ANS MC2015 - Joint International Conference on Mathematics and Computation (M&C), Supercomputing in Nuclear Applications (SNA) and the

Monte
Carlo (MC) Method Nashville, TN April 19-23, 2015, on CD-ROM, American Nuclear Society, LaGrange Park, IL (2015)

Development of a whole-body tetrahedral mesh human phantom for radiation

dose calculations using new MCNP 6.1 geometrical features
Hui Lin, Kristofer Zieb, Yiming Gao, Wei Ji, Peter F. Caracappa and X. George Xu
Rensselaer Polytechnic Institute, Troy, New York 12180
linh7@rpi.edu; xug2@rpi.edu

ABSTRACT
In this study, we developed a whole-body phantom model based on adaptive tetrahedral meshing techniques by
converting a set of segmented images of the Visible Human Project. The newly constructed phantom, called VIPMan was implemented in MCNP6 to calculate organ doses from external beams of photons and electrons with
energies less than 10 MeV in the anteriorposterior (AP) irradiation direction as well as to measure computation
speed. The dose values were then compared with those for the previously developed voxel phantom, called VIPMan . It was found that the organ doses of tetrahedral mesh phantom and voxelized phantom are in good
agreement for the photon exposures considered in this study. The computational speed of using tetrahedral mesh
phantom is about three times slower than voxelized phantom. Although limited radiation types and irradiation
geometries were tested, we are impressed by the performance. It is concluded that the tetrahedral mesh would be a
promising geometric representation for human phantoms which could be accurately and effectively implemented in
radiation transport codes such as the MCNP6.
Key Words: Human phantom, tetrahedral mesh, voxel, MCNP6

INTRODUCTION

Computational human phantoms are widely used for Monte Carlo dose calculations in many
different fields, including radiation protection, radiation therapy, medical imaging, and others
[1]. The development of computational phantoms for radiation dosimetry has been around since
the 1960s [2], increasing in complexity and detail as computer resources evolve. Full body
models have been developed to accommodate for the size differences encountered in the general
population; factors include weight, Body Mass Index (BMI), race, sex, age, and pregnancy [1].
Mathematical phantoms account for these differences by adjusting the equations and surfaces as
needed [3] while adjustments to tomographic models, though much more rigid, can also account
for these differences [1].
Voxelized computational human phantom were first constructed in the late 1980s from
tomographic images of a human body, which provided much more anatomical realism than
mathematical phantoms. Acknowledging the advantages of voxelized phantoms, the International
Commission on Radiological Protection (ICRP) officially adopted a set of male and female voxel
phantoms as the ICRP reference phantoms. However, the voxelized phantoms have several
limitations. Firstly, they show stair-stepped surfaces, causing the so-called voxel effect that
results in inaccurate dose calculations [5]. Secondly, due to the finite voxel resolution, it is
difficult to model very thin structures such as skin, oral mucosa, or the extrathoracic region,
which are very important structures for effective dose calculation. Lastly, the voxelized
phantoms are rigid, making it impossible to adjust them to model non-upright postures (e.g. that

Hui Lin, Kristofer Zieb, X. George Xu et al.

of a radiation worker sitting on a chair-type whole-body counter). Moving or deforming the

internal organs of a voxel phantom during Monte Carlo simulation is also impossible. As
advancement, surface phantoms were successfully developed to address the aforementioned
limitations of the voxelized phantoms. It allows for modeling of thin and complicated organs
with smooth surfaces as well as body size changes or posture adjustment. However, the 2D
surface phantoms have their own limitations [4]. To date, most Monte Carlo codes cannot handle
surface or tetrahedral meshes. As a result, the surface mesh based phantoms need to be converted
to voxel phantoms before the phantoms can be used in the Monte Carlo code. Recently, one
development of tetrahedral mesh-based phantom associated with GEANT4 was accomplished by
researchers from Hanyang University, the detailed results are presented in [9]. In that study,
instead of generating tetrahedral mesh phantom from segmented images of human body, they
generated a tetrahedral mesh phantom by converting a polygonal surface phantom and then
implemented in the Geant4 Monte Carlo code to calculate dose values. It is found that the dose
values calculated with the tetrahedral phantom were in good agreement to those of the original
polygonal surface phantom, and the computation speed was significantly improved comparing
with the polygonal surface phantom.
In the Version 6.1, the general purpose Monte Carlo transport code MCNP has been added a
new capability that allows particle transport with hybrid geometries [6]. Unstructured mesh
generated from Abaqus/Computer Aided Engineering (CAE) can be directly included in
MCNP6.1 geometry models together with the legacy Constructed Solid Geometry (CSG)
description. Models developed with CAE software no longer need to be voxelized or rewritten in
MCNP legacy input, saving many man-hours of conversion time while maintaining the native
geometry.
In this study, we aimed to develop a whole-body phantom in tetrahedral mesh and then to
test MCNP6s ability in calculating organ doses in this phantom for external irradiations
involving photons and electrons with energies less than 10 MeV.
2

MATERIALS AND METHODS

2.1 Visible Human Phantom

Previously we have developed the voxelized VIP-Man phantom using tomographic images
available from well-known Visible Human Project [8]. For constructing a tetrahedral mesh
phantom in this study, we converted a series of segmented tomographic images of Visible Human
Project directly the tetrahedral mesh geometry. The segmented Visible Human image dataset
contains 72 organs and tissues for organ dose calculations [8]. These organs are preserved in the
conversion. In the discussion below, we refer to these two phantoms as the VIP-Man
phantom and the VIP-Man phantom.
2.2 Construction of Tetrahedral mesh phantom
The Visible Human was tetrahedralized using the iso2mesh code developed by a research
group at Massachusetts General Hospital [7]. The code is a Matlab-based toolbox for the mesh
generation and processing. It can create 3D tetrahedral finite element (FE) mesh from surfaces,
3D binary and gray-scale volumetric images such as segmented MRI/CT scans. A detailed
description of the iso2mesh code can be found in a paper composed by Fang and Boas [7].

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In this study, the Visible Man segmented image data is converted into a tetrahedral mesh
phantom by using iso2mesh. To begin with, the organ identification information (organ IDs) was
firstly extracted from the Visible Man segmented data. The extracted file was then reshaped into
a matrix based on the dimensions of the original segmented data and read by the iso2mesh. When
going through all of the voxels, the targeted organ region will be assigned to value 1 while others
will be assigned to 0. The organ region was then tetrahedralized using the functions v2s and
s2m of iso2mesh, which firstly generated a geometric surface based on the data and then
generated the volumetric mesh from the surface. Each organ region was meshed independently
and exported as .inp file readable by Abaqus/CAE. The mesh construction time for each organ is
less than 5 minutes. Figure 1 shows the constructed tetrahedral mesh phantom VIP-Man .
The detailed workflow of the constructing the tetrahedral mesh phantom is illustrated in Figure
2.

(a)

(b)

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Hui Lin, Kristofer Zieb, X. George Xu et al.

Figure 1. VIP- phantom showing internal organs in tetrahedral meshes. (a) shows the sectional
view of whole-body phantom with organs inside. (b) shows the sectional view of the lungs.
Segmented data from VIP-Man

.raw file
Extract organ IDs using a Matlab
script

organlists.xls
Reshape the file into a matrix
based on the original dimensions

iso2mesh
Volume repairing: Fillholes3d

iso2mesh
Generate closed surface: v2s

nodes, faces
iso2mesh
Volumetric mesh generation: s2m

.inp file
MCNP6
Read in mesh elements (.inp file)
Figure 2. Work flow for constructing the tetrahedral mesh phantom

2.3 Monte Carlo Simulations with MCNP6 Unstructured Mesh Geometry

To evaluate dose values and computation speeds of the tetrahedral mesh phantom, we
compared with data derived for the VIP-Man voxelized phantom [8], using the MCNP6 code.
After assigning the materials and statistic sets to each organ region and integrating all organs
into one assembly, the mesh input was implemented by the unstructured mesh pre-processing
utility (um_pre_op) of MCNP6 to generate a basic MCNP input file containing psedo-cells,
minimal legacy cells, single surface that defines the mesh universe and minimal data card.
Further efforts to adjust the input deck such as adding the material cards, defining the source and
tally are required to create by hand. To differentiate the mesh results from the traditional MCNP
tally treatment, the results accumulated on the unstructured mesh are referred to as elemental
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Development of Whole-body Tetrahedral Mesh Phantom Using MCNP6

edits. The elemental edits, along with a generic description of the tetrahedral mesh phantom, are
output in a special file known as the .eeout (Elemental Edit Output) file. The .eeout file was then
processed by the unstructured mesh post-processing utility (um_post_op) to create instancebased tally results.
The simulations were performed using a single-core AMD Opteron 6272 CPU (@2.1 GHz,
64GB) with MCNP6.1. Prior to the comparison of the computation speed, the organ dose values
of the tetrahedral mesh phantom were compared with those of the VIP-Man voxelized phantom
in order to confirm that the tetrahedral mesh phantom was accurate. This involved calculation of
the organ doses for broad parallel photon and electron beams in the anteriorposterior (AP)
direction as well as for three energies of 0.1 MeV, 1 MeV, and 10 MeV. The number of primary
photons simulated was varied between 106 and 108 to limit the statistical errors in each organ to
below 5%.
In the computational speed comparison, computation times were calculated for two particle
types (photons and electrons) and three energies (0.1 MeV, 1 MeV, and 10 MeV) in the AP
irradiation direction. MCNP6 proton tallies for the mesh geometries were found to contain
problems and were not reported in this paper. Since the goal here is only to compare the
computation speed, a total of 104 primary particles were simulated in all cases.
3

RESULTS

3.1 Whole Body Tetrahedral Mesh Phantom

In this study, a whole-body tetrahedral mesh phantom was successfully generated by
tetrahedralizing the Visible Human images using the iso2mesh code. Figure 3 shows the
comparison view between the VIP-Man phantom and the VIP-Man phantom, which
indicates that the VIP-Man phantom maintains the original structure of the VIP-Man
phantom.

(a)

(b)

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Hui Lin, Kristofer Zieb, X. George Xu et al.

Figure 3. Comparison of detailed view of VIP- phantom and VIP- phantom. (a) VIP phantom, (b) VIP- phantom (by surface rendering which does not show the voxels). VisIt
Toolkit was used for visualization the generated tetrahedral mesh phantom [10].

Table I summarizes the comparison data between the VIP-Man phantom and the VIPMan phantom. The tetrahedral mesh phantom so far consists of 17 organs for effective dose
calculation. The masses of the organs exactly match those of the VIP-Man phantom, and the
number of tetrahedrons of each organ is at the same level of the number of voxels, which
minimized the computation time and memory usage.
Table I. Comparison of organs between VIP- phantom and the VIP phantom
Organs
VIP-
VIP-
Density(g/ )
Mass(g) Number of
Mass(g) Number
tetrahedrons
of
voxels
1.04
1247.0
24447
1247.0
18735
Brain
Lungs

0.26

910.3

42264

910.3

54709

Liver

1.05

1937.9

27747

1937.9

28802

Kidney

1.05

335.4

6757

335.4

5029

Skeleton

1.55

10961.3

76821

10961.3

92667

Heart wall

1.03

398.7

7059

398.7

6049

Upper large intestine

1.04

1430.2

21097

1430.2

21428

Lower large intestine

1.04

651.0

12875

651.0

9860

Esophagus

1.04

69.2

1071

69.2

1049

Stomach

1.04

497.7

6611

497.7

7439

Small intestine

1.04

1291.8

19708

1291.8

19375

Bladder

1.02

84.6

1222

84.6

1280

Gall bladder

1.03

33.0

593

33.0

504

Spleen

1.06

244.0

4050

244.0

3536

Thymus

1.03

11.2

160

11.2

175

Thyroid

1.05

27.6

405

27.6

409

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Development of Whole-body Tetrahedral Mesh Phantom Using MCNP6

Pancreas

1.05

82.9
20213.8

Total

1493
254425

82.9
20213.8

1232
271476

3.2 Comparison of Calculated Dose Values from External Photon and Electron Beams less
than 10 MeV
Figures 4 to 6 the calculated organ dose values of VIP-Man phantom and the VIPMan phantom from photon beams in 0.1, 1, and 10 MeV, respectively. Figure 7 to 9
compare these two phantoms for electron beams of 0.1, 1, and 10 MeV, respectively. The results
indicate that there was no significant dose discrepancy between the VIP-Man phantom and
the VIP-Man phantoms: the average dose value of the differences was as low as 4.1%
considering all of the simulations. Therefore, the VIP-Man phantom provides, within
statistical uncertainties (which were kept below 5%), dose values identical to those of the VIPMan phantom. For this study, only the photon and electron beams were used for the organ
dose comparison. In the future, we plan to consider additional radiation types and energies.

1.1

1.05

0.95

0.9

Organ
Figure 4. Comparison of organ doses for VIP- phantom with the VIP- phantom using
0.1 MeV photon source at AP direction

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Hui Lin, Kristofer Zieb, X. George Xu et al.

1.1

1.05

0.95

0.9

Organ
Figure 5. Comparison of organ doses for VIP- phantom with the VIP- phantom using
1-MeV photon source in the AP direction

AP, 10MeV
1.1

1.05

0.95

0.9

Organ
Figure 6. Comparison of organ doses for VIP- phantom with the VIP- phantom using
10 MeV photon source at AP direction

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Development of Whole-body Tetrahedral Mesh Phantom Using MCNP6

1.1

1.05

0.95

0.9

Organ
Figure 7. Comparison of organ doses for VIP- phantom with the VIP- phantom using
0.1 MeV electron source at AP direction
1.1

1.05

0.95

0.9

Organ
Figure 8. Comparison of organ doses for VIP- phantom with the VIP- phantom using
1-MeV electron source in the AP direction

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Hui Lin, Kristofer Zieb, X. George Xu et al.

AP, 10MeV
1.1

1.05

0.95

0.9

Organ
Figure 9. Comparison of organ doses for VIP- phantom and the VIP- phantom using
10 MeV electron source at AP direction

3.3 Comparison of MC Dose Computation Speed

The comparison results of computation speed between VIP-Man and VIP-Man is
shown in Table II. It was found that the computational speed of running the VIP-Man
phantom is about three times slower than of the VIP-Man phantom. This was expected since
particles are much easier to be tracked within the structured mesh (voxels) than in the
unstructured mesh geometry. With the continuing improvement of ray-tracing method in the
MCNP6, the tetrahedral mesh would be a viable geometric representation for human phantoms.
Table II. Comparison of computation time of VIP- and VIP-
phantom
Particle Type
Photon

Electron

Energy(MeV)

Computation time(min)
VIP-Man
VIP-Man

0.1

12.32

6.46

1.0

27.41

7.83

10

39.67

9.85

0.1

15.22

7.69

1.0

34.74

14.13

10

95.90

25.08

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Development of Whole-body Tetrahedral Mesh Phantom Using MCNP6

CONCLUSIONS

In this study, we developed a new type of computational human phantom, a tetrahedral mesh
phantom, VIP-Man , by constructing from a set of segmented human body images of the
Visible Human Project. The external shape and the organs of the tetrahedral mesh phantom were
kept identical to those of the voxelized phantom. The dose values calculated for the tetrahedral
phantom, likewise, were found to be in good agreement with to those of the VIP-Man voxelized
phantom. Though the computation speed of tetrahedral mesh phantom is about three times
slower than of the voxelized phantom, the tetrahedral mesh phantom offers many other
advantages. Indeed, it combines the advantages of the voxelized phantom (fast computation
speed and inhomogeneous density representation) and the surface phantom (deformability,
flexibility, and surface smoothness). Note that the density distribution in an organ or tissue can
be easily modeled using a fine tetrahedral mesh [9]. Tetrahedral mesh geometry brings good
deformability, which is useful in interactive virtual reality applications such as surgery
simulators. Furthermore, finite element analysis is typically done using unstructured meshes
[11]. With the continuing improvement of ray-tracing method in MCNP6, the tetrahedral mesh
can be a promising geometric representation for human phantoms (as well as other applications)
and effectively radiation transport simulations.
5

ACKNOWLEDGEMENTS

Former group members, Dr. Aiping Ding and Dr. Yong H. Na, have provided very helpful
advices on constructing the tetrahedral mesh phantom during this project. Research is supported
in part by a grant from National Institute of Biomedical Imaging and Bioengineering
(R01EB015478) and a graduate fellowship to the first author from the Health Physics Society (
2014-2015).
6

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