RulE baSed atrIaL fIber gENeraTor.
RESILIENT is a rule-based atrial fiber generator for generating bi-atrial fibers and interatrial bridges. The algorithm was developed at IBT and published in Wachter et al. 2015 [1]. The algorithm works with triangle, terahedron and voxel meshes. The fibers are based on 22 seedpoints: 9 in the right atrium and 13 in the left atrium. They have to be selected by the user as described in [1].
To install and run RESILIENT, you need:
- VTK (https://gitlab.kitware.com/vtk/vtk), tested with version 8
- GMP (https://gmplib.org)
- Cork (https://github.com/gilbo/cork)
- Tetgen (http://www.tetgen.org)
Install these using your package manager (apt, homebrew, macports...) or download the source code directly.
When compiling cork from source, make sure to give the correct paths to gmp in the "makeConstants" file.
The standard path where we look for cork is a subfolder "cork" here. For tetgen, it's "tetgen1.6.0".
We use CMake to configure the build process. If your dependencies are in non-standard locations, you might need to pass these paths to CMake.
git clone https://github.com/KIT-IBT/RESILIENT.git
cd RESILIENT
cmake .
make
sudo make install
The atrial mesh requires special endo/epi materials (element data array called "Material" in the input VTK file) and should be divided into left and right atrium for the algorithm. The setpum can be part of the left atrium only or split into left/right. Both options should work.
Materials
Material 32 for the right epicardium
Material 33 for the left epicardium
Material 129 for the right endocardium
Material 233 for the left endocardium
The atrial mesh requires special epi materials (element data array called "Material" in the input VTK file) and should be divided into left and right atrium for the algorithm. The artia should be closed, i.e., the valves should be filled with blood (material: 150 right / 151 left). The setpum can be part of the left atrium only or split into left/right. Both options should work.
Materials
Material 32 for the right epicardium
Material 33 for the left epicardium
The seed points defining anatomical landmarks comprise 9 points in the right atrium and 13 points in the left atrium.
These point have to be manually annotated in every mesh by the user. It is important that the points do not lie in extrema of the surface.
The first three points in the right atrium describe the orifice of the superior caval vein. "R1" is located on the back side of the right atrium at the borderline between the right and the left atrium. "R2" is located on the front side of the right atrium at the borderline between the right and the left atrium. "R3" is located on the back side of the right atrium at the junction with the right atrial appendage. With these three points, it should be possible to construct a ring. That means that the shortest path in the material between the points "R2" and "R3“ may not cross the shortest path between "R1" and "R2" or between "R3" and "R2". The points "R4" and "R5" describe the orifice of the inferior caval vein. "R4" is located on the right side of the orifice and "R5" on the left side on the front side of the right atrium. The shortest path between these points has to be on the front side of the orifice. The point "R6" marks the peak of the right atrial appendage over the opening of the right atrial appendage. The last three right atrial points describe the ring of the tricuspidal valve. Point "R7" is located below the right appendage. "R9" is the point of the orifice closest to the left atrium. "R8" is located on the other side of the orifice. It is important the shortest path in material between the points "R8" and "R9" does not cross the shortest paths between "R7" and "R8" or between "R7" and "R9". The first three points in the left atrium describe the ring of the orifice of the mitral valve. "L1" is located on the left lateral side below the left appendage. "L3" is on the right lateral side of the left atrium, approximately the point of the orifice closest to the right atrium. It is important that the shortest path in material between these two points on the front wall of the left atrium. "L2" is located approximately in the middle of the posterior side of the orifice. Point "L4" is on the top of the front side of the left atrium, it is located at the beginning of the right superior pulmonary vein. "L5" is also located on the top of the front wall at the beginning of the left superior pulmonary vein. Normally, it is between the left appendage and the left superior pulmonary vein. The next two points are on the top wall of the left atrium. "L6" marks a point between the right pulmonary veins and "L7" marks a point between both left pulmonary veins. The points "L8" and "L9" are located on the top of the posterior wall of the left atrium. "L8" marks the beginning of the right and "L9" the beginning of the left inferior pulmonary vein. The points "L10" and "L11" describe the left appendage. "L11" marks the peak of the left appendage over the opening of the right appendage and "L10" is located on the front wall of the left atrium and describes the excrescence of the left appendage on the front wall. The point "L12" is located on the left lateral wall over the left appendage between both left pulmonary veins, almost directly below of the point "L7". It is important that the points "L5", "L7" and "L12" construct a ring of the orifice of the left superior pulmonary vein. The point "L13" is located on the right lateral wall of the left atrium below the right inferior pulmonary vein. It is important that the points "L6", "L8" and "L13" construct a ring of the orifice of the right inferior pulmonary vein.
For each three points on a common opening, make sure that the shortest path between two of these points is the path that does not include the third point. For example: L1L2L3: the path from L1 to L2 in clockwise direction (on the image above) is shorter than the path between L2 and L1 also in clockwise direction, since L3 is in between.
The position of the seed points taken by the algorithm can be checked in the mesh with the tool: FindAndMarkSeedPoints.
The points have to be provided in a TXT-file with the following syntax:
SCV1 G 12.2 -23.4 57.5
SCV2 G 13 -25 79
...
...
SCV9 G 48 27 -30
LV1 G 59 -45 -98
LV2 G 97 -45 -108
...
...
LV13 G -105 23 -39
If you want an additional bridge between the atria, you can define as follows in a TXT-file.
point-left-atrium (XYZ) point-right-atrium (XYZ) material bridge-radius
xl yl zl xr yr zr Material Bridgeradius
RESILIENT rParameter1 rParameter2 rParameter3 oParameter1 oParameter2 [...]
If you need help with parameter selection, just run RESILENT on the command line. Then, the options will appear.
<path for input datafile *.vtu | vtp | vtk>
<path for output datafile *.vtu | vtp | vtk>
<path for seedpoints file *.txt>
[-intermediateResultPrefix] (default: inputdataname): prefix for intermediate results
[-writeIntermediateData]: for saving intermediate Results
[-noOpenVTPBridgeInAtrial]: open atrial Bridges in VTP
[-noRightAtrium]
[-noBachmannBundle]
[-noWideBachmann]: if you wouldn't have wide Bachmann Bundle from the right to the left atrial appendeage
[-noUpperPosteriorBridge]
[-noMiddlePosteriorBridge]
[-noCoronarySinusBridge]
[-lowerAnteriorBridge]
[-upperAnteriorBridge]
[-writeViewFiberOrientation]: write out the orginal fiber orientation in the cell for illustration
[-numberOfPectinateMuscles N] (default: 15): number of pectinate muscles
[-growPathOffestLeft N] (default: 0): additiv Offset for the path dilatation in left Atrium
[-writeViewFiberOrientation]: growPath transmural in the atria
[-growPathTransmuralPectEndo]: grow endocardial Pectinate muscles in the atria
[-growPathPectFromEndo]: grow radial endocardial Pectinate muscles in the atria from the endocardial surface
[-growPectToRAppendage]: grow Pectinate muscles in the right atria appendeage
[-growCristaDepOnWallthick]: grow Crista Teriminals depending on avarage atrial wall thickness
[-markCoronary]: mark the coronary sinus
[-debug]: if you would have more information when program abort
[-freeBridge PATH]: if you would set free define bridges + definitionfilepath
[-noInitialClean]: no inital clean of the mesh e.g. when they are disconnected
[-noEndCleanup]: no end clean of the mesh e.g. when they are disconnected
[-debug]: if you would have more information when program abort
TestTetrahedralize: This programm can used for testing if a bridge can be tetrahedralized with tetgen.
<path for input datafile *.vtu | vtp | vtk>
FindAndMarkSeedPoints: Mark the localization of the seed points in the mesh by using the material class.
<path for input datafile *.vtu | vtp | vtk>
<path for output datafile *.vtu|vtp|vtk>
<path for seedpoints file *.txt>
Some tissue classes are substituted at the end of the calculation for the simulation.
| Region | algorithm material class | output material class for simulation |
|---|---|---|
| SVC | 159 | 32 |
| IntercavanalBundel | 175 | 32 |
| not right Isthmus | 131 | 32 |
| other right | 187 | 32 |
| Tricusline | 176 | 32 |
| left atrium endo | 233 | 33 |
| other left | 188 | 33 |
| subendo | 130 | 33 |
| subepi | 99 | 33 |
The example meshes provided with the program are stored using git lfs. If are not familiar with using git lfs, just download the meshes from the Gitlab website: https://github.com/KIT-IBT/RESILIENT/tree/main/example
If you don't know if the points are good for the mesh, it makes sense to start RESILENT with the optional Parameter:
RESILENT inputMesh.vtp/vtu/vtk inputMesh_wafo.vtp/vtu/vtk seedPoint.txt -writeIntermediateData -debug
RESILIENT ./example/surface_mesh/mesh_material.vtp ./example/surface_mesh/mesh_with_fiber.vtp ./example/surface_mesh/seedPoint.txt -noInitialClean
RESILIENT ./example/volume_mesh/mesh_material.vtu ./example/volume_mesh/mesh_with_fiber.vtu ./example/volume_mesh/seedPoint.txt -noInitialClean
If the fibers could not be calculated, run RESILIENT again and use the "-writeIntermediateData" flag as well as "-debug" to get additional information useful to track down the issue. In most cases, one or two points are misplaced, so the base paths run incorrectly. Find them and replace them to fix the problem. For this, there is an array "basePath" in the network file where the base paths are stored. Compare them with the following figures.
The basic paths that are calculated in the process of RESILIENT. This can help you if you want to find the possible error in the fiber orientation calculation.
The basic paths in the right atrium, the left atrial epicardium and the automatic bridges:
The basic paths in the right atrial and the left atrial endocardium:
Another problem can be that the dilated paths do not isolate a region. As a result, adjacent areas of the mesh may be annotated. In most cases, you can fix this problem by replacing seed points or with the additional "-dilatation" flag.
The bridges sometimes can't be inserted in the tetrahedral mesh. Then, you'll have to edit the bridge manually. To do this, it is best to use the programs Blender and Meshlab in sequence. Mostly self-intersecting elements and multiple edges are the problem. When you are done, you can test it with the tool TestTetrahedralize.
When using this program, please cite
[1] Andreas Wachter, Axel Loewe, Martin W. Krueger, Olaf Dössel and Gunnar Seemann. "Mesh structure-independent modeling of patient-specific atrial fiber orientation". Current Directions in Biomedical Engineering, 2015, 1(1), 409-412.
When using the example mesh (#5 in [1], please cite:
[2] Axel Loewe, Martin W. Krueger, Fredrik Holmqvist, Olaf Dössel, Gunnar Seemann, Pyotr G. Platonov. "Influence of the earliest right atrial activation site and its proximity to interatrial connections on P-wave morphology". Europace, 2016, 18, iv35-iv43.
@article{Wachter_2015
author = {Andreas Wachter and Axel Loewe and Martin W Krueger and Olaf Dössel and Gunnar Seemann},
doi = {10.1515/cdbme-2015-0099},
url = {https://doi.org/10.1515/cdbme-2015-0099},
title = {Mesh structure-independent modeling of patient-specific atrial fiber orientation},
journal = {Current Directions in Biomedical Engineering},
number = {1},
volume = {1},
year = {2015},
pages = {409--412}
}
Andreas Wachter, Luca Azzolin, Axel Loewe
Institute of Biomedical Engineering, Karlsruhe Institute of Technology (KIT)