Dataset Open Access

Virtual cohort of extreme and average four-chamber heart meshes from statistical shape model

Rodero, Cristobal; Strocchi, Marina; Marciniak, Maciej; Longobardi, Stefano; Whitaker, John; O'Neill, Mark D.; Gillette, Karli; Augustin, Christoph; Plank, Gernot; Vigmond, Edward J.; Lamata, Pablo; Niederer, Steven A.

Dataset Description: We present a database of four-chamber heart models derived from a statistical shape model (SSM) suitable for electro-mechanical (EM) simulations. Our database consists of 39 four-chamber heart models generated from end-diastolic CT-derived meshes (available in the repository called ("Virtual cohort of adult healthy four-chamber heart meshes from CT images"). These meshes were used for EM simulations. The output of the simulations and the weights of the SSM are also provided.

Cardiac meshes: To build the SSM, we rigidly aligned the CT cohort and extracted the surfaces, representing them as deRham currents. The registration between meshes and computation of the average shape was done using a Large Deformation Diffeomorphic Metric Mapping method. The deformation functions depend on a set of uniformly distributed control points in which the shapes are embedded, and on the deformation vectors attached to these points. It is in this spatial field of deformation vectors (one per each control point) where the Principal Component Analysis is applied. Case #20 of the CT cohort was not included. More information on the details can be found in Supplement 3 of the reference paper. We created two extra cohorts by modifying the weight of the modes explaining 90%of the variance in shape (corresponding to modes 1 to 9). We created these meshes with either ±2 or ±3 standard deviations (SD) of each mode added to the average mesh (extreme2 and extreme3 cohorts respectively). We also created two additional meshes with ±1 SD for mode 2 (extreme1 cohort). The elements of all the meshes are labelled as follows:

  1. Left ventricle myocardium
  2. Right ventricle myocardium
  3. Left atrium myocardium
  4. Right atrium myocardium
  5. Aorta wall
  6. Pulmonary artery wall
  7. Mitral valve plane
  8. Tricuspid valve plane
  9. Aortic valve plane
  10. Pulmonary valve plane
  11. Left atrium appendage "inlet"
  12. Left superior pulmonary vein inlet
  13. Left inferior pulmonary vein inlet
  14. Right inferior pulmonary vein inlet
  15. Right superior pulmonary vein inlet
  16. Superior vena cava inlet
  17. Inferior vena cava inlet
  18. Left atrial appendage border
  19. Right inferior pulmonary vein border
  20. Left inferior pulmonary vein border
  21. Left superior pulmonary vein border
  22. Right superior pulmonary vein border
  23. Superior vena cava border
  24. Inferior vena cava border

Ventricular fibres were generated using a rule-based method, with a fibre orientation varying transmurally from endocardium to epicardium from 80˚ to -60˚, respectively.  We defined a system of universal ventricular coordinates on the meshes: an apico-basal coordinate (Z) varying continuously from 0 at the apex to 1 at the base (defined with the mitral and tricuspid valve); a transmural coordinate (\(\rho\)) varying continuously from 0 at the endocardium to 1 at the epicardium; a rotational coordinate (\(\phi\)) varying continuously from – π at the left ventricular free wall, 0 at the septum and then back to + π at the left ventricular free wall; intra-ventricular coordinate (V) defined at -1 at the left ventricle and +1 at the right ventricle. This coordinate system was assigned to the ventricles in the four-chamber meshes and all the other labels were assigned with -10.  

 We provide a zipped folder for each mesh, A VTK file for each mesh was included (in ASCII) as an UNSTRUCTURED GRID. In all the cases the following fields were included:

  • POINTS, with the coordinates of the points in mm.
  • CELL_TYPES, having all of the points the value 10 since they are tetrahedra.
  • CELLS, with the indices of the vertices of every element.
  • CELL_DATA, corresponding to the meshing tags. 
  • VECTORS, with the directions of the fibres.
  • POINT_DATA, with four LOOKUP_TABLE subfields corresponding to the UVC in the order \(\rho\), \(\phi\), Z and V.

We provide the average mesh, and the extreme1, extreme2 and extreme3 cohorts. These correspond to the files of the form modeX±1SD for extreme 1, modeX±2SD for extreme2 and modeX±3SD for extreme3. These meshes have been used to interpret the anatomical meaning of modifying each mode.

Cardiac simulations: For the cardiac EM simulations we used CARP (Cardiac Arrhythmia Research Package). We used the reaction-eikonal model for electrophysiology, stimulating as initial condition the bottom third (Z < 0.33) of the endocardium. We simulated the large deformation mechanics in a Lagrangian reference system. The ventricular myocardium was modelled as a hyperelastic transversely isotropic material with Guccione's strain energy function. The remaining tissues were modelled as non-contracting neo-Hookean materials. Simulations diverged for cases mode2-3SD, mode3+3SD, mode6-3SD, mode9-3SD and mode2-2SD . Details on the specific parametrisation can be found in the supplements of the reference paper.

We provide comma-separated-values files with the output of the simulations used in the reference paper for validation purposes. The simulations of the cases that did not converge were not included. The acronyms used in the names of columns are:

  • EDP: End-diastolic pressure
  • EDV: End-diastolic volume
  • Myo_vol: Myocardial volume of the ventricle (as sum of its elements)
  • ESV: End-systolic volume
  • SV: Stroke volume 
  • EF: Ejection fraction
  • V1: Volume at time of peak flow
  • EF1: First-Phase Ejection Fraction
  • ESP: End-systolic pressure
  • dPdtmax: Maximum increase of pressure
  • dPdtmin: Maximum decrease of pressure
  • PeakP: Peak pressure
  • tpeak: Time to peak pressure
  • ET: Ejection time
  • ICT: Isovolumic contraction time
  • IRT: Isovolumic relaxation time
  • tsys: Duration of systole
  • QRS: QRS duration
  • AT1090: Time taken to activate from 10% to 90% of the mesh
  • AT: Activation time of the left ventricle

Besides the output value name, in each column is specified the ventricle where that output was extracted from with the suffixes "_LV" or "_RV".

SSM weights:  Each one of the meshes can be approximated as a linear combination of the shape modes, extracted using Principal Component Analysis on the space where the meshes are located. We provide the weights for each mesh in a comma-separated-values file.

We have added 1000 more meshes from the same statistical shape model, modifying the weights from the PCA randomly within the 2SD range. These meshes are provided in the repository named "Virtual cohort of 1000 synthetic heart meshes from the adult human healthy population".

GP received support from the Austrian Science Fund (FWF) (https://fwf.ac.at/en/); grant number PI2760-B30. PL is supported by BHF [PG/16/75/32383]. SAN is supported by NIH R01-HL152256, ERC PREDICT-HF 453 (864055) and BHF (RG/20/4/34803).
Files (2.3 GB)
Name Size
average.tar.gz
md5:992f31e20c1aa73c10c5d9a6b6ac903a
58.2 MB Download
mode1+2SD.tar.gz
md5:a5956442c48f124f272db79503d50edd
59.7 MB Download
mode1+3SD.tar.gz
md5:18fb9f9f837e8305a742c860e54a9081
62.9 MB Download
mode1-2SD.tar.gz
md5:b37f771a566090c16bd3a5677c525d9f
61.9 MB Download
mode1-3SD.tar.gz
md5:0b5c14da3a309a48fd3da3f586007cf9
65.8 MB Download
mode2+1SD.tar.gz
md5:d710264ed1de6262eab517e29974f321
65.0 MB Download
mode2+2SD.tar.gz
md5:41e49922a06e225bb0669edd7f4bceff
74.0 MB Download
mode2+3SD.tar.gz
md5:897cc3127db94cd87f703bd7f6a20d1d
85.0 MB Download
mode2-1SD.tar.gz
md5:6a0bbee8a0b26c4d966d37a20eca2ce2
53.3 MB Download
mode2-2SD.tar.gz
md5:edde5399825d250d1017afcfeba60ea2
51.2 MB Download
mode2-3SD.tar.gz
md5:540bb6c3040f653db104b25da2ab0eda
52.4 MB Download
mode3+2SD.tar.gz
md5:1d3f54cc0c429177292a26dada36022e
66.3 MB Download
mode3+3SD.tar.gz
md5:e0a53d0b98c39565404bf2d258c219fd
71.7 MB Download
mode3-2SD.tar.gz
md5:23ef8798e6180d0b66ff11cb92d98bb6
53.3 MB Download
mode3-3SD.tar.gz
md5:7de3fd0508ba25dcea192cca5a6b72ac
52.6 MB Download
mode4+2SD.tar.gz
md5:75a4df9a240b77d867cfeed1f6597ed6
58.5 MB Download
mode4+3SD.tar.gz
md5:dfdb5316d31b86544cfd03ca42165f61
59.0 MB Download
mode4-2SD.tar.gz
md5:9b0f7c63ee15d6f293159c4bbbb17b85
59.2 MB Download
mode4-3SD.tar.gz
md5:8ac4dee6a6745aa45f48fe08fa5ca2f7
60.5 MB Download
mode5+2SD.tar.gz
md5:9bf8087ac4ddf6e1d45d459a5e9e6ad2
58.0 MB Download
mode5+3SD.tar.gz
md5:06e94a4578a88f04821ce83c9af2ee5c
58.6 MB Download
mode5-2SD.tar.gz
md5:19d8c8410d909b6b463a036c7d889c70
59.9 MB Download
mode5-3SD.tar.gz
md5:5fbd459848e01fdd1d7fbe1b893863bf
61.2 MB Download
mode6+2SD.tar.gz
md5:6401ab97a2aaa9426173ab3420f3d9ef
58.0 MB Download
mode6+3SD.tar.gz
md5:84b01087014007ae9e4f4702420feb79
61.5 MB Download
mode6-2SD.tar.gz
md5:82d0ce9fe76cabda8f8627e3b5e11325
56.8 MB Download
mode6-3SD.tar.gz
md5:3bcfca61a7ec86102d1e368b2023611c
56.3 MB Download
mode7+2SD.tar.gz
md5:4bc86b068cc884f8662fb35f2c90f3d8
55.8 MB Download
mode7+3SD.tar.gz
md5:461a8a87546ce73804596147e6f219ea
54.9 MB Download
mode7-2SD.tar.gz
md5:3761c62bebbebcb548a79facfc48d1ae
61.3 MB Download
mode7-3SD.tar.gz
md5:fc62b7b4ac34648f013cc83e7793104a
63.1 MB Download
mode8+2SD.tar.gz
md5:3ea1a98b4552247dfac8e10d4a3c8fa0
59.3 MB Download
mode8+3SD.tar.gz
md5:0679972fd4ea22b7ebceb08f3d5ce447
60.0 MB Download
mode8-2SD.tar.gz
md5:1f6a7a906caec73d82d776bdec11aff6
57.6 MB Download
mode8-3SD.tar.gz
md5:2f69ba6f1df4eb01647d8a86bb6e1605
57.5 MB Download
mode9+2SD.tar.gz
md5:66e85bf686e01614d59733639d40c48a
62.5 MB Download
mode9+3SD.tar.gz
md5:eb22db85eb0f99059a31a23bc961837d
64.7 MB Download
mode9-2SD.tar.gz
md5:a9a41f8bc5b6ec87eee7bcaf582af706
54.1 MB Download
mode9-3SD.tar.gz
md5:2d20faf8c24382f5d5ee48d8e42bcca4
52.1 MB Download
modes_weights.csv
md5:fdccb9bdba01d7f6ca2d83b9a4bfb27e
2.3 kB Download
simulation_output.csv
md5:d355c1e073a389abccf16f12d3b79c63
8.1 kB Download
  • Rodero et al. (2021), "Linking statistical shape models and simulated function in the healthy adult human heart". DOI: 10.1371/journal.pcbi.1008851

650
739
views
downloads
All versions This version
Views 650650
Downloads 739739
Data volume 22.0 GB22.0 GB
Unique views 595595
Unique downloads 421421

Share

Cite as