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Asai, M., Cortes-Giraldo, M. A., Gimenez-Alventosa, V., Gimenez, V., & Salvat, F. (2021). The PENELOPE Physics Models and Transport Mechanics. Implementation into Geant4. Front. Physics, 9, 738735–20pp.
Abstract: A translation of the penelope physics subroutines to C++, designed as an extension of the Geant4 toolkit, is presented. The Fortran code system penelope performs Monte Carlo simulation of coupled electron-photon transport in arbitrary materials for a wide energy range, nominally from 50 eV up to 1 GeV. Penelope implements the most reliable interaction models that are currently available, limited only by the required generality of the code. In addition, the transport of electrons and positrons is simulated by means of an elaborate class II scheme in which hard interactions (involving deflection angles or energy transfers larger than pre-defined cutoffs) are simulated from the associated restricted differential cross sections. After a brief description of the interaction models adopted for photons and electrons/positrons, we describe the details of the class-II algorithm used for tracking electrons and positrons. The C++ classes are adapted to the specific code structure of Geant4. They provide a complete description of the interactions and transport mechanics of electrons/positrons and photons in arbitrary materials, which can be activated from the G4ProcessManager to produce simulation results equivalent to those from the original penelope programs. The combined code, named PenG4, benefits from the multi-threading capabilities and advanced geometry and statistical tools of Geant4.
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Gimenez-Alventosa, V., Antunes, P. C. G., Vijande, J., Ballester, F., Perez-Calatayud, J., & Andreo, P. (2017). Collision-kerma conversion between dose-to-tissue and dose-to-water by photon energy-fluence corrections in low-energy brachytherapy. Phys. Med. Biol., 62(1), 146–164.
Abstract: The AAPM TG-43 brachytherapy dosimetry formalism, introduced in 1995, has become a standard for brachytherapy dosimetry worldwide; it implicitly assumes that charged-particle equilibrium (CPE) exists for the determination of absorbed dose to water at different locations, except in the vicinity of the source capsule. Subsequent dosimetry developments, based on Monte Carlo calculations or analytical solutions of transport equations, do not rely on the CPE assumption and determine directly the dose to different tissues. At the time of relating dose to tissue and dose to water, or vice versa, it is usually assumed that the photon fluence in water and in tissues are practically identical, so that the absorbed dose in the two media can be related by their ratio of mass energy-absorption coefficients. In this work, an efficient way to correlate absorbed dose to water and absorbed dose to tissue in brachytherapy calculations at clinically relevant distances for low-energy photon emitting seeds is proposed. A correction is introduced that is based on the ratio of the water-to-tissue photon energy-fluences. State-of-the art Monte Carlo calculations are used to score photon fluence differential in energy in water and in various human tissues (muscle, adipose and bone), which in all cases include a realistic modelling of low-energy brachytherapy sources in order to benchmark the formalism proposed. The energy-fluence based corrections given in this work are able to correlate absorbed dose to tissue and absorbed dose to water with an accuracy better than 0.5% in the most critical cases (e.g. bone tissue).
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Gimenez-Alventosa, V., Ballester, F., & Vijande, J. (2016). VoxelMages: a general-purpose graphical interface for designing geometries and processing DICOM images for PENELOPE. Appl. Radiat. Isot., 118, 251–257.
Abstract: The design and construction of geometries for Monte Carlo calculations is an error-prone, time-consuming, and complex step in simulations describing particle interactions and transport in the field of medical physics. The software VoxelMages has been developed to help the user in this task. It allows to design complex geometries and to process DICOM image files for simulations with the general-purpose Monte Carlo code PENELOPE in an easy and straightforward way. VoxelMages also allows to import DICOM-RT structure contour information as delivered by a treatment planning system. Its main characteristics, usage and performance benchmarking are described in detail.
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Gimenez-Alventosa, V., Gimenez, V., Ballester, F., Vijande, J., & Andreo, P. (2020). Monte Carlo calculation of beam quality correction factors for PTW cylindrical ionization chambers in photon beams. Phys. Med. Biol., 65(20), 205005–11pp.
Abstract: The beam quality correction factork(Q)for megavoltage photon beams has been calculated for eight PTW (Freiburg, Germany) ionization chambers (Farmer chambers PTW30010, PTW30011, PTW30012, and PTW30013, Semiflex 3D chambers PTW31021, PTW31010, and PTW31013, and the PinPoint 3D chamber PTW31016). Simulations performed on the widely used NE-2571 ionization chamber have been used to benchmark the results. The Monte Carlo code PENELOPE/penEasy was used to calculate the absorbed dose to a point in water and the absorbed dose to the active air volume of the chambers for photon beams in the range 4 to 24 MV. Of the nine ionization chambers analysed, only five are included in the current version of the International Code of Practice for dosimetry based on standards of absorbed dose to water (IAEA TRS 398). The values reported in this work agree with those in the literature within the uncertainty estimates and are to be included in the average values of the data obtained by different working groups for the forthcoming update of TRS 398.
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Gimenez-Alventosa, V., Gimenez, V., Ballester, F., Vijande, J., & Andreo, P. (2018). Correction factors for ionization chamber measurements with the 'Valencia' and 'large field Valencia' brachytherapy applicators. Phys. Med. Biol., 63(12), 125004–10pp.
Abstract: Treatment of small skin lesions using HDR brachytherapy applicators is a widely used technique. The shielded applicators currently available in clinical practice are based on a tungsten-alloy cup that collimates the source-emitted radiation into a small region, hence protecting nearby tissues. The goal of this manuscript is to evaluate the correction factors required for dose measurements with a plane-parallel ionization chamber typically used in clinical brachytherapy for the 'Valencia' and 'large field Valencia' shielded applicators. Monte Carlo simulations have been performed using the PENELOPE-2014 system to determine the absorbed dose deposited in a water phantom and in the chamber active volume with a Type A uncertainty of the order of 0.1%. The average energies of the photon spectra arriving at the surface of the water phantom differ by approximately 10%, being 384 keV for the 'Valencia' and 343 keV for the 'large field Valencia'. The ionization chamber correction factors have been obtained for both applicators using three methods, their values depending on the applicator being considered. Using a depth-independent global chamber perturbation correction factor and no shift of the effective point of measurement yields depth-dose differences of up to 1% for the 'Valencia' applicator. Calculations using a depth-dependent global perturbation factor, or a shift of the effective point of measurement combined with a constant partial perturbation factor, result in differences of about 0.1% for both applicators. The results emphasize the relevance of carrying out detailed Monte Carlo studies for each shielded brachytherapy applicator and ionization chamber.
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Gimenez-Alventosa, V., Gimenez, V., & Oliver, S. (2021). PenRed: An extensible and parallel Monte-Carlo framework for radiation transport based on PENELOPE. Comput. Phys. Commun., 267, 108065–12pp.
Abstract: Monte Carlo methods provide detailed and accurate results for radiation transport simulations. Unfortunately, the high computational cost of these methods limits its usage in real-time applications. Moreover, existing computer codes do not provide a methodology for adapting these kinds of simulations to specific problems without advanced knowledge of the corresponding code system, and this restricts their applicability. To help solve these current limitations, we present PenRed, a general-purpose, standalone, extensible and modular framework code based on PENELOPE for parallel Monte Carlo simulations of electron-photon transport through matter. It has been implemented in C++ programming language and takes advantage of modern object-oriented technologies. In addition, PenRed offers the capability to read and process DICOM images as well as to construct and simulate image-based voxelized geometries, so as to facilitate its usage in medical applications. Our framework has been successfully verified against the original PENELOPE Fortran code. Furthermore, the implemented parallelism has been tested showing a significant improvement in the simulation time without any loss in precision of results. Program summary Program title: PenRed: Parallel Engine for Radiation Energy Deposition. CPC Library link to program files: https://doi .org /10 .17632/rkw6tvtngy.1 Licensing provision: GNU Affero General Public License (AGPL). Programming language: C++ standard 2011. Nature of problem: Monte Carlo simulations usually require a huge amount of computation time to achieve low statistical uncertainties. In addition, many applications necessitate particular characteristics or the extraction of specific quantities from the simulation. However, most available Monte Carlo codes do not provide an efficient parallel and truly modular structure which allows users to easily customise their code to suit their needs without an in-depth knowledge of the code system. Solution method: PenRed is a fully parallel, modular and customizable framework for Monte Carlo simulations of the passage of radiation through matter. It is based on the PENELOPE [1] code system, from which inherits its unique physics models and tracking algorithms for charged particles. PenRed has been coded in C++ following an object-oriented programming paradigm restricted to the C++11 standard. Our engine implements parallelism via a double approach: on the one hand, by using standard C++ threads for shared memory, improving the access and usage of the memory, and, on the other hand, via the MPI standard for distributed memory infrastructures. Notice that both kinds of parallelism can be combined together in the same simulation. Moreover, both threads and MPI processes, can be balanced using the builtin load balance system (RUPER-LB [30]) to maximise the performance on heterogeneous infrastructures. In addition, PenRed provides a modular structure with methods designed to easily extend its functionality. Thus, users can create their own independent modules to adapt our engine to their needs without changing the original modules. Furthermore, user extensions will take advantage of the builtin parallelism without any extra effort or knowledge of parallel programming. Additional comments including restrictions and unusual features: PenRed has been compiled in linux systems withg++ of GCC versions 4.8.5, 7.3.1, 8.3.1 and 9; clang version 3.4.2 and intel C++ compiler (icc) version 19.0.5.281. Since it is a C++11-standard compliant code, PenRed should be able to compile with any compiler with C++11 support. In addition, if the code is compiled without MPI support, it does not require any non standard library. To enable MPI capabilities, the user needs to install whatever available MPI implementation, such as openMPI [24] or mpich [25], which can be found in the repositories of any linux distribution. Finally, to provide DICOM processing support, PenRed can be optionally compiled using the dicom toolkit (dcmtk) [32] library. Thus, PenRed has only two optional dependencies, an MPI implementation and the dcmtk library.
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Gimenez-Alventosa, V., Vijande, J., Ballester, F., & Perez-Calatayud, J. (2016). Transit dose comparisons for Co-60 and Ir-192 HDR sources. J. Radiol. Prot., 36(4), 858–864.
Abstract: The goal of this study is to evaluate the ambient dose due to the transit of high dose rate (HDR) Co-60 sources along a transfer tube as compared to Ir-192 ones in a realistic clinical scenario. This goal is accomplished by evaluating air-kerma differences with Monte Carlo calculations using PENELOPE2011. Scatter from both the afterloader and the patient was not taken into account. Two sources, mHDR-v2 and Flexisource Co-60, (Elekta Brachytherapy, Veenendaal, the Netherlands) have been considered. These sources were simulated within a standard transfer tube located in an infinite air phantom. The movement of the source was included by displacing their positions along the connecting tube from z = – 75 cm to z = + 75 cm and combining them. Since modern afterloaders like Flexitron (Elekta) or Saginova (BEBIG GmbH) are able to use equally 192Ir and 60Co sources, it was assumed that both sources are displaced with equal speed. Typical HDR source activity content values were provided by the manufacturer. 2D distributions were obtained with type-A uncertainties (k = 2) less than 0.01%. From those, the air-kerma ratio Co-60/Ir-192 was evaluated weighted by their corresponding typical activities. It was found that it varies slowly with distance (less than 10% variation at 75 cm) but strongly in time due to the shorter half-life of the 192Ir (73.83 d). The maximum ratio is located close to the tube. It reaches a value of 0.57 when the typical activity of the sources at the time when they were installed by the vendor was used. Such ratio increases up to 1.28 at the end of the recommended working life (90 d) of the Ir-192 source. Co-60/Ir-192 air-kerma ratios are almost constant (0.51-0.57) in the vicinity of the source-tube with recent installed sources. Nevertheless, air-kerma ratios increase rapidly (1.15-1.29) whenever the Ir-192 is approaching the end of its life. In case of a medical event requiring the medical staff to access the treatment room, these ratios indicate that the dosimetric impact on the medical team will be lower, with a few exceptions, in the case of Co-60-based HDR brachytherapy as compared to Ir-192-based one when typical air-kerma strength values are considered.
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Oliver, S., Gimenez-Alventosa, V., Berumen, F., Gimenez, V., Beaulieu, L., Ballester, F., et al. (2023). Benchmark of the PenRed Monte Carlo framework for HDR brachytherapy. Z. Med. Phys., 33(4), 511–528.
Abstract: Purpose: The purpose of this study is to validate the PenRed Monte Carlo framework for clinical applications in brachytherapy. PenRed is a C++ version of Penelope Monte Carlo code with additional tallies and utilities. Methods and materials: Six benchmarking scenarios are explored to validate the use of PenRed and its improved bachytherapy-oriented capabilities for HDR brachytherapy. A new tally allowing the evaluation of collisional kerma for any material using the track length kerma estimator and the possibility to obtain the seed positions, weights and directions processing directly the DICOM file are now implemented in the PenRed distribution. The four non-clinical test cases developed by the Joint AAPM-ESTRO-ABG-ABS WG-DCAB were evaluated by comparing local and global absorbed dose differences with respect to established reference datasets. A prostate and a palliative lung cases, were also studied. For them, absorbed dose ratios, global absorbed dose differences, and cumulative dose-volume histograms were obtained and discussed. Results: The air-kerma strength and the dose rate constant corresponding to the two sources agree with the reference datatests within 0.3% (Sk) and 0.1% (K). With respect to the first three WG-DCAB test cases, more than 99.8% of the voxels present local (global) differences within +/- 1%(+/- 0.1%) of the reference datasets. For test Case 4 reference dataset, more than 94.9%(97.5%) of voxels show an agreement within +/- 1%(+/- 0.1%), better than similar benchmarking calculations in the literature. The track length kerma estimator scorer implemented increases the numerical efficiency of brachytherapy calculations two orders of magnitude, while the specific brachytherapy source allows the user to avoid the use of error-prone intermediate steps to translate the DICOM information into the simulation. In both clinical cases, only minor absorbed dose differences arise in the low-dose isodoses. 99.8% and 100% of the voxels have a global absorbed dose difference ratio within +/- 0.2%for the prostate and lung cases, respectively. The role played by the different segmentation and composition material in the bone structures was discussed, obtaining negligible absorbed dose differ-ences. Dose-volume histograms were in agreement with the reference data.Conclusions: PenRed incorporates new tallies and utilities and has been validated for its use for detailed and precise high-dose-rate brachytherapy simulations.
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Oliver, S., Rodriguez Bosca, S., & Gimenez-Alventosa, V. (2024). Enabling particle transport on CAD-based geometries for radiation simulations with penRed. Comput. Phys. Commun., 298, 109091–11pp.
Abstract: Geometry construction is a fundamental aspect of any radiation transport simulation, regardless of the Monte Carlo code being used. Typically, this process is tedious, time-consuming, and error-prone. The conventional approach involves defining geometries using mathematical objects or surfaces. However, this method comes with several limitations, especially when dealing with complex models, particularly those with organic shapes. Furthermore, since each code employs its own format and methodology for defining geometries, sharing and reproducing simulations among researchers becomes a challenging task. Consequently, many codes have implemented support for simulating over geometries constructed via Computer-Aided Design (CAD) tools. Unfortunately, this feature is lacking in penRed and other PENELOPE physics-based codes. Therefore, the objective of this work is to implement such support within the penRed framework. New version program summary Program Title: Parallel Engine for Radiation Energy Deposition (penRed) CPC Library link to program files: https://doi.org/10.17632/rkw6tvtngy.2 Developer's repository link: https://github.com/PenRed/PenRed Code Ocean capsule: https://codeocean.com/capsule/1041417/tree Licensing provisions: GNU Affero General Public License v3 Programming language: C++ standard 2011. Journal reference of previous version: V. Gimenez-Alventosa, V. Gimenez Gomez, S. Oliver, PenRed: An extensible and parallel Monte-Carlo framework for radiation transport based on PENELOPE, Computer Physics Communications 267 (2021) 108065. doi:https://doi.org/10.1016/j.cpc.2021.108065. Does the new version supersede the previous version?: Yes Reasons for the new version: Implements the capability to simulate on CAD constructed geometries, among many other features and fixes. Summary of revisions: All changes applied through the code versions are summarized in the file CHANGELOG.md in the repository package. Nature of problem: While Monte Carlo codes have proven valuable in simulating complex radiation scenarios, they rely heavily on accurate geometrical representations. In the same way as many other Monte Carlo codes, penRed employs simple geometric quadric surfaces like planes, spheres and cylinders to define geometries. However, since these geometric models offer a certain level of flexibility, these representations have limitations when it comes to simulating highly intricate and irregular shapes. Anatomic structures, for example, require detailed representations of organs, tissues and bones, which are difficult to achieve using basic geometric objects. Similarly, complex devices or intricate mechanical systems may have designs that cannot be accurately represented within the constraints of such geometric models. Moreover, when the complexity of the model increases, geometry construction process becomes more difficult, tedious, time-consuming and error-prone [2]. Also, as each Monte Carlo geometry library uses its own format and construction method, reproducing the same geometry among different codes is a challenging task. Solution method: To face the problems stated above, the objective of this work is to implement the capability to simulate using irregular and adaptable meshed geometries in the penRed framework. This kind of meshes can be constructed using Computer-Aided Design (CAD) tools, the use of which is very widespread and streamline the design process. This feature has been implemented in a new geometry module named “MESH_BODY” specific for this kind of geometries. This one is freely available and usable within the official penRed package1. It can be used since penRed version 1.9.3b and above.
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Valdes-Cortez, C., Ballester, F., Vijande, J., Gimenez, V., Gimenez-Alventosa, V., Perez-Calatayud, J., et al. (2020). Depth-dose measurement corrections for the surface electronic brachytherapy beams of an Esteya(R) unit: a Monte Carlo study. Phys. Med. Biol., 65(24), 245026–12pp.
Abstract: Three different correction factors for measurements with the parallel-plate ionization chamber PTW T34013 on the Esteya electronic brachytherapy unit have been investigated. This chamber type is recommended by AAPM TG-253 for depth-dose measurements in the 69.5 kV x-ray beam generated by the Esteya unit. Monte Carlo simulations using the PENELOPE-2018 system were performed to determine the absorbed dose deposited in water and in the chamber sensitive volume at different depths with a Type A uncertainty smaller than 0.1%. Chamber-to-chamber differences have been explored performing measurements using three different chambers. The range of conical applicators available, from 10 to 30 mm in diameter, has been explored. Using a depth-independent global chamber perturbation correction factor without a shift of the effective point of measurement yielded differences between the absorbed dose to water and the corrected absorbed dose in the sensitive volume of the chamber of up to 1% and 0.6% for the 10 mm and 30 mm applicators, respectively. Calculations using a depth-dependent perturbation factor, including or excluding a shift of the effective point of measurement, resulted in depth-dose differences of about +/- 0.5% or less for both applicators. The smallest depth-dose differences were obtained when a shift of the effective point of measurement was implemented, being displaced 0.4 mm towards the center of the sensitive volume of the chamber. The correction factors were obtained with combined uncertainties of 0.4% (k = 2). Uncertainties due to chamber-to-chamber differences are found to be lower than 2%. The results emphasize the relevance of carrying out detailed Monte Carlo studies for each electronic brachytherapy device and ionization chamber used for its dosimetry.
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