├── .gitignore ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── Example_BCS_leg_right.m ├── Example_ankle_model.m ├── Example_bilateral_model.m ├── Example_create_kinetic_models.m ├── Example_extract_ankle_artic_surf.m ├── Example_extract_tibiofem_artic_surf.m ├── Example_full_leg_left.m ├── Example_full_leg_right.m ├── Example_hip_model.m ├── Example_knee_model.m ├── Example_use_Kai2014.m ├── LICENSE.txt ├── NOTICE.txt ├── README.md ├── STAPLE ├── GIBOC-core │ ├── LICENSE │ ├── README.md │ ├── SubFunctions │ │ ├── FittingFun │ │ │ ├── LSGE │ │ │ │ ├── csr.m │ │ │ │ ├── drrot3.m │ │ │ │ ├── fg2dcircle.m │ │ │ │ ├── fg3dcircle.m │ │ │ │ ├── fgbrrt3.m │ │ │ │ ├── fgcone.m │ │ │ │ ├── fgcylinder.m │ │ │ │ ├── fgrrot3.m │ │ │ │ ├── fgsphere.m │ │ │ │ ├── fgtorus.m │ │ │ │ ├── frrot3.m │ │ │ │ ├── gncc2.m │ │ │ │ ├── gr.m │ │ │ │ ├── licence.pdf │ │ │ │ ├── licence.txt │ │ │ │ ├── ls2dcircle.m │ │ │ │ ├── ls2dline.m │ │ │ │ ├── ls3dcircle.m │ │ │ │ ├── ls3dline.m │ │ │ │ ├── lscone.m │ │ │ │ ├── lscylinder.m │ │ │ │ ├── lsplane.m │ │ │ │ ├── lssphere.m │ │ │ │ ├── lstorus.m │ │ │ │ ├── nlss11.m │ │ │ │ ├── readme.txt │ │ │ │ └── rot3z.m │ │ │ ├── LSSLFitPatellaRidge.m │ │ │ ├── ankleSurfFit.m │ │ │ ├── ellipsoid_fit.m │ │ │ ├── fitCSA.m │ │ │ ├── fitCSATalus.m │ │ │ ├── fitEllipseOnTibialCondylesEdge.m │ │ │ ├── fitQuadriTalus.m │ │ │ ├── fit_ellipse.m │ │ │ ├── patRidgeFit.m │ │ │ ├── patRidgeRainbow.m │ │ │ └── sphereFit.m │ │ ├── GeometricFun │ │ │ ├── LargestEdgeConvHull.m │ │ │ ├── PCRegionGrowing.m │ │ │ ├── PlanPolygonCentroid3D.m │ │ │ ├── ProjectOnPlan.m │ │ │ ├── PtsOnCondylesFemur.m │ │ │ ├── TriangleClosestPointPair.m │ │ │ ├── computeMassProperties_Mirtich1996.m │ │ │ ├── computeTriCoeffMorpho.m │ │ │ ├── cutLongBoneMesh.m │ │ │ ├── getLargerPlanarSect.m │ │ │ └── normalizeV.m │ │ ├── MeshReadFun │ │ │ ├── ReadMesh.m │ │ │ ├── readGMSH.m │ │ │ └── stlTools │ │ │ │ ├── license_stlTools.txt │ │ │ │ ├── readme.txt │ │ │ │ ├── stlAddVerts.m │ │ │ │ ├── stlDelVerts.m │ │ │ │ ├── stlDemo.m │ │ │ │ ├── stlGetFormat.m │ │ │ │ ├── stlGetVerts.m │ │ │ │ ├── stlPlot.m │ │ │ │ ├── stlRead.m │ │ │ │ ├── stlReadAscii.m │ │ │ │ ├── stlReadBinary.m │ │ │ │ ├── stlSlimVerts.m │ │ │ │ └── stlWrite.m │ │ ├── PlotFun │ │ │ ├── original_TriPlots │ │ │ │ ├── PlotFemur.m │ │ │ │ ├── PlotPatella.m │ │ │ │ └── PlotTibia.m │ │ │ ├── pl3t.m │ │ │ ├── pl3tVectors.m │ │ │ ├── plotArrow.m │ │ │ ├── plotBoneLandmarks.m │ │ │ ├── plotCylinder.m │ │ │ ├── plotDot.m │ │ │ ├── plotEllipsoid.m │ │ │ ├── plotPlan.m │ │ │ ├── plotSphere.m │ │ │ ├── plotTriangLight.m │ │ │ ├── quickPlotRefSystem.m │ │ │ └── quickPlotTriang.m │ │ └── TriangulationFun │ │ │ ├── NotNaN.m │ │ │ ├── Subexpressions.m │ │ │ ├── TriChangeCS.m │ │ │ ├── TriCloseMesh.m │ │ │ ├── TriConnectedPatch.m │ │ │ ├── TriCovMatrix.m │ │ │ ├── TriCurvature.m │ │ │ ├── TriDifferenceMesh.m │ │ │ ├── TriDilateMesh.m │ │ │ ├── TriErodeMesh.m │ │ │ ├── TriFillPlanarHoles.m │ │ │ ├── TriFixNormals.m │ │ │ ├── TriInertiaPpties.m │ │ │ ├── TriKeepLargestPatch.m │ │ │ ├── TriMesh2DProperties.m │ │ │ ├── TriOpenMesh.m │ │ │ ├── TriPlanIntersect.m │ │ │ ├── TriPointOnMesh.m │ │ │ ├── TriReduceMesh.m │ │ │ ├── TriSliceObjAlongAxis.m │ │ │ ├── TriSplitObjects.m │ │ │ └── TriUnite.m │ └── ThirdPartyLicenses │ │ ├── licence_LSGE.txt │ │ ├── license_Ellipsoid_fit.txt │ │ ├── license_Patch_Curvature.txt │ │ ├── license_fit_ellipse.txt │ │ ├── license_sphereFit.txt │ │ └── license_stlTools.txt ├── algorithms │ ├── CS_femur_CylinderOnCondyles.m │ ├── CS_femur_EllipsoidsOnCondyles.m │ ├── CS_femur_SpheresOnCondyles.m │ ├── CS_pelvis_ISB.m │ ├── CS_talus_subtalarSpheres.m │ ├── CS_talus_trochleaCylinder.m │ ├── CS_tibia_ArtSurfCentroids.m │ ├── CS_tibia_Ellipse.m │ ├── CS_tibia_PlateauLayer.m │ ├── FemPatTibACS │ │ ├── .gitignore │ │ └── .gitkeep │ ├── GIBOC_femur.m │ ├── GIBOC_tibia.m │ ├── Kai2014_femur.m │ ├── Kai2014_pelvis.m │ ├── Kai2014_tibia.m │ ├── STAPLE_foot.m │ ├── STAPLE_pelvis.m │ ├── STAPLE_talus.m │ ├── STAPLE_toes.m │ └── private │ │ ├── GIBOC_femur_ArticSurf.m │ │ ├── GIBOC_femur_filterCondyleSurf.m │ │ ├── GIBOC_femur_fitSphere2FemHead.m │ │ ├── GIBOC_femur_getCondyleMostProxPoint.m │ │ ├── GIBOC_femur_processEpiPhysis.m │ │ ├── GIBOC_femur_smoothCondyles.m │ │ ├── GIBOC_isolate_epiphysis.m │ │ ├── GIBOC_tibia_DistArtSurf.m │ │ ├── GIBOC_tibia_DistMaxSectCentre.m │ │ ├── GIBOC_tibia_FullProxArtSurf.m │ │ ├── GIBOC_tibia_ProxArtSurf_it1.m │ │ ├── GIBOC_tibia_ProxArtSurf_it2.m │ │ ├── GIBOC_tibia_removePartBetweenRidges_it1.m │ │ ├── Kai2014_femur_fitSphere2FemHead.m │ │ ├── Kai2014_femur_fitSpheres2Condyles.m │ │ ├── convertBoolean2OnOff.m │ │ ├── femur_guess_CS.m │ │ ├── pelvis_guess_CS.m │ │ ├── removeFibulaFromProxTibia.m │ │ ├── sliceFemoralCondyles.m │ │ ├── tibia_guess_CS.m │ │ └── tibia_identify_lateral_direction.m ├── anthropometry │ ├── assignMassPropsToSegments.m │ ├── calcOsimModelMass.m │ ├── gait2392MassProps.m │ ├── mapGait2392MassPropToModel.m │ └── scaleMassProps.m ├── geometry │ ├── bodySide2Sign.m │ ├── compileListOfJointsInJCSStruct.m │ ├── createTriGeomSet.m │ ├── findLandmarkCoords.m │ ├── getBoneLandmarkList.m │ ├── inferBodySideFromAnatomicStruct.m │ ├── jointDefinitions_Modenese2018.m │ ├── jointDefinitions_auto2020.m │ ├── landmarkBoneGeom.m │ ├── load_mesh.m │ ├── processTriGeomBoneSet.m │ ├── reduceTriObjGeometry.m │ ├── transformToBodyCS.m │ ├── transformTriGeomSet.m │ └── writeOBJfile.m ├── opensim │ ├── addBodiesFromTriGeomBoneSet.m │ ├── addBodyFromTriGeomObj.m │ ├── addBoneLandmarksAsMarkers.m │ ├── addJointsFromStruct.m │ ├── assembleJointStruct.m │ ├── attachPatellaGeom.m │ ├── computeXYZAngleSeq.m │ ├── createCustomJointFromStruct.m │ ├── createOpenSimModelJoints.m │ ├── createSpatialTransformFromStruct.m │ ├── finalizeJointStruct.m │ ├── getAxisVecFromStringLabel.m │ ├── getJointParams.m │ ├── initializeOpenSimModel.m │ ├── logConsolePrintout.m │ ├── mergeOpenSimModels.m │ ├── mergeOpenSimSets.m │ ├── orientation2MatRot.m │ ├── osimVec3ToArray.m │ ├── reduceOpenSimModel.m │ ├── renameBodyAndAdjustOpenSimModel.m │ ├── updTransformAxis.m │ ├── updTransformAxisCoordName.m │ ├── verifyJointStructCompleteness.m │ └── writeModelGeometriesFolder.m └── sandbox │ ├── GIBOC_Miranda2010_tibia.m │ ├── MeshLabServer_scripts │ ├── MeshLab_scripts │ │ ├── Cleaning_Filters.mlx │ │ ├── Matlab_functions │ │ ├── Poisson_Pass1.mlx │ │ ├── Poisson_Pass3.mlx │ │ └── other scripts │ │ │ ├── AutomaticAligment.mlx │ │ │ ├── FlattenLayers.mlx │ │ │ ├── FreezeCurrentMatrix.mlx │ │ │ ├── HC_Laplacian_Smooth.mlx │ │ │ ├── Laplacian_Smooth.mlx │ │ │ ├── Merge_Close_Vertices.mlx │ │ │ ├── Preprocessing_PoissonRemesh.mlx │ │ │ ├── Remove_Duplicate_Faces.mlx │ │ │ ├── Remove_Duplicate_Vertex.mlx │ │ │ ├── Remove_Faces_from_Non_Manifold_Edges.mlx │ │ │ ├── Remove_Unreferenced_Vertex.mlx │ │ │ ├── Remove_Zero_Area_Faces.mlx │ │ │ ├── Surface_Reconstruction_Poisson.mlx │ │ │ └── Tranform_Align_to_Principal_Axis.mlx │ ├── call_MeshLab_v2.m │ └── runMeshLabScript.m │ ├── README.md │ ├── STAPLE_tibia.m │ ├── TODOs.md │ ├── carpentry │ ├── addMarkersFromStruct.m │ ├── createJointSet.m │ ├── setCustomJointSpatialTransform.m │ └── setJointCoords.m │ ├── list_MATLAB structures.xlsx │ ├── multiple_choices_input.m │ ├── patfem │ └── .gitkeep │ ├── suppl_mat_tibiofemoral_alignment.m │ ├── transf_geom │ └── writeTransformedBoneGeom.m │ └── workflows_gallery.m ├── advanced_examples ├── README.md ├── joints_with_custom_DoF │ ├── README.md │ ├── getJointParams3DoFKnee.m │ └── leg_model_3DoF_knee.m ├── merge_STAPLE_model_to_gait2392 │ ├── README.md │ ├── example_auto2020_ankle_R.osim │ ├── final_STAPLEfoot+gait2392.osim │ ├── gait2392_scaled_0.82.osim │ ├── merge_STAPLEfoot_gait2392.m │ └── output_STAPLEfoot+gait2392.osim └── upper_limb │ ├── GIBOC_humerus.m │ ├── README.md │ ├── bone_geom │ └── tri │ │ └── humerus_r.mat │ └── process_humerus_r.m ├── bone_datasets ├── ICL_MRI │ ├── README.md │ └── tri │ │ ├── calcn_r.mat │ │ ├── femur_r.mat │ │ ├── fibula_r.mat │ │ ├── patella_r.mat │ │ ├── pelvis.mat │ │ ├── pelvis_l.mat │ │ ├── pelvis_no_sacrum.mat │ │ ├── pelvis_r.mat │ │ ├── sacrum.mat │ │ ├── talus_r.mat │ │ ├── tibia_r.mat │ │ └── toes_r.mat ├── JIA_ANKLE_MRI │ ├── README.md │ └── tri │ │ ├── calcn_l.mat │ │ ├── calcn_r.mat │ │ ├── talus_l.mat │ │ ├── talus_r.mat │ │ ├── tibia_l.mat │ │ ├── tibia_r.mat │ │ ├── toes_l.mat │ │ └── toes_r.mat ├── JIA_MRI │ ├── README.md │ └── tri │ │ ├── calcn_l.mat │ │ ├── calcn_r.mat │ │ ├── femur_l.mat │ │ ├── femur_r.mat │ │ ├── patella_l.mat │ │ ├── patella_r.mat │ │ ├── pelvis.mat │ │ ├── pelvis_no_sacrum.mat │ │ ├── talus_l.mat │ │ ├── talus_r.mat │ │ ├── tibia_l.mat │ │ ├── tibia_r.mat │ │ ├── toes_l.mat │ │ └── toes_r.mat ├── LHDL_CT │ ├── LICENSE_LHDL.pdf │ ├── README.md │ └── tri │ │ ├── calcn_r.mat │ │ ├── femur_r.mat │ │ ├── patella_r.mat │ │ ├── pelvis_no_sacrum.mat │ │ ├── talus_r.mat │ │ ├── tibia_no_fib_r.mat │ │ ├── tibia_r.mat │ │ └── toes_r.mat ├── MC22 │ ├── README.md │ └── tri │ │ ├── femur_l.mat │ │ ├── femur_r.mat │ │ ├── foot_l.mat │ │ ├── foot_r.mat │ │ ├── patella_r.mat │ │ ├── pelvis.mat │ │ ├── pelvis_no_sacrum.mat │ │ ├── tibia_l.mat │ │ └── tibia_r.mat ├── TLEM2 │ ├── README.md │ └── stl │ │ ├── femur_r.stl │ │ ├── foot_r.stl │ │ ├── pelvis.stl │ │ ├── talus_r.stl │ │ └── tibia_r.stl ├── TLEM2_CT │ ├── README.md │ └── tri │ │ ├── calcn_l.mat │ │ ├── calcn_r.mat │ │ ├── femur_l.mat │ │ ├── femur_r.mat │ │ ├── patella_l.mat │ │ ├── patella_r.mat │ │ ├── pelvis.mat │ │ ├── pelvis_no_sacrum.mat │ │ ├── talus_l.mat │ │ ├── talus_r.mat │ │ ├── tibia_l.mat │ │ ├── tibia_r.mat │ │ ├── toes_l.mat │ │ └── toes_r.mat ├── TLEM2_MRI │ ├── README.md │ └── tri │ │ ├── calcn_l.mat │ │ ├── calcn_r.mat │ │ ├── femur_l.mat │ │ ├── femur_r.mat │ │ ├── patella_l.mat │ │ ├── patella_r.mat │ │ ├── pelvis.mat │ │ ├── pelvis_no_sacrum.mat │ │ ├── talus_l.mat │ │ ├── talus_r.mat │ │ ├── tibia_l.mat │ │ ├── tibia_r.mat │ │ ├── toes_l.mat │ │ └── toes_r.mat └── VAKHUM_CT │ ├── README.md │ ├── VAKHUM_resources_license_agreement.pdf │ └── tri │ ├── femur_r.mat │ ├── patella_r.mat │ ├── pelvis_no_sacrum.mat │ ├── talus_r.mat │ └── tibia_r.mat ├── convert_stl2triang.m ├── convert_triang2STL.m ├── docs ├── GIBOC_algorithms_explained.pdf ├── STAPLE_algorithms_suppl_mat.pdf └── _docs_mass_properties │ ├── Eberly 2003 Polyhedral Mass Properties Revisited.pdf │ └── Mirtich Mass properties of mesh 1996.pdf ├── images ├── ICL_MRI_bones.PNG ├── JIA-MRI_bones.PNG ├── LHDL_CT_bones.PNG ├── MRI_foot_bones.PNG ├── Montefiori2020.PNG ├── STAPLE_overview.png ├── STAPLEfoot_gait2392_merged.png ├── TLEM2_CT_bones.PNG ├── TLEM2_MRI_bones.PNG ├── VAKHUM-CT_bones.PNG ├── adv_example_humerus.png ├── artic_surfaces.png ├── complete_osim_model.png ├── partial_osim_models.png └── reference_systems.png └── tests ├── ref_models ├── bilateral │ ├── JIA_MRI_bilateral.osim │ └── TLEM2_MRI_bilateral.osim ├── mass │ ├── README.md │ └── 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