metric.cpp
diff --git a/cmd/warpconvert.cpp → cpp/cmd/warpconvert.cpp b/cmd/warpconvert.cpp → cpp/cmd/warpconvert.cpp
diff --git a/cmd/warpcorrect.cpp → cpp/cmd/warpcorrect.cpp b/cmd/warpcorrect.cpp → cpp/cmd/warpcorrect.cpp
diff --git a/cmd/warpinit.cpp → cpp/cmd/warpinit.cpp b/cmd/warpinit.cpp → cpp/cmd/warpinit.cpp
diff --git a/cmd/warpinvert.cpp → cpp/cmd/warpinvert.cpp b/cmd/warpinvert.cpp → cpp/cmd/warpinvert.cpp