├── .gitignore ├── @cobiveco ├── cobiveco.asv ├── cobiveco.m ├── computeApicobasal.m ├── computeApicobasalBridges.m ├── computeApicobasalVentricles.m ├── computeHeartAxesAndApex.m ├── computeRotational.m ├── computeRotationalBridges.m ├── computeRotationalVentricles.m ├── computeTransmural.m ├── computeTransventricular.m ├── createGraphandSplitMesh.asv ├── createGraphandSplitMesh.m ├── exportResult.m ├── prepareMesh0.m ├── prepareMesh1.m └── prepareMesh2.m ├── @uvc ├── computeApicobasal.m ├── computeRotational.m ├── computeTransmural.m ├── computeTransventricular.m ├── prepareMesh.m ├── splitMesh.m └── uvc.m ├── CITATION.cff ├── LICENSE ├── README.md ├── cobivecox.yml ├── dependencies ├── install_cobiveco.sh └── install_uvc.sh ├── examples ├── HeatGeodesic │ ├── computeHeatGeodesic.m │ ├── solveHeat.m │ └── solvePoisson.m ├── Pictures_parcellation_results │ ├── anteriorGeo2View.png │ ├── anteriorMeanTOF.png │ ├── apexViewMeanTOF.png │ ├── inferiorGeo2View.png │ ├── inferiorMeanTOF.png │ ├── topViewGeo2.png │ ├── topViewGeo2TiltLeft.png │ ├── topViewGeo2TiltRight.png │ ├── topViewTOF.png │ ├── topViewTruncatedMeanTOF.png │ └── topViewTruncatedMeanTOFTilted.png ├── README_AHA_parcellation.md ├── example_CobivecoX.m ├── example_CobivecoX_batch.m ├── example_CobivecoX_batch_strings.m ├── example_aha_parcellation.m ├── example_assignTissue.m ├── example_extended_aha_parcellation.m ├── example_extended_parcellation.m ├── example_geo1.m ├── example_geo1_uvc.m ├── example_geo2.m ├── example_inputPreparation.m ├── example_mapping_Cobiveco.m ├── example_mapping_batch_CobivecoX.m ├── example_parcellation.m ├── example_parcellation_geo2.m ├── example_polarProjection.m ├── extractExtraTriangles.py ├── extractfunc_bridge.py ├── geo1 │ ├── heart.vtp │ ├── heart.vtu │ └── heart_for_UVC.vtp ├── geo1_fine │ ├── heart.vtp │ ├── heart.vtu │ └── heart_for_UVC.vtp ├── geo2 │ ├── heart.vtu │ ├── heart_base.ply │ ├── heart_endo_lv.ply │ ├── heart_endo_rv.ply │ └── heart_epi.ply └── geo3 │ └── heart_original.vtu ├── functions ├── AxelRot.m ├── baryInterpMat.m ├── calculatePointsAligningWithRotatedVector.m ├── calculateValveReferenceVector.m ├── calculateValveReferenceVector_update.m ├── colormapCoolWarm.m ├── colormapDiverging.m ├── computeLongAxis.m ├── createBoundarySurfaceRVLVOnVentricle.m ├── createBoundarySurfacesAB.m ├── createBoundarySurfacesRT.m ├── createGraphFromStruct.m ├── createTissueArea.m ├── createValveCenterConnectingVectors.m ├── defineBridgesShortestPath.m ├── filterGlobalIndicesEndo.m ├── findMatchingPointinEpi.m ├── findPointInGraph.m ├── functionsForCreatingEllipsoidAndSmallSpheres │ ├── constructTissueEllipsoid.asv │ ├── constructTissueEllipsoidWithSmallSpheres.m │ ├── constructTissueEllipsoidWithoutSavingIndices.m │ ├── determiningCentroidInCartesian.m │ ├── determiningPointIndicesTissueEllipsoid.m │ └── determiningSphereCentersCartesian.m ├── ichol_autocomp.m ├── mapCartesianToCobivecoX.m ├── mapCoordinateFromMeshToSubmeshBary.m ├── mapGlobalIndexToGraphIndex.m ├── mapSurfaceClassesOnToBridge.m ├── mmg.m ├── mmgReadMesh.m ├── mmgWriteMesh.m ├── mmgWriteSol.m ├── normalizedGradField.m ├── pcaSurfaceNormal.m ├── plotImages2Grid.ipynb ├── plotValveAxis.m ├── polydata2unstrucgrid.py ├── prepareMeshVentricularVolume.m ├── prepareSeptalSurface.m ├── projectSurOnToPlane.m ├── secant.m ├── solveLaplace.m ├── solveTrajectDist.m ├── updateOutliersWithNeighborValues.m └── visualizeStartingPointsPath.m ├── requirements.txt └── utilities ├── cobiveco_applyAlignmentMatrix.m ├── cobiveco_computeMappingMatrix.m ├── cobiveco_computeMappingMatrix_briges.m ├── cobiveco_createPolarProjection.m └── inputPreparation ├── SplitMesh.m ├── cobivecoX_surface_preparation ├── README_Input_file_preparation_CobivecoX.md ├── data │ ├── input │ │ └── README.md │ └── output │ │ └── README.md └── scripts │ ├── cp2cobiveco.py │ ├── extract.py │ ├── extract_midmyocard.py │ ├── extractfunc.py │ ├── extractfunc_orig.py │ ├── msh2ply.py │ ├── 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