├── .codespellrc ├── .github └── workflows │ └── validation.yml ├── .gitignore ├── CITATION.cff ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE ├── Makefile ├── README.md ├── README_APPENDIX.md ├── archive ├── LN2_COLTRIAN.cpp ├── LN2_DIFFUSE.cpp ├── LN2_FLATTEN.cpp ├── LN2_LLOYD.cpp ├── LN_GRADSMOOTH_ITER.cpp ├── LN_INFO_standalone_template.cpp └── README.md ├── dep ├── laynii_lib.cpp ├── laynii_lib.h ├── nifti1.h ├── nifti2.h ├── nifti2_io.cpp ├── nifti2_io.h ├── znzlib.cpp └── znzlib.h ├── ida ├── README.md ├── dep │ ├── idalib.cpp │ └── idalib.h ├── imgui │ ├── backends │ │ ├── imgui_impl_opengl3.cpp │ │ ├── imgui_impl_opengl3.h │ │ ├── imgui_impl_opengl3_loader.h │ │ ├── imgui_impl_sdl2.cpp │ │ └── imgui_impl_sdl2.h │ ├── imconfig.h │ ├── imgui.cpp │ ├── imgui.h │ ├── imgui_demo.cpp │ ├── imgui_draw.cpp │ ├── imgui_internal.h │ ├── imgui_tables.cpp │ ├── imgui_widgets.cpp │ ├── imstb_rectpack.h │ ├── imstb_textedit.h │ └── imstb_truetype.h └── src │ ├── Makefile │ ├── ida_GUI.cpp │ ├── ida_GUI.h │ ├── ida_GUI_slices.h │ ├── ida_IO.h │ ├── imgui.ini │ ├── imgui_ini_embed.h │ └── main.cpp ├── obj └── readme.txt ├── src ├── LN2_BORDERIZE.cpp ├── LN2_CHOLMO.cpp ├── LN2_COLUMNS.cpp ├── LN2_CONNECTED_CLUSTERS.cpp ├── LN2_DEVEIN.cpp ├── LN2_DIRECTIONALITY_BIN.cpp ├── LN2_GEODISTANCE.cpp ├── LN2_GRADIENTS.cpp ├── LN2_GRAMAG.cpp ├── LN2_HEXBIN.cpp ├── LN2_IFPOINTS.cpp ├── LN2_INTPRO.cpp ├── LN2_LAPLACIAN.cpp ├── LN2_LAYERDIMENSION.cpp ├── LN2_LAYERS.cpp ├── LN2_LAYER_SMOOTH.cpp ├── LN2_MASK.cpp ├── LN2_MULTILATERATE.cpp ├── LN2_NEIGHBORS.cpp ├── LN2_PATCH_FLATTEN.cpp ├── LN2_PATCH_FLATTEN_2D.cpp ├── LN2_PATCH_UNFLATTEN.cpp ├── LN2_PEAK_DETECT.cpp ├── LN2_PHASE_GRADIENTS.cpp ├── LN2_PHASE_JOLT.cpp ├── LN2_PHASE_LAPLACIAN.cpp ├── LN2_PROFILE.cpp ├── LN2_REGRESS_OUT.cpp ├── LN2_RIMIFY.cpp ├── LN2_RIM_BORDERIZE.cpp ├── LN2_RIM_POLISH.cpp ├── LN2_SENSITIVITY.cpp ├── LN2_SKELETONIZE.cpp ├── LN2_SPECIFICITY.cpp ├── LN2_UVD_FILTER.cpp ├── LN2_UVD_LSTSQR.cpp ├── LN2_VORONOI.cpp ├── LN2_WINDOWED_COUNTER_2D.cpp ├── LN2_ZERO_CROSSING.cpp ├── LN3_LAYERS.cpp ├── LN3_NOLAD.cpp ├── LN_3DCOLUMNS.cpp ├── LN_BOCO.cpp ├── LN_COLUMNAR_DIST.cpp ├── LN_CONLAY.cpp ├── LN_CORREL2FILES.cpp ├── LN_DIRECT_SMOOTH.cpp ├── LN_EXTREMETR.cpp ├── LN_FLOAT_ME.cpp ├── LN_GFACTOR.cpp ├── LN_GRADSMOOTH.cpp ├── LN_GROW_LAYERS.cpp ├── LN_IMAGIRO.cpp ├── LN_INFO.cpp ├── LN_INTPRO.cpp ├── LN_INT_ME.cpp ├── LN_LAYER_SMOOTH.cpp ├── LN_LEAKY_LAYERS.cpp ├── LN_LOITUMA.cpp ├── LN_MP2RAGE_DNOISE.cpp ├── LN_NOISEME.cpp ├── LN_NOISE_KERNEL.cpp ├── LN_PHYSIO_PARS.cpp ├── LN_RAGRUG.cpp ├── LN_SHORT_ME.cpp ├── LN_SKEW.cpp ├── LN_TEMPSMOOTH.cpp ├── LN_TRIAL.cpp └── LN_ZOOM.cpp ├── test_data ├── Ding2016_occip_ROI.nii.gz ├── Ding2016_occip_T2starweighted_filtered_for_tests.nii.gz ├── Ding2016_occip_rim.nii.gz ├── Ding2016_occipital_rim_midGM_equidist_control_point0.nii.gz ├── Smagn_t-001.nii.gz ├── Sphase_t-001.nii.gz ├── lo_ALF.nii.gz ├── lo_BOLD_act.nii.gz ├── lo_BOLD_intemp.nii.gz ├── lo_Nulled_intemp.nii.gz ├── lo_T1EPI.nii.gz ├── lo_VASO_act.nii.gz ├── lo_columns.nii.gz ├── lo_gradT1.nii.gz ├── lo_layers.nii.gz ├── lo_rim_LL.nii.gz ├── lo_sc_layers.nii.gz ├── rim_M.nii.gz ├── sc_BOLD_act.nii.gz ├── sc_INV1.nii.gz ├── sc_INV2.nii.gz ├── sc_T1EPI.nii.gz ├── sc_UNI.nii.gz ├── sc_VASO_act.nii.gz ├── sc_columns_3dcolumns.nii.gz ├── sc_distlay_1000.nii.gz ├── sc_landmarks.nii.gz ├── sc_landmarks_3dcolumns.nii.gz ├── sc_layers.nii.gz ├── sc_layers_3dcolumns.nii.gz ├── sc_leakylay_1000.nii.gz ├── sc_midGM.nii.gz ├── sc_rim.nii.gz ├── tests.sh └── tests_on_windows.sh └── visuals ├── LayNii_Logo_v02_optimized.gif ├── LayNii_logo.svg └── supporting.svg /.codespellrc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/.codespellrc -------------------------------------------------------------------------------- /.github/workflows/validation.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/.github/workflows/validation.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/.gitignore -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/CITATION.cff -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/CONTRIBUTING.md -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/Dockerfile -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/LICENSE -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/README.md -------------------------------------------------------------------------------- /README_APPENDIX.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/README_APPENDIX.md -------------------------------------------------------------------------------- /archive/LN2_COLTRIAN.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/archive/LN2_COLTRIAN.cpp -------------------------------------------------------------------------------- /archive/LN2_DIFFUSE.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/archive/LN2_DIFFUSE.cpp -------------------------------------------------------------------------------- /archive/LN2_FLATTEN.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/archive/LN2_FLATTEN.cpp -------------------------------------------------------------------------------- /archive/LN2_LLOYD.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/archive/LN2_LLOYD.cpp -------------------------------------------------------------------------------- /archive/LN_GRADSMOOTH_ITER.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/archive/LN_GRADSMOOTH_ITER.cpp -------------------------------------------------------------------------------- /archive/LN_INFO_standalone_template.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/archive/LN_INFO_standalone_template.cpp -------------------------------------------------------------------------------- /archive/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/archive/README.md -------------------------------------------------------------------------------- /dep/laynii_lib.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/dep/laynii_lib.cpp -------------------------------------------------------------------------------- /dep/laynii_lib.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/dep/laynii_lib.h -------------------------------------------------------------------------------- /dep/nifti1.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/dep/nifti1.h -------------------------------------------------------------------------------- /dep/nifti2.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/dep/nifti2.h -------------------------------------------------------------------------------- /dep/nifti2_io.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/dep/nifti2_io.cpp -------------------------------------------------------------------------------- /dep/nifti2_io.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/dep/nifti2_io.h -------------------------------------------------------------------------------- /dep/znzlib.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/dep/znzlib.cpp -------------------------------------------------------------------------------- /dep/znzlib.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/dep/znzlib.h -------------------------------------------------------------------------------- /ida/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/README.md -------------------------------------------------------------------------------- /ida/dep/idalib.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/dep/idalib.cpp -------------------------------------------------------------------------------- /ida/dep/idalib.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/dep/idalib.h -------------------------------------------------------------------------------- /ida/imgui/backends/imgui_impl_opengl3.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/imgui/backends/imgui_impl_opengl3.cpp -------------------------------------------------------------------------------- /ida/imgui/backends/imgui_impl_opengl3.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/imgui/backends/imgui_impl_opengl3.h -------------------------------------------------------------------------------- /ida/imgui/backends/imgui_impl_opengl3_loader.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/imgui/backends/imgui_impl_opengl3_loader.h -------------------------------------------------------------------------------- /ida/imgui/backends/imgui_impl_sdl2.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/imgui/backends/imgui_impl_sdl2.cpp -------------------------------------------------------------------------------- /ida/imgui/backends/imgui_impl_sdl2.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/imgui/backends/imgui_impl_sdl2.h -------------------------------------------------------------------------------- /ida/imgui/imconfig.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/imgui/imconfig.h -------------------------------------------------------------------------------- /ida/imgui/imgui.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/imgui/imgui.cpp -------------------------------------------------------------------------------- /ida/imgui/imgui.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/imgui/imgui.h -------------------------------------------------------------------------------- /ida/imgui/imgui_demo.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/imgui/imgui_demo.cpp -------------------------------------------------------------------------------- /ida/imgui/imgui_draw.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/imgui/imgui_draw.cpp -------------------------------------------------------------------------------- /ida/imgui/imgui_internal.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/imgui/imgui_internal.h -------------------------------------------------------------------------------- /ida/imgui/imgui_tables.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/imgui/imgui_tables.cpp -------------------------------------------------------------------------------- /ida/imgui/imgui_widgets.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/imgui/imgui_widgets.cpp -------------------------------------------------------------------------------- /ida/imgui/imstb_rectpack.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/imgui/imstb_rectpack.h -------------------------------------------------------------------------------- /ida/imgui/imstb_textedit.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/imgui/imstb_textedit.h -------------------------------------------------------------------------------- /ida/imgui/imstb_truetype.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/imgui/imstb_truetype.h -------------------------------------------------------------------------------- /ida/src/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/src/Makefile -------------------------------------------------------------------------------- /ida/src/ida_GUI.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/src/ida_GUI.cpp -------------------------------------------------------------------------------- /ida/src/ida_GUI.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/src/ida_GUI.h -------------------------------------------------------------------------------- /ida/src/ida_GUI_slices.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/src/ida_GUI_slices.h -------------------------------------------------------------------------------- /ida/src/ida_IO.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/src/ida_IO.h -------------------------------------------------------------------------------- /ida/src/imgui.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/src/imgui.ini -------------------------------------------------------------------------------- /ida/src/imgui_ini_embed.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/src/imgui_ini_embed.h -------------------------------------------------------------------------------- /ida/src/main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/ida/src/main.cpp -------------------------------------------------------------------------------- /obj/readme.txt: -------------------------------------------------------------------------------- 1 | # for obj folder in github 2 | -------------------------------------------------------------------------------- /src/LN2_BORDERIZE.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_BORDERIZE.cpp -------------------------------------------------------------------------------- /src/LN2_CHOLMO.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_CHOLMO.cpp -------------------------------------------------------------------------------- /src/LN2_COLUMNS.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_COLUMNS.cpp -------------------------------------------------------------------------------- /src/LN2_CONNECTED_CLUSTERS.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_CONNECTED_CLUSTERS.cpp -------------------------------------------------------------------------------- /src/LN2_DEVEIN.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_DEVEIN.cpp -------------------------------------------------------------------------------- /src/LN2_DIRECTIONALITY_BIN.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_DIRECTIONALITY_BIN.cpp -------------------------------------------------------------------------------- /src/LN2_GEODISTANCE.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_GEODISTANCE.cpp -------------------------------------------------------------------------------- /src/LN2_GRADIENTS.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_GRADIENTS.cpp -------------------------------------------------------------------------------- /src/LN2_GRAMAG.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_GRAMAG.cpp -------------------------------------------------------------------------------- /src/LN2_HEXBIN.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_HEXBIN.cpp -------------------------------------------------------------------------------- /src/LN2_IFPOINTS.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_IFPOINTS.cpp -------------------------------------------------------------------------------- /src/LN2_INTPRO.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_INTPRO.cpp -------------------------------------------------------------------------------- /src/LN2_LAPLACIAN.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_LAPLACIAN.cpp -------------------------------------------------------------------------------- /src/LN2_LAYERDIMENSION.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_LAYERDIMENSION.cpp -------------------------------------------------------------------------------- /src/LN2_LAYERS.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_LAYERS.cpp -------------------------------------------------------------------------------- /src/LN2_LAYER_SMOOTH.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_LAYER_SMOOTH.cpp -------------------------------------------------------------------------------- /src/LN2_MASK.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_MASK.cpp -------------------------------------------------------------------------------- /src/LN2_MULTILATERATE.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_MULTILATERATE.cpp -------------------------------------------------------------------------------- /src/LN2_NEIGHBORS.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_NEIGHBORS.cpp -------------------------------------------------------------------------------- /src/LN2_PATCH_FLATTEN.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_PATCH_FLATTEN.cpp -------------------------------------------------------------------------------- /src/LN2_PATCH_FLATTEN_2D.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_PATCH_FLATTEN_2D.cpp -------------------------------------------------------------------------------- /src/LN2_PATCH_UNFLATTEN.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_PATCH_UNFLATTEN.cpp -------------------------------------------------------------------------------- /src/LN2_PEAK_DETECT.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_PEAK_DETECT.cpp -------------------------------------------------------------------------------- /src/LN2_PHASE_GRADIENTS.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_PHASE_GRADIENTS.cpp -------------------------------------------------------------------------------- /src/LN2_PHASE_JOLT.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_PHASE_JOLT.cpp -------------------------------------------------------------------------------- /src/LN2_PHASE_LAPLACIAN.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_PHASE_LAPLACIAN.cpp -------------------------------------------------------------------------------- /src/LN2_PROFILE.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_PROFILE.cpp -------------------------------------------------------------------------------- /src/LN2_REGRESS_OUT.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_REGRESS_OUT.cpp -------------------------------------------------------------------------------- /src/LN2_RIMIFY.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_RIMIFY.cpp -------------------------------------------------------------------------------- /src/LN2_RIM_BORDERIZE.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_RIM_BORDERIZE.cpp -------------------------------------------------------------------------------- /src/LN2_RIM_POLISH.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_RIM_POLISH.cpp -------------------------------------------------------------------------------- /src/LN2_SENSITIVITY.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_SENSITIVITY.cpp -------------------------------------------------------------------------------- /src/LN2_SKELETONIZE.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_SKELETONIZE.cpp -------------------------------------------------------------------------------- /src/LN2_SPECIFICITY.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_SPECIFICITY.cpp -------------------------------------------------------------------------------- /src/LN2_UVD_FILTER.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_UVD_FILTER.cpp -------------------------------------------------------------------------------- /src/LN2_UVD_LSTSQR.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_UVD_LSTSQR.cpp -------------------------------------------------------------------------------- /src/LN2_VORONOI.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_VORONOI.cpp -------------------------------------------------------------------------------- /src/LN2_WINDOWED_COUNTER_2D.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_WINDOWED_COUNTER_2D.cpp -------------------------------------------------------------------------------- /src/LN2_ZERO_CROSSING.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN2_ZERO_CROSSING.cpp -------------------------------------------------------------------------------- /src/LN3_LAYERS.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN3_LAYERS.cpp -------------------------------------------------------------------------------- /src/LN3_NOLAD.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN3_NOLAD.cpp -------------------------------------------------------------------------------- /src/LN_3DCOLUMNS.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_3DCOLUMNS.cpp -------------------------------------------------------------------------------- /src/LN_BOCO.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_BOCO.cpp -------------------------------------------------------------------------------- /src/LN_COLUMNAR_DIST.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_COLUMNAR_DIST.cpp -------------------------------------------------------------------------------- /src/LN_CONLAY.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_CONLAY.cpp -------------------------------------------------------------------------------- /src/LN_CORREL2FILES.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_CORREL2FILES.cpp -------------------------------------------------------------------------------- /src/LN_DIRECT_SMOOTH.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_DIRECT_SMOOTH.cpp -------------------------------------------------------------------------------- /src/LN_EXTREMETR.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_EXTREMETR.cpp -------------------------------------------------------------------------------- /src/LN_FLOAT_ME.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_FLOAT_ME.cpp -------------------------------------------------------------------------------- /src/LN_GFACTOR.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_GFACTOR.cpp -------------------------------------------------------------------------------- /src/LN_GRADSMOOTH.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_GRADSMOOTH.cpp -------------------------------------------------------------------------------- /src/LN_GROW_LAYERS.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_GROW_LAYERS.cpp -------------------------------------------------------------------------------- /src/LN_IMAGIRO.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_IMAGIRO.cpp -------------------------------------------------------------------------------- /src/LN_INFO.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_INFO.cpp -------------------------------------------------------------------------------- /src/LN_INTPRO.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_INTPRO.cpp -------------------------------------------------------------------------------- /src/LN_INT_ME.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_INT_ME.cpp -------------------------------------------------------------------------------- /src/LN_LAYER_SMOOTH.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_LAYER_SMOOTH.cpp -------------------------------------------------------------------------------- /src/LN_LEAKY_LAYERS.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_LEAKY_LAYERS.cpp -------------------------------------------------------------------------------- /src/LN_LOITUMA.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_LOITUMA.cpp -------------------------------------------------------------------------------- /src/LN_MP2RAGE_DNOISE.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_MP2RAGE_DNOISE.cpp -------------------------------------------------------------------------------- /src/LN_NOISEME.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_NOISEME.cpp -------------------------------------------------------------------------------- /src/LN_NOISE_KERNEL.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_NOISE_KERNEL.cpp -------------------------------------------------------------------------------- /src/LN_PHYSIO_PARS.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_PHYSIO_PARS.cpp -------------------------------------------------------------------------------- /src/LN_RAGRUG.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_RAGRUG.cpp -------------------------------------------------------------------------------- /src/LN_SHORT_ME.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_SHORT_ME.cpp -------------------------------------------------------------------------------- /src/LN_SKEW.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_SKEW.cpp -------------------------------------------------------------------------------- /src/LN_TEMPSMOOTH.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_TEMPSMOOTH.cpp -------------------------------------------------------------------------------- /src/LN_TRIAL.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_TRIAL.cpp -------------------------------------------------------------------------------- /src/LN_ZOOM.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/src/LN_ZOOM.cpp -------------------------------------------------------------------------------- /test_data/Ding2016_occip_ROI.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/Ding2016_occip_ROI.nii.gz -------------------------------------------------------------------------------- /test_data/Ding2016_occip_T2starweighted_filtered_for_tests.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/Ding2016_occip_T2starweighted_filtered_for_tests.nii.gz -------------------------------------------------------------------------------- /test_data/Ding2016_occip_rim.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/Ding2016_occip_rim.nii.gz -------------------------------------------------------------------------------- /test_data/Ding2016_occipital_rim_midGM_equidist_control_point0.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/Ding2016_occipital_rim_midGM_equidist_control_point0.nii.gz -------------------------------------------------------------------------------- /test_data/Smagn_t-001.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/Smagn_t-001.nii.gz -------------------------------------------------------------------------------- /test_data/Sphase_t-001.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/Sphase_t-001.nii.gz -------------------------------------------------------------------------------- /test_data/lo_ALF.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/lo_ALF.nii.gz -------------------------------------------------------------------------------- /test_data/lo_BOLD_act.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/lo_BOLD_act.nii.gz -------------------------------------------------------------------------------- /test_data/lo_BOLD_intemp.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/lo_BOLD_intemp.nii.gz -------------------------------------------------------------------------------- /test_data/lo_Nulled_intemp.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/lo_Nulled_intemp.nii.gz -------------------------------------------------------------------------------- /test_data/lo_T1EPI.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/lo_T1EPI.nii.gz -------------------------------------------------------------------------------- /test_data/lo_VASO_act.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/lo_VASO_act.nii.gz -------------------------------------------------------------------------------- /test_data/lo_columns.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/lo_columns.nii.gz -------------------------------------------------------------------------------- /test_data/lo_gradT1.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/lo_gradT1.nii.gz -------------------------------------------------------------------------------- /test_data/lo_layers.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/lo_layers.nii.gz -------------------------------------------------------------------------------- /test_data/lo_rim_LL.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/lo_rim_LL.nii.gz -------------------------------------------------------------------------------- /test_data/lo_sc_layers.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/lo_sc_layers.nii.gz -------------------------------------------------------------------------------- /test_data/rim_M.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/rim_M.nii.gz -------------------------------------------------------------------------------- /test_data/sc_BOLD_act.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/sc_BOLD_act.nii.gz -------------------------------------------------------------------------------- /test_data/sc_INV1.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/sc_INV1.nii.gz -------------------------------------------------------------------------------- /test_data/sc_INV2.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/sc_INV2.nii.gz -------------------------------------------------------------------------------- /test_data/sc_T1EPI.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/sc_T1EPI.nii.gz -------------------------------------------------------------------------------- /test_data/sc_UNI.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/sc_UNI.nii.gz -------------------------------------------------------------------------------- /test_data/sc_VASO_act.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/sc_VASO_act.nii.gz -------------------------------------------------------------------------------- /test_data/sc_columns_3dcolumns.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/sc_columns_3dcolumns.nii.gz -------------------------------------------------------------------------------- /test_data/sc_distlay_1000.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/sc_distlay_1000.nii.gz -------------------------------------------------------------------------------- /test_data/sc_landmarks.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/sc_landmarks.nii.gz -------------------------------------------------------------------------------- /test_data/sc_landmarks_3dcolumns.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/sc_landmarks_3dcolumns.nii.gz -------------------------------------------------------------------------------- /test_data/sc_layers.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/sc_layers.nii.gz -------------------------------------------------------------------------------- /test_data/sc_layers_3dcolumns.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/sc_layers_3dcolumns.nii.gz -------------------------------------------------------------------------------- /test_data/sc_leakylay_1000.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/sc_leakylay_1000.nii.gz -------------------------------------------------------------------------------- /test_data/sc_midGM.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/sc_midGM.nii.gz -------------------------------------------------------------------------------- /test_data/sc_rim.nii.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/sc_rim.nii.gz -------------------------------------------------------------------------------- /test_data/tests.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/tests.sh -------------------------------------------------------------------------------- /test_data/tests_on_windows.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/test_data/tests_on_windows.sh -------------------------------------------------------------------------------- /visuals/LayNii_Logo_v02_optimized.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/visuals/LayNii_Logo_v02_optimized.gif -------------------------------------------------------------------------------- /visuals/LayNii_logo.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/visuals/LayNii_logo.svg -------------------------------------------------------------------------------- /visuals/supporting.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/layerfMRI/LAYNII/HEAD/visuals/supporting.svg --------------------------------------------------------------------------------