.gitignore
CODE_OF_CONDUCT.md
CONTRIBUTING.md
Makefile
README.md
environment.yml
environment_no_builds.yml
get_test_MESE_info.py
meniscus_subregions.nrrd
pyproject.toml
requirements-conda.txt
requirements-dev.txt
requirements.txt
setup.py
test_seg_men_split.nrrd
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/build-test.yml
.github/workflows/building-pypi-linux.yml
.github/workflows/docs.yml
data/SAG_3D_DESS_RIGHT_bones_cart_men_fib-label.nrrd
data/femur_cart_smoothed_binary_no_surface_resampling.vtk
data/femur_cart_smoothed_binary_resampled_10k_pts.vtk
data/femur_cropped_cartilage_thick_10k_pts.vtk
data/femur_cropped_cartilage_thick_roi_10k_pts.vtk
data/femur_cropped_cartilage_thick_roi_full_pts.vtk
data/femur_cropped_cartilage_thick_smoothed_1.25_sigma_10k_pts.vtk
data/femur_cropped_test.vtk
data/femur_mesh_10k_pts.vtk
data/femur_mesh_orig.vtk
data/femur_orig_no_image_smoothing.vtk
data/femur_thickness_mm_10k_pts.vtk
data/femur_thickness_mm_regions_10k_pts.vtk
data/femur_thickness_mm_regions_10k_pts_thick_smoothed_1.25_sigma.vtk
data/femur_thickness_mm_regions_10k_pts_thick_smoothed_3_sigma.vtk
data/lat_tib_cart_smoothed_binary_no_surface_resampling.vtk
data/med_tib_cart_smoothed_binary_no_surface_resampling.vtk
data/right_knee_example.nrrd
data/tibia_cropped_test.vtk
data/tibia_smoothed_image_10k_pts_thick_regions.vtk
data/tibia_smoothed_image_cropped.vtk
data/tibia_smoothed_image_full_size.vtk
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data/femur_meshes_registration/2_RIGHT_femur_Nov_02_2021.vtk
data/femur_meshes_registration/3_RIGHT_femur_Nov_02_2021.vtk
data/femur_meshes_registration/4_RIGHT_femur_Nov_02_2021.vtk
data/femur_meshes_registration/5_RIGHT_femur_Nov_02_2021.vtk
data/femur_meshes_registration/temp/temp_ref_mesh.vtk
data/muscles/AM17_08_baseline_segmentation.nii
data/muscles/segmentation.nii.gz
docs/cython_functions.html
docs/index.html
docs/image/cartilage_processing.html
docs/image/index.html
docs/image/main.html
docs/mesh/createMesh.html
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docs/mesh/io.html
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docs/mesh/meshTools.html
docs/mesh/meshTransform.html
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docs/mesh/anatomical/femur_anatomical_coordinate_system.html
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examples/anatomic_coordinate_system/anatomic_coordinate_system_example_Sept.21.2022.ipynb
examples/create meshes/Create Muscle Mesh Jan.28.2022.ipynb
examples/create meshes/Create_Femur_Mesh_Assign_Cartilage_Thickness_and_Regions_Feb.3.2022.ipynb
examples/create meshes/Create_Femur_Mesh_with_All_Sub_Regions_Feb.11.2022.ipynb
examples/create meshes/Create_Tibia_Mesh_Assign_Cartilage_Thickness_and_Regions_Feb.3.2022.ipynb
examples/create meshes/Create_whole_knee_Feb.3.2022.ipynb
examples/create meshes/Detailed Example of setting and updating parameters for pymskt Feb.3.2022.ipynb
examples/create ssm/ssm_femur_example_March.3.2022.ipynb
examples/superficial_deep_cartilage_regions/femur_subregions_depth_subregions_Dec.5.2024.ipynb
examples/superficial_deep_cartilage_regions/simple_depth_subregions_Dec.5.2024.ipynb
examples/testing_meniscus_subregions/creat_meniscus_subregions_April.20.2025.ipynb
examples/testing_meniscus_subregions/creat_meniscus_subregions_visualization_May.7.2025.ipynb
examples/testing_meniscus_subregions/create_meniscus_subregions_visualization_May.7.2025_V2.ipynb
examples/testing_meniscus_subregions/lat_meniscus_mesh.vtk
examples/testing_meniscus_subregions/lat_tib_cart_mesh.vtk
examples/testing_meniscus_subregions/med_meniscus_mesh.vtk
examples/testing_meniscus_subregions/med_tib_cart_mesh.vtk
examples/testing_meniscus_subregions/tibia_mesh.vtk
examples/testing_meniscus_subregions.ipynb/creat_meniscus_subregions_April.20.2025.ipynb
examples/view_thickness_calculations/thick_calc_visuals.ipynb
images/cartilage_thickness_analysis.pdf
images/cartilage_thickness_analysis.png
images/cartilage_thickness_analysis.pptx
images/femur_acs.png
images/femur_acs_v2.png
images/femur_acs_v3.png
images/femur_itkwidgets.png
images/femur_subregions.png
images/whole_knee_1.png
images/whole_knee_2.png
mskt.egg-info/PKG-INFO
mskt.egg-info/SOURCES.txt
mskt.egg-info/dependency_links.txt
mskt.egg-info/not-zip-safe
mskt.egg-info/requires.txt
mskt.egg-info/top_level.txt
planning/t2_mapping_integration_plan.md
pymskt/__init__.py
pymskt/__init__.pyc
pymskt/cython_functions.cpython-38-darwin.so
pymskt/cython/cython_functions.c
pymskt/cython/cython_functions.pyx
pymskt/image/__init__.py
pymskt/image/__init__.pyc
pymskt/image/cartilage_processing.py
pymskt/image/main.py
pymskt/image/main.pyc
pymskt/image/meniscus_processing.py
pymskt/image/t2.py
pymskt/mesh/__init__.py
pymskt/mesh/createMesh.py
pymskt/mesh/io.py
pymskt/mesh/meshCartilage.py
pymskt/mesh/meshRegistration.py
pymskt/mesh/meshTools.py
pymskt/mesh/meshTransform.py
pymskt/mesh/mesh_meniscus.py
pymskt/mesh/meshes.py
pymskt/mesh/utils.py
pymskt/mesh/anatomical/__init__.py
pymskt/mesh/anatomical/femur_anatomical_coordinate_system.py
pymskt/mesh/anatomical/femur_cylinder.py
pymskt/mesh/anatomical/femur_long_axis.py
pymskt/statistics/__init__.py
pymskt/statistics/main.py
pymskt/statistics/pca.py
pymskt/statistics/ssm.py
pymskt/utils/__init__.py
pymskt/utils/main.py
pymskt/utils/testing.py
testing/bone_surface_data_test.py
testing/create_bone_mesh_test.py
testing/image/apply_transform_retain_array_test.py
testing/image/create_vtk_image_test.py
testing/image/set_vtk_image_origin_test.py
testing/image/test_femur_subregion_aligned.py
testing/image/test_meniscus_processing.py
testing/image/test_t2.py
testing/image/test_t2_loader.py
testing/mesh/meshMeniscus/MeniscusMesh_create_test.py
testing/mesh/meshMeniscus/compute_meniscal_coverage_test.py
testing/mesh/meshMeniscus/compute_meniscal_extrusion_test.py
testing/mesh/meshRegistration/get_icp_transform_test.py
testing/mesh/meshTools/gaussian_smooth_surface_scalars_test.py
testing/mesh/meshTools/get_cartilage_properties_at_points_test.py
testing/mesh/meshTools/get_mesh_physical_point_coords.test.py
testing/mesh/meshTools/get_smoothed_scalars_test.py
testing/mesh/meshTools/pcu_sdf_single_point_test.py
testing/mesh/meshTools/smooth_scalars_from_second_mesh_onto_base_test.py
testing/mesh/meshTools/transfer_mesh_scalars_get_weighted_average_n_closest_test.py
testing/mesh/meshTools/ProbeVtkImageDataAlongLine/ProbeVtkImageDataAlongLine_get_data_along_line_test.py
testing/mesh/meshTools/ProbeVtkImageDataAlongLine/ProbeVtkImageDataAlongLine_getters_test.py
testing/mesh/meshTools/ProbeVtkImageDataAlongLine/ProbeVtkImageDataAlongLine_save_data_along_line_test.py
testing/mesh/meshTools/rand_notes/general_test.py
testing/mesh/meshTools/rand_notes/plot_gaussian.py
testing/mesh/meshTools/rand_notes/random.py
testing/mesh/meshTransform/apply_transform_test.py
testing/mesh/meshTransform/break_versor_into_center_rotate_translate_translate_transforms_test.py
testing/mesh/meshTransform/copy_image_transform_to_mesh_test.py
testing/mesh/meshTransform/get_versor_from_transform_test.py
testing/mesh/meshTransform/meshTransform_apply_transform_to_mesh_test.py
testing/mesh/meshTransform/SitkVtkTransformer/SitkVtkTransformer_apply_transform_test.py
testing/mesh/meshTransform/SitkVtkTransformer/SitkVtkTransformer_get_inverse_test.py
testing/mesh/meshTransform/SitkVtkTransformer/SitkVtkTransformer_get_transform_test.py
testing/mesh/meshes/BoneMesh_calc_cartilage_regions_test.py
testing/mesh/meshes/BoneMesh_calc_cartilage_thickness_test.py
testing/mesh/meshes/BoneMesh_create_cartilage_meshes_test.py
testing/mesh/meshes/BoneMesh_create_mesh_test.py
testing/mesh/meshes/BoneMesh_setters_getters_test.py
testing/mesh/meshes/BoneMesh_smooth_surface_scalars_test.py
testing/mesh/meshes/Mesh_apply_transform_to_mesh_test.py
testing/mesh/meshes/Mesh_copy_scalars_categorical_test.py
testing/mesh/meshes/Mesh_copy_scalars_vectors_test.py
testing/mesh/meshes/Mesh_create_mesh_test.py
testing/mesh/meshes/Mesh_fixmesh_pcu_test.py
testing/mesh/meshes/Mesh_read_seg_image_test.py
testing/mesh/meshes/Mesh_resample_surface_test.py
testing/mesh/meshes/Mesh_save_mesh_test.py
testing/mesh/meshes/Mesh_scalar_properties_test.py
testing/mesh/meshes/Mesh_setters_getters_test.py
testing/scratch/meniscal_extrusion_Oct.29.2025.ipynb
testing/scratch/meniscal_extrusion_function_test_Oct.20.2025.ipynb
testing/scratch/python39_BoneMesh_create_mesh_test.ipynb
testing/scratch/python_39_Mesh_resample_surface_test.ipynb
testing/scratch/view_cropped_femur_tibia_June.17.2025.ipynb
testing/statistics/ProcrustesRegistration_test.py