Personalization of cubic Hermite meshes for efficient biomechanical simulations.
ABSTRACT Cubic Hermite meshes provide an efficient representation of anatomy, and are useful for simulating soft tissue mechanics. However, their personalization can be a complex, time consuming and labour-intensive process. This paper presents a method based on image registration and using an existing template for deriving a patient-specific cubic Hermite mesh. Its key contribution is a solution to customise a Hermite continuous description of a shape with the use of a discrete warping field. Fitting accuracy is first tested and quantified against an analytical ground truth solution. To then demonstrate its clinical utility, a generic cubic Hermite heart ventricular model is personalized to the anatomy of a patient, and its mechanical stability is successfully tested. The method achieves an easy, fast and accurate personalization of cubic Hermite meshes, constituting a crucial step for the clinical adoption of physiological simulations.
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ABSTRACT: Anatomically based finite element geometries are becoming increasingly popular in physiological modelling, owing to the demand for modelling that links organ function to spatially distributed properties at the protein, cell and tissue level. We present a collection of anatomically based finite element geometries of the musculo-skeletal system and other organs suitable for use in continuum analysis. These meshes are derived from the widely used Visible Human (VH) dataset and constitute a contribution to the world wide International Union of Physiological Sciences (IUPS) Physiome Project (www.physiome.org.nz). The method of mesh generation and fitting of tricubic Hermite volume meshes to a given dataset is illustrated using a least-squares algorithm that is modified with smoothing (Sobolev) constraints via the penalty method to account for sparse and scattered data. A technique ("host mesh" fitting) based on "free-form" deformation (FFD) is used to customise the fitted (generic) geometry. Lung lobes, the rectus femoris muscle and the lower limb bones are used as examples to illustrate these methods. Geometries of the lower limb, knee joint, forearm and neck are also presented. Finally, the issues and limitations of the methods are discussed.Biomechanics and Modeling in Mechanobiology 04/2004; 2(3):139-55. · 3.33 Impact Factor
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ABSTRACT: A computational framework is presented for integrating the electrical, mechanical and biochemical functions of the heart. Finite element techniques are used to solve the large-deformation soft tissue mechanics using orthotropic constitutive laws based in the measured fibre-sheet structure of myocardial (heart muscle) tissue. The reaction-diffusion equations governing electrical current flow in the heart are solved on a grid of deforming material points which access systems of ODEs representing the cellular processes underlying the cardiac action potential. Navier-Stokes equations are solved for coronary blood flow in a system of branching blood vessels embedded in the deforming myocardium and the delivery of oxygen and metabolites is coupled to the energy-dependent cellular processes. The framework presented here for modelling coupled physical conservation laws at the tissue and organ levels is also appropriate for other organ systems in the body and we briefly discuss applications to the lungs and the musculo-skeletal system. The computational framework is also designed to reach down to subcellular processes, including signal transduction cascades and metabolic pathways as well as ion channel electrophysiology, and we discuss the development of ontologies and markup language standards that will help link the tissue and organ level models to the vast array of gene and protein data that are now available in web-accessible databases.Acta Numerica 01/2004; 13.
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ABSTRACT: In this study, we review the development and application of multi-physics and multi-scale coupling in the construction of whole-heart physiological models. Through an examination of recent computational modelling developments, we analyse the significance of coupling mechanisms for the increased understanding of cardiac function in the areas of excitation-contraction, coronary blood flow and ventricular fluid mechanical coupling. Within these physiological domains, we demonstrate and discuss the importance of model parametrization, imaging-based model anatomy and computational implementation.Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences 07/2009; 367(1896):2311-31. · 2.89 Impact Factor
Personalization of Cubic Hermite Meshes for
Efficient Biomechanical Simulations
Pablo Lamata1, Steven Niederer1, David Barber2, David Norsletten1,
Jack Lee1, Rod Hose2, and Nic Smith1
1Computing Laboratory, University of Oxford, UK
2Department of Cardiovascular Science, University of Sheffield, UK
Abstract. Cubic Hermite meshes provide an efficient representation of
anatomy, and are useful for simulating soft tissue mechanics. However,
their personalization can be a complex, time consuming and labour-
intensive process. This paper presents a method based on image reg-
istration and using an existing template for deriving a patient-specific
cubic Hermite mesh. Its key contribution is a solution to customise a
Hermite continuous description of a shape with the use of a discrete
warping field. Fitting accuracy is first tested and quantified against an
analytical ground truth solution. To then demonstrate its clinical utility,
a generic cubic Hermite heart ventricular model is personalized to the
anatomy of a patient, and its mechanical stability is successfully tested.
The method achieves an easy, fast and accurate personalization of cubic
Hermite meshes, constituting a crucial step for the clinical adoption of
Computational physiology provides tools to quantitatively describe physiological
behaviour across a range of time scales and anatomical levels using mathemat-
ical and computational models [1,2]. The heart is arguably the most advanced
current exemplar of this approach [3,4], and ongoing developments now have the
potential to provide a significant impact in the management of cardiovascular
diseases. One of the key challenges in fulfilling this potential is the personaliza-
tion of models to represent the clinical status of a patient. This work focuses on
the efficient and automated development of patient-specific geometrical descrip-
tion of organs for biomechanical simulations.
A computational model requires the geometrical description of the solution do-
main where material constitutive equations are solved. The most popular choice
is linearly interpolated tetrahedral meshes, mainly due to its conceptual simplic-
ity and availability of tools for an automatic mesh generation . Nevertheless,
they introduce significant numerical error in the solution of the displacements in
the soft tissue deformation problem . Alternatively, cubic Hermite meshes are
T. Jiang et al. (Eds.): MICCAI 2010, Part II, LNCS 6362, pp. 380–387, 2010.
c ? Springer-Verlag Berlin Heidelberg 2010
Cubic Hermite Personalization381
an efficient representation of the geometrical state of an organ, and a more suit-
able choice for biomechanical simulations compared to tetrahedral meshes .
Another important requirement is mesh robustness, related to the convergence
of simulation results in changing physiological conditions. For these reasons, cu-
bic Hermite meshes are a popular choice for the simulation of heart mechanical
deformations [7,8,9]. Nevertheless, construction of these meshes can be a com-
plex, time consuming and labour-intense process. There is thus a need for a fast,
accurate, robust and easy to use cubic Hermite personalization method.
There are two broad approaches for the personalization of geometrical meshes:
construction from segmented images [5,10] or customization from an existing
mesh model [11,10]. Whereas the literature for linear meshes is extensive , its
translation to Hermite meshes is not straightforward.The change of interpolation
scheme, from linear to Hermite functions, requires a completely different meshing
strategy, like the adaptation of the Iterative Closest Point proposed in . In a
Hermite mesh shape is interpolated, not only from the 3D Cartesian coordinates
of nodes, but also from the derivatives of shape versus local finite element (FE)
coordinates. This enables a compact representation, but results in a complex
mesh construction and customization. This article presents an image registration
based solution for cubic Hermite mesh personalization.
2Material and Methods
The proposed personalization method combines a fast binary image registration
with a cubic Hermite warping technique. A schematic illustration of the complete
process is provided in Fig.1.
Fig.1. Dataflow designed to generate patient specific cubic Hermite meshes
382P. Lamata et al.
2.1 Image Registration
A binary image registration technique using a fast optical flow algorithm pro-
posed in  is chosen for its robustness, accuracy and computational efficiency.
It requires a preliminary segmentation of the patient’s anatomy, which in the
case of heart ventricles from static MRI or CT is a quite mature field of research.
Discrete values of the warping field between the two binary images are defined
at nodes of a regular hexahedral grid superimposed on the binary image of the
template shape. The two main parameters of the registration technique are the
spacing between nodes D and the smoothing weighting factor λ (based on a
Tikhonov regularisation of the linear least squares problem). Registration is ini-
tialised by aligning the principal axis of the shapes after a Principal Component
Analysis of the 3D coordinates of each shape.
2.2 Cubic Hermite Mesh Warping
A cubic Hermite mesh is a set of 3D FE that uses Hermite interpolation func-
tions. Mesh nodes have both coordinate values and derivatives (single, double
and triple cross derivatives) in order to encode a C1shape. Let u(ξ1,ξ2,ξ3) be
a shape defined in the Cartesian space as a function of the material coordinates
ξ. The four 1D Hermite interpolation basis functions are described in (1), and
interpolation in a line element u(ξ) is given by a linear combination of these four
basis functions (2). This scheme can be extended to 3D as illustrated in Fig.2,
u(ξ1,ξ2,ξ3) is then interpolated from a total of 192 variables in each element.
1(ξ) = 1 − 3ξ2+ 2ξ3; ψ0
2(ξ) = ξ2(3 − 2ξ)
2(ξ) = ξ2(ξ − 1)
1(ξ) = ξ(ξ − 1)2; ψ1
u(ξ) = ψ0
Warping a cubic Hermite mesh therefore implies calculation of a deformed state
of its three coordinate fields (x,y,z). The total number of degrees of freedom is
therefore Ndof = 3 × 8 × n = 24n, being n the number of nodes of the mesh.
Note that this number will be slightly smaller if the mesh has collapsed elements,
and slightly bigger if there are discontinuities modelled with different versions
of node values. For further details about these meshes see .
The solution for the warping of a cubic Hermite mesh is the core contribution
of this work. This third step in Fig.1 calculates the optimal description of a
warped shape with Hermite interpolation functions. This is built on three basic
concepts. First, it is important to realise that the warping of a FE requires know-
ing the warping field throughout the complete domain, and not only in the local
neighbourhood of mesh nodes. Second, the solution uses a FEM technique for
finding an optimal representation of a field in a domain, i.e. it uses a variational
formulation of the problem based on a dot product of functions. And third, a
numerical technique is required to handle continuous domains with computer
discrete representations, i.e. a numerical integration method is used to calculate
the dot product of functions.
Cubic Hermite Personalization383
Fig.2. Cubic Hermite meshes. (a) A two element mesh, showing the vectors corre-
sponding to the 7 derivatives at each node; (b) template of truncated left and right
ventricles of the heart. This complex shape is represented with only 112 cubic elements
(cubes with black lines) and 183 nodes.
The central idea is that warping of a cubic Hermite mesh is an addition of a FE
description of a warping field. It requires finding the adequate FE description,
with a set of Ndof variables as described before, of the warping field. And this
description is then added to the corresponding Ndof nodal variables describing
the 3 coordinate fields, i.e. the shape. Let us define a variational problem for
finding the C1continuous function g that approximates w, one of the three
components of the warping field W in the domain defined by the cubic Hermite
template ΘT. Let g be formulated as a linear combination of the set of Ndof/3
basis functions φTof the mesh. Note that each φTis a combination of 3D Hermite
basis from adjacent elements in order to enforce the continuity of the function
and its derivatives. Let us introduce the definition of a dot product of functions:
Finding g becomes the problem of finding the ci coefficients (or nodal values)
which satisfy a set of Ndof/3 equations, one for each basis φT:
(g,φj) = (w,φj)∀φj
Mx = b
where vector x is the set of Ndof/3 coefficients ci, and integrals required to
calculate matrix M and vector b are computed using Gaussian Quadrature.
Calculi of vector b uses order 4, and cubic interpolation of the warping field is
used to calculate the data (deformation field) at Gauss Points. The linear system
of the fitting process requires the solution of a sparse matrix system. This matrix
is symmetric and positive definite, allowing the use of fast, low-memory solvers
such as Conjugate Gradients.
384P. Lamata et al.
3.1Analytical Workbench for Accuracy and Robustness Analysis
Accuracy and sensitivity to parameters are analysed using a virtual workbench
with known analytical solutions. Three experiments study the accuracy of (1)
proposed warping scheme, step 3 in Fig.1, (2) the binary image registration, step
2 in Fig.1, and (3) the concatenation of the two processes. Template cylinders are
built with dimensions 30, 10 and 5mm in length, outer and internal radius, and
with 24, 81 and 192 elements. Warped versions of these cylinders are generated
under two known warping fields W1and W2, see Fig.3. Shape error is calculated
in each element as the integral of the RMS error between warped coordinates
field and their ground truth. An order 5 Gaussian Quadrature volume-weighted
integration of error is used, which is independent of the mesh discretisation
resolution and topology.
The warping step is analysed by using a perfect solution of the registration
step, obtained by sampling the ground truth warping fields. This experiment is
repeated for W1and W2, for the three cylinder mesh resolutions and for a range
of node spacings in the discretisation of the warping field (SW, with 9 values from
1 to 5 mm in steps of 0.5mm). Average shape error is 5.5e−3and 5.5e−2mm2
for W1 and W2 respectively, and the dependence with the two factors (mesh
resolution and SW) is illustrated in Fig.4.
The registration step is analysed by comparison of obtained warping fields
with their analytical expression. Binary images are generated from the Ground
Truth shapes. Registration is performed for each W1and W2, for a total of 49
binary image resolutions (from 0.2mm to 5mm in steps of 0.1mm), and for 9
values of node spacing (D from 2 to 10 voxels). The smoothing coefficient λ is
set automatically by an empirical theorem proposed in . Average registration
volume-weighted error is 1.86 and 0.69mm RMS for W1 and W2 respectively,
results are shown in Fig.5.
(b) W1 = (x3,x3,1)
(c) W2 = (sin(z),0,0)
Fig.3. GroundTruth. All three shapes (template, customised by W1 and customised
by W2) are created with three resolutions (24, 81 and 192 elements).
Cubic Hermite Personalization 385
Shape error (mm RMS)
Shape error (mm RMS)
Fig.4. Error introduced in the warping of cubic Hermite meshes using a discrete ver-
sion of the ideal warping fields W1 and W2. (a) Dependence on sampling resolution,
(SW), averaging results with three mesh resolutions. (b) Dependence on mesh resolu-
tion, averaging results with nine sampling resolutions.
Binary image voxel length (mm)
Shape error (mm RMS)
Node spacing (voxels)
Shape error (mm RMS)
Fig.5. Registration error (volume-weighted integral) for warping fields W1 and W2.
(a) Dependence on image resolution, averaging results with 9 node spacings. (b) De-
pendence on node spacing, averaging results with 49 image resolutions.
The previous two steps are concatenated, and template cylinder meshes are
warped with the result of binary image registrations. The mesh resolution of 81
elements is chosen for this experiment, since higher resolutions did not introduce
any significant improvement in accuracy, see Fig.4b. The analysis is repeated for
W1and W2, for all 49 binary image resolutions (from 0.2mm to 5mm in steps of
0.1mm), and for 9 node spacing (from 2 to 10 voxels). The average shape error
for W1and W2is 1.90 and 0.702mm RMS respectively, an increment of roughly a
1.5% with respect to the registration error. The dependence on binary resolution
and node spacing is the same as reported for the registration step, see Fig.5.
A patient specific cubic Hermite mesh of heart ventricles is constructed following
the process of Fig.1. The template mesh chosen is the result of fitting a mesh to
the anatomy of a first patient following the methodology described in  and
386P. Lamata et al.
illustrated in Fig.2. A T1 MRI heart study of a second patient (0.88x0.88x0.75
mm voxel resolution) is manually segmented and truncated just underneath of
the opening of valve planes after vertical alignment. The agreement between
segmentation and resulting cubic Hermite mesh is shown in Fig.6, and the av-
erage distance between the two surfaces is measured as 1.32mm. The process
from image segmentation to mesh fitting for this biventricular dataset of 903
voxels requires about one minute. Mechanical stability of personalised geometry
is successfully tested by simulating a passive inflation and an isochronous active
contraction of the heart following the methods described in .
Fig.6. Shape personalization result. Comparison of the isosurface of the binary manual
segmentation (red wireframe) to the Cubic Hermite mesh (white solid).
Cubic Hermite mesh warping requires the addition of an adequate representation
of the warping field in nodal values and derivatives. The proposed solution finds
an optimal description of this field, leading to reasonable accurate results.
Results show the importance of the registration step, which is limited by
image resolution. Interpolation errors also become significant when the topology
of the mesh is not able to represent the warped shape. These cases require an
interpolation order higher than cubic or higher element refinement, such as case
W2. An inherent limitation of proposed approach is that binary registration only
aligns the surfaces of models, interpolating the warping inside. This is a valid
approach for vessels and computational fluid dynamics , and preliminary
results suggest that this is also adequate for the flat walls of the heart.
The proposed method is its simpler and more robust compared to the state of
the art alternatives, the ”host mesh” technique  or the mesh generation by
fitting Hermite surfaces from a linear scaffold . Proposed method is fast and
requires minimal user interaction. In comparison, the two alternative methods
greatly depend on users expertise, and it can take hours of manual interaction
and fitting to get satisfactory results. A second advantage is that, because it
uses a voxelized description of the shape and not a selection of pairs of control
points and degrees of freedom as required in a ”host mesh” technique, it is
immune to subjective and sometimes arbitrary selection of parameters. Finally,
warping an existing high quality template mesh under a smoothness constraint
is a reasonable warranty of simulation stability in the resulting mesh. This does
not occur using a mesh generation from an arbitrary initial linear mesh .
Further experiments with higher number of cases are nevertheless required to
Cubic Hermite Personalization 387
generalise and accept these desirable properties. Future works will also address
the characterization and development of a metric of mechanical stability of cubic
Hermite meshes, a metric to be optimised during the personalization process.
Proposed method achieves an easy, fast and accurate personalization of cubic
Hermite meshes, constituting a crucial step for the clinical adoption of biome-
chanical physiological simulations.
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