InterDosi: In-House Tool For Internal Dosimetry Using Primitive and Voxelized Phantoms

In-house tool for internal dosimetry using
primitive and voxelized phantoms
Dr. Jaafar EL Bakkali

Professor in nuclear physics, associated member to RNSL laboratory, UAE,
Faculty of Sciences of Tetuan, Morocco.
18 September 2023
Outlines

InterDosi :

Acronyme & essence

Main features

Software overview

Installation and user support

Novice examples

Summary
2
InterDosi acronyme & essence

As a word InterDosi stands for Internal Dosimetry.

As code, InterDosi is a new Monte Carlo simulation tool primarily coded in C++
language and uses Geant4 library to perform internal dosimetry studies using
voxelized and primitive phantoms.

We chosed Geant4 toolkit as dose calculation engine for InterDosi code for one
main reason; Geant4 being the most powerful and widely used simulation toolkit
around the world for various applications involving the simulation of ionizing
radiation transport and its interaction with matter.
3
InterDosi main features

Learning of a general purpose code such Geant4 is not generally straightforward as
the coding with it is done usually by C++ programming language that requires
considerable time to learn.

InterDosi has been developed especially to reduce this complexity for researchers
that prefer the use of Geant4 simulation toolkit among others to establish studies
related to internal dosimetry research area.

To do so, by providing a scripting language the setting of simulation parameters is
simpler and more robust and the analyzing of results is done almost automatically.

It has been designed with user-friendliness in mind, thanks to its well-developed
graphical interface which has been coded using the Java programming language.

InterDosi supports the calculation of internal dosimetric coefficients such as AF, SAF
and S-value defined by MIRD in a voxelized phantom.
4

InterDosi allows the visualization of a voxelized phantom slice in different view modes
(sagittal, coronal, axial and 3D).

Within InterDosi, it is possible to individually display the 3D geometry of a selected
organ.

2D Dose heat map feature is also supported which is a color-based technique that
displays the absorbed dose distribution on a defined voxelized phantom slice.

InterDosi also allows the estimation of internal dosimetric coefficients in a tumor model
represented by spherical or spheroidal geometry (oblate and prolate) of different sizes
and filled with varying chemical composition.

InterDosi coming with robust install scripts that supporting some Linux distribution that
make the getting, compiling and installing of Geant4 and InterDosi prerequisite libraries
more easy.
5

InterDosi offers three specific techniques to optimize the calculation of internal
dosimetric coefficients in voxelized and primitive phantoms.

The first technique is called VoxIsle (Voxel Isle) developed based on the LRAH algorithm
which is used to create a compressed voxelized phantom thus combining adjacent voxels
belonging to the same organ/tissue. The phantom created is therefore assembled from a
set of rectangular voxels of different sizes.

The second technique denoted SVSCM (S-Value Simplified Calculation Method) developed
to optimize computational performances of S-value calculation either in voxelized or
primitive phantom. The idea is very simple; reduce the size of a vector of SAFs to be
calculated to obtain a S-value of a particular radionuclide can enhance simulation
computation performance. This can be achieved by reducing the number of decimal
digits in a SAF energy to only one or two significant digits. The vector size of SAFs of
1252 radionuclides decreases from 454345 to only 586 when this technique is applied.
6

The third technique is OBEAMON, consists of optimizing the number of histories by
running a simulation test with a small histories while the uncertainty is inversely
proportional to the square root of histories, the latter providing a least statistical
uncertainty greater than 1% can be easily determined using the rule of three.

In addition to native optimization techniques, as InterDosi by nature a Geant4-based
code, it provides the use of the Geant4 tracking optimization method that optimizes
particle tracking in a voxelized geometry when a particle travels frontiers between
adjacent voxels filled with a same material.

InterDosi can automatically do voxelization of geometries created using well-known
3D geometry formats like as OBJ and STL or Monte Carlo 3D specific models as
GDML and MCNP lattice.

InterDosi comes with novice examples demonstrating the full capabilities of the code.
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Software overview
Programming languages

C++ language and Geant4 C++ classes were especially used in writing most
parts of InterDosi modules.

In order to make the InterDosi code more user-friendly, the Java
programming language has been used to build a user-friendly Java GUI
which contains essential modules and tools to cover all the requirements
for establishing a complete internal dosimetry study using a voxel-based or
primitive phantom.

Linux Bash scripting language was used through a set of scripts to ensure
various aspects of connections between C++ modules and the main Java-
based GUI application.
8
Software overview
Description of all supported input/output file formats
Common 3D geometry file formats supported by code

InterDosi can easily handle four common 3D models by translating them into InterDosi
voxelized geometries, with the aim of making the code more suitable for the requirements
of dosimetry researchers who may prefer certain 3D model types over others.

Famous STL geometry which can be encoded using the Standard Triangle Language can be
easily translated into voxelized geometry provided that the 3D STL model was read from
an ASCII file.

Another known format that has been developed by Wavefront Technologies to define and
store geometric objects known as the OBJ file format is also supported; the corresponding
3D model can be integrated into InterDosi code since the loaded model was written in an
ASCII file format.
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Software overview
Common 3D geometry file formats supported by code

Voxelized phantom geometry coded using a hexahedral structure lattice
with a MCNP Monte Carlo code can be easily imported into InterDosi
code via the corresponding conversion tool.

As InterDosi is by nature an application created on the top of the
Geant4 toolkit and knowing that GDML is a markup language native to
the Geant4 collaboration and being the most preferred method to
encode geometries due to its simplicity, InterDosi also supported this 3D
model.
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Software overview
InterDosi native I/O file formats

To make InterDosi code an easy tool in the hands of internal dosimetry
researchers a set of file formats has been developed accordingly.

The developed file formats are classed into four main categories,
namely: geometry file format, material file format, configuration file
format, and dose file format.
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Software overview
Geometry file format Description
IJKID It stores voxelized phantom specified data in an ASCII text file consisting of one line followed by
another line. The line count is equal to the number of phantom voxels and each line records four
parameters: voxel IDs along the x, y, and z axes, and a material ID.
IRVOX It stores voxelized phantom specified data in a compressed manner, this means that the number of
voxels assembled a phantom will be decreased by applying VoxIsle compression algorithm. The
stored information includes voxel and phantom dimensions as well as organ identifiers. Other
recorded parameters are dimensions of world volume and for each rectangular irregular voxel
volume its solid/logical volume dimensions. It should be noted here that this file implicitly uses the
IJKID file to extract geometry information and organ IDs.
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Software overview
Description of all supported input/output file formats InterDosi_Test4.ijkid
InterDosi native I/O file formats 2 1 0 2
3 1 0 2

Example of an IJKID file 4 1 0 2
5 1 0 2
6 1 0 2
Phantom details: 7 1 0 2
2 2 0 2
Name: InterDosi_Test4.ijkid 3 2 0 2
4 2 0 2
>>>
Dimension along X,Y and Z axis (mm): 1600 1591.23 900
Number of voxels along X,Y and Z axis : 128 128 128
Voxel dimensions along X,Y and Z axis (mm): 12.5 12.4315 7.03125
ORGAN_NAME ORGAN_ID
MyWorld -1
InterDosi_Test2_Tissue_Adipose 0
InterDosi_Test2_Tissue_Muscle 1
InterDosi_Test2_Tissue_Skin 2
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Software overview
InterDosi_Test4.irvox

Example of an IRVOX file
VOXEL_DIMENSIONS (mm, mm, mm) 10.000000|10.000000|
Phantom compression details: 10.000000
PHANTOM_DIMENSIONS (mm, mm, mm) 100.000000|60.000000|
30.000000
VoxIsle data processing CPU time(s) 0.00111914 WORLD_VOLUME (VOL(cm^3),ID )
108 -1
DIM_VOLUMES (cm^3)
Total number of whole body uniform voxels: 72 24.000000 24.000000 24.000000
SOLID_VOLUMES 1
Total number of no merged voxels: 0 6x4
LOGICAL_VOLUMES 3
2@0 3@0 4@0
Total number of merged voxels: 72
ORGAN_ID 2
0 2:1:7:4
Percent of merged voxels is: 100%. ORGAN_ID 3
1 2:1:7:4
ORGAN_ID 4
2 2:1:7:4
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Software overview
Material file format Description
MAT Its development was based on the fact that the storage of material data defining a given organ can
facilitate its reuse. This means that several organs sharing the same material in the same or another
phantom can read their material specification from a predefined relevant material. InterDosi contains a
comprehensive database of predefined materials which can be easily enlarged to support new materials.
Structurally, MAT is a native file format in which material that makes up each phantom organ is written
in an ASCII text format consisting of one line followed by another, this according to the following
structure:
OrganName Density(in g/cm3) NumberOfChemicalElements

ChemicalElement_1 Fraction_1
......
ChemicalElement_N Fraction_N
As can be seen above, the first line contains three parameters: the name of a tissue/organ, its density
and the number of chemical elements composing it. While the other lines each contain an abbreviation
of a chemical element and its corresponding mass fraction.
15
Software overview
 InterDosi Material database repository (contains more than 900 files)
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Software overview
Configuration file format Description
VOXPH It stores phantom configuration data in an ASCII text format. The data are regrouped into lines in pairs
of a binary flag starting with @ and one or more values.
PHANTINFO It stores interesting information about phantom organs, including: organ name, its ID, its material, its
mass, its number of voxels and its volume.
RAD It is reserved to stock radionuclide data like as a radionuclide name and a 3D vector storing particle
name, energy and energy yield.
SPC It keeps mandatory configuration parameters automatically created when a tumor S-value simulation is
started, including radius of a spherical tumor expressed in mm, tumor mass fractions of a pair of soft and
bone tissues. It should be noted here that this file is created automatically when performing a spherical
tumor S-value calculation using the PriGeoTumorSAFs module.
17
Software overview

Example of a VOXPH file
InterDosi_Test1.voxph
@VoxelizedPhantomName InterDosi_Test1
@VoxelizedPhantomFileName InterDosi_Test1.ijkid
@Voxelizedimensions 180 180 600
@NumberOfVoxels 100 100 100
@NumberOfPhantomOrgans 5
@NumberOfPhantomAnatomicalRegions 0
@BackgroundID -1
@PhantomOrganItem -1 background Air 0 204 204
@PhantomOrganItem 3 Skin_Tissue Skin_Male_ICRP_110 255 204 204
@PhantomOrganItem 2 Adipose_Tissue Adipose_Tissue_Male_ICRP_110 255 153 51
@PhantomOrganItem 1 Muscle_Tissue Muscle_Tissue_Male_ICRP_110 255 102 102
@PhantomOrganItem 0 Bone_Tissue Mineral_Bone_Male_ICRP_110 153 153 153
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Software overview

Example of a PHANTINFO file
InterDosi_Test1.phantinfo
ORGAN_NAME ORGAN_ID ORGAN_MATERIAL ORGAN_MASSE(g) ORGAN_VOLUME(CM_3)

ORGAN_NVOXELS ORGAN_DENSITY(g/CM_3)
background -1 Air 5.01212 4160.16 214000 0.00120479
Skin_Tissue 3 Skin_Male_ICRP_110 1432.42 1314.14 67600 1.09
Adipose_Tissue 2 Adipose_Tissue_Male_ICRP_110 7667.91 8071.49 415200 0.95
Muscle_Tissue 1 Muscle_Tissue_Male_ICRP_110 3608.84 3436.99 176800 1.05
Bone_Tissue 0 Mineral_Bone_Male_ICRP_110 4717.85 2457.22 126400 1.92
BODY MASSE (g) 17432
TOTAL NUMBER OF VOXELS 1000000
BODY VOLUME(CM_3) 19440
NVOXELS_X 100
NVOXELS_Y 100
NVOXELS_Z 100
DIM_X 180
DIM_Y 180
DIM_Z600 19
Software overview

Examples of RAD and SPC files
Radionuclide : Na-22 Tumor sphere radius : 1 mm , 100 % soft 0 % bone
Na-22 1 1.0 0.0

gamma 1.79797 0.5
gamma 0.99944 1.3
positron 0.898436 0.2
positron 5.50022E-4 0.85
electron 6.42858E-6 1.3
electron 3.77188E-7 1.3
electron 2.07187E-10 1.3
electron 3.39931E-10 1.3
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Software overview
Dose file format Description
DVOX Default file format used by InterDosi built-in visualization tool to draw a 2D dose heat map, which is
structured as follows: the first line contains a full path to a VOXPH file. The remaining lines contain four
parameters spaced by a white character: voxel IDs along the x,y and z axes and a relative absorbed dose.
SAF SAF which sends dosimetric data produced in a voxelized geometry to a file with .saf extension output
by the VoxGeoSAFs C++ module.The saved data include SAF and its corresponding uncertainty in all
phantom organs and some useful simulation parameters such as file creation date, simulation CPU time
and number of simulated histories.
SVALUE ASCII file with .svalue extension that stores simulation outputs of VoxGeoSAFs C++ module taken as
input a vector of radionuclide emitted energies into a file, including S-value and its corresponding
uncertainty in all phantom organs and some statistics information as file creation date, CPU simulation
time, radionuclide name, number of running threads and physics parameters. It should be noted here
that InterDosi through SValueCalcs GUI module implicitly uses radioisotope decay data of the ICRP
publication 107
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Software overview

Example of a DVOX file
Bone_Tissue-0.15-gamma-EMLVP-SM0-unidist.dvox
home/elbakkali/Monte_Carlo_Simulation/InterDosi_Version1.3/InterDosi/inputs/PhantomConfiguration_files/InterDosi_Test1.voxph
0 43 3 0.0793079
0 43 11 0.366993
0 43 12 0.0642457
0 43 21 0.0418227
0 43 33 1.36128
0 43 35 0.959387
0 43 37 0.930406
0 43 62 0.44383
0 43 77 1.50857
0 43 91 0.0390615
0 44 0 2.15841
0 44 10 0.331413
0 44 29 1.96432
0 44 33 0.686266
0 44 45 0.785795
0 44 48 1.9894
>>>
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Software overview

Examples of SAF and SVALUE file
Bone_Tissue-0.1-gamma-EMLVP-SM0-unidist.saf Muscle_Tissue-O-15-EMLVP-SM0-unidist-no-full.svalue
CREATION DATE Mon Sep 4 10:49:48 2023 CREATION DATE Fri Sep 1 09:35:44 2023
CPU TIME (S) 0.435411 CPU TIME (S) 63.9103
SOURCE_EMITTED_ENERGY (MeV) 0.1 NUMBER_THREADS 12
PARTICLE NUMBER OF TIMES OF USE 1 NUMBER_EVENTS 120000
NUMBER OF THREADS 10 RADIOISOTOPE O-15
NUMBER OF SIMULATED EVENTS 10000 SOURCE_NAME Muscle_Tissue
TOT NUMBER OF SIMULATED EVENTS 10000 PHYSICS_LIST EMLVP
ORGAN NAME AF SAF(kg^-1) STD_DEV(kg^-1) N_EVENTS Organ/Region Name S-Value(mGy/MBq/s) STD(mGy/MBq/s)
STATISTICAL_ERROR(%) background 1.43897e-06 1.71966e-07
background 2.849239e-05 5.684700e-03 3.474969e-02 149 6.112846e+02 Skin_Tissue 2.71978e-06 2.2786e-09
Skin_Tissue 7.062652e-03 4.930584e-03 1.019119e-03 1861 2.066934e+01 Adipose_Tissue4.95922e-06 1.35507e-10
Adipose_Tissue5.611537e-02 7.318206e-03 5.710632e-05 16976 7.803323e-01 Muscle_Tissue 4.09899e-05 2.72843e-10
Muscle_Tissue 6.428920e-02 1.781436e-02 1.365226e-04 16800 7.663628e-01 Bone_Tissue 7.46822e-06 2.74163e-10
Bone_Tissue 4.314557e-01 9.145166e-02 7.956993e-05 65702 8.700764e-02
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Software overview
C++ modules of InterDosi code

VoxGeoSAFs
Responsible for producing dosimetric coefficients such as AF and SAF in a voxelized
geometry, these coefficients are produced by a set of running threads in separate
HDF5 files which are created based on HDF5 C++ scientific library [13]. If score
dose at voxel level is enabled this module will also output a set of voxel-dose
ASCII files.

DoseOrgMerger
Combines different HDF5 files output by VoxGeoSAFs into a single file written in
SAF file format.

DoseVoxMerger
Combines different voxel-dose ASCII files calculated using VoxGeoSAFs module in
each running thread into a single file having DVOX file format.
24
Software overview
C++ modules of InterDosi code

VoxGeoBldr
Translate a GDML geometry into a voxelized geometry encoded in IJKID file format.

VoxGeoSvalue
Accepts as input a vector of SAF files produced by VoxGeoSAFs for a radionuclide irradiating a voxelized
phantom and generates a file in the SVALUE file format.

PriGeoTumorSAFs
Calculates a vector of SAFs corresponding to all the energies emitted by a radionuclide irradiating a
primitive geometry of a tumor dosimetric model. Currently, only the sphere, flattened spheroid and
elongated spheroid can be used.

PriGeoTumorSvalue
Accepts as input a vector of SAF files produced by PriGeoTumorSAFs for a particular radionuclide
irradiating a primitive tumor phantom and generates a file in the SVALUE file format.
25
Software overview
GUI of InterDosi code (main window)
26
Software overview
GUI of InterDosi code (VoxPhantomBldr tab)
27
Software overview
GUI of InterDosi code (SAFCalcs, SValueCalcs and PTGSValueCalcs tabs)
28
Software overview
GUI of InterDosi code (VoxGeomVis tab)
29
Software overview
GUI tools of InterDosi code
GUI tool Short description
PhantomDetails As its name indicated, this tool provides detailed information about the voxelized phantom displayed in a tabular form, including: phantom data (name, dimensions, voxels,
mass and volume) and organ/region data (name, ID, material, mass, volume, voxels and density).
STL-to-GDML converter Serves to convert 3D geometry model written STL language into its equivalent in the GDML markup language.
OBJ-to-GDML converter Called to translate 3D geometry model written OBJ language into its equivalent in the GDML markup language.
GDML-to-IJKID converter Translates tessellated geometries of phantom organs and described in GDML files into voxelized data which is stored in a single IJKID file. The voxelization process requires
the settings of the number of voxels along the three cartesian axes.
MCNP-Lattice-To-IJKID Transforms 3D geometries describing different phantom organs into voxelized data which is stored in a single IJKID file. The voxelization of the MCNP-based phantom is
converter achieved by setting the number of voxels along the x,y and z axis. It should be emphasized here that at this time, only the hexahedral lattice is supported.
IJKID-to-IRVOX converter Creates an IRVOX file from an existing IJKID voxelized geometry input file. We must mention that the IRVOX file format reserves data of a compressed phantom.
Dose-HeatMap Visualizer Used to visualize in a color-based technique called heatmap, the absorbed dose distribution on a defined image plane. This can be useful for quickly analyzing dosimetric data
by making a visual assessment. Additionally, it may be possible to apply the logarithmic scale to the plotted data which can be saved into a PNG image file format.
Dosimetric Data Plotter Used to plot graphs in the form of histograms to represent SAF and S-Value dosimetry data. The SAF or S-value file must be loaded in order to create a plot that can be related
to some selected organs or all.
Dosimetric file explorer Displays a file tree shown all created SAF and S-values files which can be opened by clicking on.
30
Software overview
31
Software overview
32
Software overview
33
Software overview
InterDosi GUI layers
InterDosi.GUI
VoxPhantomBldr SAFCalcs SValueCalcs TPGSValueCalcs VoxGeomVis Tools
Linux scripts
-----------------------------------
VoxGeoSAFs VoxGeoSvalue PriGeoTumorSAFs PriGeoTumorSvalue VoxGeoBuilder PhantomDetails
-----------------------------------
STL-to-GDML
-----------------------------------
OBJ-to-GDML
-----------------------------------
IJKID-to-IRVOX
-----------------------------------
Linux scripts MCNP-Lattice-To-IJKID
-----------------------------------
GDML-to-IJKID
-----------------------------------
Dose-HeatMap Visualizer
-----------------------------------
Dosimetric Data Plotter
OptNEvents -----------------------------------
Dosimetric File Explorer
DoseOrgMerger DoseVoxMerger -----------------------------------
C++ Java
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
During the development of InterDosi, it was taken into account that the installation of a
Monte Carlo code is often a complex task for non-habitual software users. For this reason,
a great effort has been made to make the installation of InterDosi simpler and more
robust. This is achieved through a number of Linux scripts that have been developed to
automate the configuration and installation of the prerequisite libraries required by the
InterDosi code in its proper functioning. Currently, InterDosi can be successfully run under
Ubuntu 18, Ubuntu 20 and Centos 7 Linux operating systems.
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
As all software, InterDosi package contains a user guide to help user
understand how to install InterDosi and run it as well as a full details
of its architecture and demonstrative examples are provided in.
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
InterDosi can be freely downloaded from the following link:
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Novice examples
Example 1: Internal dosimetry on a voxelized phantom created from GDML
geometries.

What do we propose to learn from the following example?

Answer:

Create a voxelized phantom from GDML geometries.

Create an InterDosi phantom configuration file for the created voxel-based phantom.

Do an internal dosimetry study using a voxelized phantom and get SAFs and plot
them.

Display a 2D dose heat map of a particular voxelized phantom slice.
38
Novice examples
geometries.

We consider a phantom called InterDosi_Test1 written in GDML markup language
assembled by four cylinders of equal length of 30 cm, but of varying diameter: the
inner cylinder of green color and diameter 36 mm is filled with mineral bone
material, the next two cylinders of red and gray color of diameter 20 and 30 mm
are respectively filled with muscle and adipose material, while the cylinder exterior
of yellow color and with a diameter of 4 mm is filled with a skin material.
39
Novice examples
geometries.

First step: using GDML-to-IJKID Converter tool, one should set parameters as
displayed in the below figure. By clicking on CREATE_IJKID_FILE button, the
converter tool will process the GDML data and create, separately, two file at
/InterDosi/nput/IJKIDPhantom_files, namely InterDosi_Test1.ijkid and
InterDosi_Test1.ijkid.info.
InterDosi_Test1.ijkid.info
Phantom dimension along X,Y and Z axis (mm): 180 180

600
Number of voxels along X,Y and Z axis : 100 100 100
Voxel dimensions along X,Y and Z axis (mm): 1.8 1.8 6
ORGAN_NAME ORGAN_ID
world -1
Tissue_Bone 0
Tissue_Muscle 1
Tissue_Adipose 2
Tissue_Skin 3
40
Novice examples
Example 1: Internal dosimetry on a voxelized
phantom created from GDML geometries.

Second step: using VoxPhantomBldr tab one should
create a voxelized phantom configuration file that
requires phantom geometry data written in
InterDosi_Test1.ijkid.info file.

Phantom material and color specifications can
be done also through this GUI tab.

Once the specifying of voxelized phantom is done,
one can create voxel-based configuration file by
clicking on SAVE_PHANCONFG button.
41
Novice examples
Example 1: Internal dosimetry on a voxelized phantom created from GDML geometries.

Third step: using VoxPhantomBldr tab one should create a voxelized phantom configuration file
that requires phantom geometry data written in InterDosi_Test1.ijkid.info file.

Phantom material and color specifications can
be done also through this GUI tab.

Once the specifying of voxelized phantom is done,
one can create voxel-based configuration file called InterDosi_Test1.voxph
By clicking on SAVE_PHANCONFG button.
InterDosi_Test1.voxph
@VoxelizedPhantomName InterDosi_Test1
@VoxelizedPhantomFileName InterDosi_Test1.ijkid
@Voxelizedimensions 180 180 600
@NumberOfVoxels 100 100 100
@NumberOfPhantomOrgans 5
@NumberOfPhantomAnatomicalRegions 0
@BackgroundID -1
@PhantomOrganItem -1 background Air 0 204 204
@PhantomOrganItem 3 Skin_Tissue Skin_Male_ICRP_110 255 204 204
@PhantomOrganItem 2 Adipose_TissueAdipose_Tissue_Male_ICRP_110 255 153 51
@PhantomOrganItem 1 Muscle_Tissue Muscle_Tissue_Male_ICRP_110 255 102 102 42
@PhantomOrganItem 0 Bone_Tissue Mineral_Bone_Male_ICRP_110 153 153 153
Novice examples
Example 1: Internal dosimetry on a voxelized
phantom created from GDML geometries.

Last step: the phantom is ready to be used for internal
dose calculation. To do that, in the tab named
VoxPhantomBldr user should select
LOAD_EXISTING_PHANTOM_CONFIG_FILE option,
choose InterDosi_Test1.voxph file and click on
LOAD_PHACONF button.

We calculate Specific absorbed fractions (SAFs) of a
monoenergetic photon of 1000 keV in all organs while
bone is the source organ. By clicking on the next tab
called SAFCalcs, user should fill parameters as follows:
43
Novice examples
geometries.

After clicking on CALC_SAFS button, InterDosi will generate a SAF file called
Bone_Tissue-0.1-gamma-EMLVP-SM0-unidist.saf at
/outputs/DosiFiles/SAFs/InterDosi_Test1, which its content may look like:

The SAF can be plotted by the means of Dosimetric Data Plotter tool.
Bone_Tissue-0.1-gamma-EMLVP-SM0-unidist.saf
CREATION DATE Mon Sep 4 10:49:48 2023

CPU TIME (S) 0.435411
SOURCE_EMITTED_ENERGY (MeV) 0.1
PARTICLE NUMBER OF TIMES OF USE 1
NUMBER OF THREADS 10
NUMBER OF SIMULATED EVENTS 10000
TOT NUMBER OF SIMULATED EVENTS 10000
ORGAN NAME AF SAF(kg^-1) STD_DEV(kg^-1) N_EVENTS STATISTICAL_ERROR(%)
background 2.849239e-05 5.684700e-03 3.474969e-02 149 6.112846e+02
Skin_Tissue 7.062652e-03 4.930584e-03 1.019119e-03 1861 2.066934e+01
Adipose_Tissue5.611537e-02 7.318206e-03 5.710632e-05 16976 7.803323e-01
Muscle_Tissue 6.428920e-02 1.781436e-02 1.365226e-04 16800 7.663628e-01
Bone_Tissue 4.314557e-01 9.145166e-02 7.956993e-05 65702 8.700764e-02
44
Novice examples
geometries.
With InterDosi code, the scoring of absorbed dose at voxel level is also provided, which
can be activated by enabling the SDVOX option. New file called
muscle_0.75_gamma.dvox, will be produced at
/InterDosi/outputs/DvoxFiles//InterDosi_Test1/ which can be visualized by clicking on
Tools Dose-Heat-Map Visualizer. Here bellow a screenshot of the expected result:
45
Novice examples
Example 2: Internal dosimetry on a voxelized phantom created from STL
geometries.

What are the main objectives of this example?

Answer:

Create a voxelized phantom from STL geometries and write the concerned
InterDosi phantom configuration file.
46
Novice examples
geometries.
 We consider a phantom called InterDosi_Test2 InterDosi_Test2 that was developed to
show the capabilities of InterDosi code to deal with STL files. The STL-based phantom was
developed using OpenSCAD software, it is located into
/InterDosi/inputs/STLPhantom_files/InterDosi_Test2 directory and composed by three STL
files, namely: InterDosi_Test2_Tissue_Adipose.stl, InterDosi_Test2_Tissue_Muscle.stl and
InterDosi_Test2_Tissue_Skin.stl
47
Novice examples
geometries.

To convert the STL-based files to a suitable format recognized by the InterDosi code, they should
be first converted to GDML files by means of STL-to-GDML converter tool. The other steps are
similar to ones described in the previous example.
48
Novice examples
Example 3: Internal dosimetry on a voxelized phantom created from OBJ
geometries.


Answer:

Create a voxelized phantom from OBJ geometries and write the concerned

Visualize phantom geometry using different view modes.
49
Novice examples
Example 3: Internal dosimetry on a voxelized phantom created from OBJ geometries.

InterDosi_Test3 Phantom was developed to show the capabilities of InterDosi code to deal
with OBJ files. The OBJ-based phantom geometry is same as used in previous example, it is
located into /InterDosi/inputs/OBJPhantom_files/InterDosi_Test3 directory and composed by
three OBJ files namely: InterDosi_Test3_Tissue_Adipose.obj,
InterDosi_Test3_Tissue_Muscle.obj and InterDosi_Test3_Tissue_Skin.obj.

To convert the OBJ-based phantom to a suitable format recognized by the InterDosi code,
the OBJ-based files should be first converted into GDML files by means of OBJ-to-GDML
converter tool.

The GDML files are created at /inputs/GDMLTesselatedPhantom_files/InterDosi_Test3
directory. These files should be converted to an IJKID file by using the GDML-to-IJKID
converter tool. The last step is to create a phantom configuration file as described in the
first example.
50
Novice examples
geometries.
51
Novice examples
geometries.

Visualize phantom geometry using different 2D and 3D view modes.
52
Novice examples
Example 4: Internal dosimetry on a voxelized phantom created based on
MCNP geometry file.


Answer:

Create a voxelized phantom from MCNP geometry file and write the concerned

Calculate Svalues for muscle as source of C-14 radionuclide.

Compress the built voxelized phantom using VoxIsle technique and recalculate
SValues.
53
Novice examples
MCNP geometry file.

InterDosi_Test4 Phantom was developed to show the capabilities of InterDosi
code to deal with MCNP hexahedral lattice data. The MCNP phantom geometry
is shown in /inputs/MCNP-Lattice-basedPhantom_files/InterDosi_Test4.inp, the
whole geometry consists of three rectangular layers surrounded by a background
medium, filled by three different materials with ids respectively of 2, 3 and 4,
that corresponding to skin, adipose and muscle. The background has a material
id of value of 1.

The MCNP file can be directly converted into IJKID file format, this is done by
means of MCNP-Lattice-to-IJKID converter tool.
54
Novice examples
MCNP geometry file.

Once the InterDosi_Test4.ijkid file is created, the build of InterDosi
configuration file for this phantom can be done as it was previously
described in the first example.
55
Novice examples
MCNP geometry file.

Calculate Svalues in InterDosi_Test4 while muscle is the source of C-14.
56
Novice examples
MCNP geometry file.

Compress the phantom using VoxIsle technique
57
Novice examples
MCNP geometry file.

Calculate Svalues in InterDosi_Test4 compress phantom while muscle is
the source of C-14.
58
Novice examples
MCNP geometry file.

Calculate Svalues in compress phantom while muscle is source of C-14.
59
Novice examples
Example 5: Na-22 Svalue in a sphere-based phantom filled by a soft tumor


Answer:

Calculate Svalue for Na-22 radioisotope in a spherical soft tumor without
optimization method.

Calculate SValue for Na-22 radioisotope in a spherical soft tumor with
optimization method.

Compare computation time and Svalue in the two cases.
60
Novice examples

Using the TPGSvalueCalcs GUI tab, it is proposed to calculate the S-value (without optimization)
of Na-22 radionuclide in a spherical tumor of r=1 mm filled by soft tissue.
Parameter Meaning Value(s)
TMNAME Tumor model name. tumor
TMGEOM Tumor model geometry type. SPHERE
TSPHRER Equivalent sphere radius. 1 mm
SFTBNTISSRTO Tumor soft/bone tissue ratios. 100.0%;0.0%
PHYSICS_PACKAGE Physics package. G4EmLivermorePhysics_option3
THREADS_NUMBER Number of running threads. 12
NEVENTS_PTHREAD Number of histories per running thread. 10000
RHIQNQ Ratio histories for charged and no charged particules. 1
SECPCUT Secondary parcticle production cuts. 0.001mm; 0.001mm; 0.001mm
PART_RECYCL Particule recycling option.
SLCT_RADFILE Selected ICRP RAD file. /InterDosi/inputs/RAD_files/ICRP-07.RAD
SLCT_RDNCLDE Selected radionuclide. Na-22
VERBOSITY Simulation detailled messages. Yes

61
SVSCM Svalue Simplified Computing Method. No
Novice examples
62
Novice examples

This time we repeat same example by enabling SVSCM technique.
63
Novice examples

Comparison of Svalue and it required CPU time for simulation without and with
SVSCM optimization technique.
SVSCM S-Value(mGy/MBq/s) CPU time (S)

Off 6.110 115.443
On 5.83593 70.03

We conclude that a diff in Svalue < 5% and an acceleration in Svalue
computing up to 40% are achieved when the optimization technique was applied.
64
Summary

InterDosi is a new internal dosimetry tool developed on the top of the Geant4
simulation toolkit.

InterDosi allows one to get internal dosimetric coefficients either in voxelized or
primitive phantom as AF, SAF and S-value with less effort thanks to its user-
friendless nature.

InterDosi provides rich functionalities allow user to import their models written in
common 3D file format into the code, visualize phantom geometry with different
view modes, display heat map of dose distribution in a 2D slice, etc.

InterDosi encapsulates its own optimization techniques to improve computational and
memory performances.

In the next version of InterDosi, we plan to implement hybrid computational
phantoms into the code.
65

InterDosi: In-House Tool For Internal Dosimetry Using Primitive and Voxelized Phantoms

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InterDosi: In-House Tool For Internal Dosimetry Using Primitive and Voxelized Phantoms

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In-house tool for internal dosimetry using

primitive and voxelized phantoms

Dr. Jaafar EL Bakkali

Geometry file format Description

Material file format Description

OrganName Density(in g/cm3) NumberOfChemicalElements

ORGAN_NAME ORGAN_ID ORGAN_MATERIAL ORGAN_MASSE(g) ORGAN_VOLUME(CM_3)

Radionuclide : Na-22 Tumor sphere radius : 1 mm , 100 % soft 0 % bone

Na-22 1 1.0 0.0

GUI tool Short description

Phantom dimension along X,Y and Z axis (mm): 180 180

CREATION DATE Mon Sep 4 10:49:48 2023

TMNAME Tumor model name. tumor

TMGEOM Tumor model geometry type. SPHERE

TSPHRER Equivalent sphere radius. 1 mm

SFTBNTISSRTO Tumor soft/bone tissue ratios. 100.0%;0.0%

PHYSICS_PACKAGE Physics package. G4EmLivermorePhysics_option3

THREADS_NUMBER Number of running threads. 12

NEVENTS_PTHREAD Number of histories per running thread. 10000

RHIQNQ Ratio histories for charged and no charged particules. 1

SECPCUT Secondary parcticle production cuts. 0.001mm; 0.001mm; 0.001mm

PART_RECYCL Particule recycling option.

SLCT_RADFILE Selected ICRP RAD file. /InterDosi/inputs/RAD_files/ICRP-07.RAD

SLCT_RDNCLDE Selected radionuclide. Na-22

VERBOSITY Simulation detailled messages. Yes

SVSCM S-Value(mGy/MBq/s) CPU time (S)

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