Fast Monte Carlo Simulations for Quality Assurance in Radiation Therapy

Monte Carlo (MC) simulation is generally considered to be the most accurate method for dose calculation in radiation therapy. However, it suffers from the low simulation efficiency (hours to days) and complex configuration, which impede its applications in clinical studies. The recent rise of MRI-guided radiation platform (e.g. ViewRay’s MRIdian system) brings urgent need of fast MC algorithms because the introduced strong magnetic field may cause big errors to other algorithms. My dissertation focuses on resolving the conflict between accuracy and efficiency of MC simulations through 4 different approaches: (1) GPU parallel computation, (2) Transport mechanism simplification, (3) Variance reduction, (4) DVH constraint. Accordingly, we took several steps to thoroughly study the performance and accuracy influence of these methods. As a result, three Monte Carlo simulation packages named gPENELOPE, gDPMvr and gDVH were developed for subtle balance between performance and accuracy in different application scenarios. For example, the most accurate gPENELOPE is usually used as golden standard for radiation meter model, while the fastest gDVH is usually used for quick in-patient dose calculation, which significantly reduces the calculation time from 5 hours to 1.2 minutes (250 times faster) with only 1% error introduced. In addition, a cross-platform GUI integrating simulation kernels and 3D visualization was developed to make the toolkit more user-friendly. After the fast MC infrastructure was established, we successfully applied it to four radiotherapy scenarios: (1) Validate the vender provided Co60 radiation head model by comparing the dose calculated by gPENELOPE to experiment data; (2) Quantitatively study the effect of magnetic field to dose distribution and proposed a strategy to improve treatment planning efficiency; (3) Evaluate the accuracy of the build-in MC algorithm of MRIdian’s treatment planning system. (4) Perform quick quality assurance (QA) for the “online adaptive radiation therapy” that doesn’t permit enough time to perform experiment QA. Many other time-sensitive applications (e.g. motional dose accumulation) will also benefit a lot from our fast MC infrastructure

Development of advanced geometric models and acceleration techniques for Monte Carlo simulation in Medical Physics

Els programes de simulació Monte Carlo de caràcter general s'utilitzen actualment en una gran varietat d'aplicacions.Tot i això, els models geomètrics implementats en la majoria de programes imposen certes limitacions a la forma dels objectes que es poden definir. Aquests models no són adequats per descriure les superfícies arbitràries que es troben en estructures anatòmiques o en certs aparells mèdics i, conseqüentment, algunes aplicacions que requereixen l'ús de models geomètrics molt detallats no poden ser acuradament estudiades amb aquests programes.L'objectiu d'aquesta tesi doctoral és el desenvolupament de models geomètrics i computacionals que facilitin la descripció dels objectes complexes que es troben en aplicacions de física mèdica. Concretament, dos nous programes de simulació Monte Carlo basats en PENELOPE han sigut desenvolupats. El primer programa, penEasy, utilitza un algoritme de caràcter general estructurat i inclou diversos models de fonts de radiació i detectors que permeten simular fàcilment un gran nombre d'aplicacions. Les noves rutines geomètriques utilitzades per aquest programa, penVox, extenen el model geomètric estàndard de PENELOPE, basat en superfícices quàdriques, per permetre la utilització d'objectes voxelitzats. Aquests objectes poden ser creats utilitzant la informació anatòmica obtinguda amb una tomografia computeritzada i, per tant, aquest model geomètric és útil per simular aplicacions que requereixen l'ús de l'anatomia de pacients reals (per exemple, la planificació radioterapèutica). El segon programa, penMesh, utilitza malles de triangles per definir la forma dels objectes simulats. Aquesta tècnica, que s'utilitza freqüentment en el camp del disseny per ordinador, permet representar superfícies arbitràries i és útil per simulacions que requereixen un gran detall en la descripció de la geometria, com per exemple l'obtenció d'imatges de raig x del cos humà.Per reduir els inconvenients causats pels llargs temps d'execució, els algoritmes implementats en els nous programes s'han accelerat utilitzant tècniques sofisticades, com per exemple una estructura octree. També s'ha desenvolupat un paquet de programari per a la paral·lelització de simulacions Monte Carlo, anomentat clonEasy, que redueix el temps real de càlcul de forma proporcional al nombre de processadors que s'utilitzen.Els programes de simulació que es presenten en aquesta tesi són gratuïts i de codi lliures. Aquests programes s'han provat en aplicacions realistes de física mèdica i s'han comparat amb altres programes i amb mesures experimentals.Per tant, actualment ja estan llestos per la seva distribució pública i per la seva aplicació a problemes reals.Monte Carlo simulation of radiation transport is currently applied in a large variety of areas. However, the geometric models implemented in most general-purpose codes impose limitations on the shape of the objects that can be defined. These models are not well suited to represent the free-form (i.e., arbitrary) shapes found in anatomic structures or complex medical devices. As a result, some clinical applications that require the use of highly detailed phantoms can not be properly addressed.This thesis is devoted to the development of advanced geometric models and accelration techniques that facilitate the use of state-of-the-art Monte Carlo simulation in medical physics applications involving detailed anatomical phantoms. To this end, two new codes, based on the PENELOPE package, have been developed. The first code, penEasy, implements a modular, general-purpose main program and provides various source models and tallies that can be readily used to simulate a wide spectrum of problems. Its associated geometry routines, penVox, extend the standard PENELOPE geometry, based on quadric surfaces, to allow the definition of voxelised phantoms. This kind of phantoms can be generated using the information provided by a computed tomography and, therefore, penVox is convenient for simulating problems that require the use of the anatomy of real patients (e.g., radiotherapy treatment planning). The second code, penMesh, utilises closed triangle meshes to define the boundary of each simulated object. This approach, which is frequently used in computer graphics and computer-aided design, makes it possible to represent arbitrary surfaces and it is suitable for simulations requiring a high anatomical detail (e.g., medical imaging).A set of software tools for the parallelisation of Monte Carlo simulations, clonEasy, has also been developed. These tools can reduce the simulation time by a factor that is roughly proportional to the number of processors available and, therefore, facilitate the study of complex settings that may require unaffordable execution times in a sequential simulation.The computer codes presented in this thesis have been tested in realistic medical physics applications and compared with other Monte Carlo codes and experimental data. Therefore, these codes are ready to be publicly distributed as free and open software and applied to real-life problems.Postprint (published version

Development and assessment of estimate methods for internal dosimetry using PET/CT

The aim of this thesis was to assess and develop internal dose calculations methods in diagnostic and therapeutic nuclear medicine procedures to patients undergone PET/CT explorations. Towards this objective, the accuracy and precision of different classical methods commonly used to estimate internal dosimetry were investigated. Biodistribution studies were used in order to compare these methods. The main study aspects included region-of-interest (ROI) delineation methods, reconstruction algorithms, scatter correction and radiopharmaceutical's biokinetic. Optimization of internal dosimetry in this thesis was completed with the development of a Monte Carlo (MC) technique for estimating the patient-specific PET/CT dosimetry. The development of a mathematical model using MC techniques allowed us to have a gold standard to which compare classical techniques and study the aspects discussed previously. It was observed that effective dose (ED) estimations were sensitive to whichever delineation ROI method was applied. Furthermore, it was perceived that the biokinetics of the radioligand also influences in the ED estimation. On the other hand, similar quantitative accuracy was found regarding image reconstruction (FBP and OSEM) and scatter correction methods studied (FSC and SSC). Analysis of the impact of inter- and intra-operator variability in dose estimations revealed higher reproducibility in 3D methods in comparison with 2D planar method. The last one, showed the highest interoperator variability, which implies an overestimation of the ED. In this dissertation, specific routines were developed to be applied with the MC code PENELOPE/penEasy to perform individualized internal dosimetry estimations. Voxel-level absorbed dose maps which include self- and cross-irradiation doses were generated from the morphological and functional patient images. Further parameters such as cumulative organ dose, maximum and minimum voxel organ values, volume of the organ and dose-volume histograms of interest were reported. The model implemented was applied to a theoretical study using simulated PET images of a voxelized Zubal phantom. The results were benchmarked with the ones obtained using the OLINDA/EXM software. The comparison was in good agreement for those organs were both phantoms considered (Zubal and the reference one in OLINDA/EXM) were close. Undoubtedly, the implementation of a patient-specific internal dosimetry method not only leads to an improvement in diagnostic examinations where the risk could be quantified, but also NM therapy could become more effective in terms that patients receiving an optimal care.L'objectiu d'aquesta tesi va ser avaluar i desenvolupar mètodes de càlcul de dosis interna en procediments de diagnòstic i terapèutics de medicina nuclear per a pacients sotmesos a exploracions PET / TC. Amb aquest objectiu, es va investigar l'exactitud i la precisió dels diferents mètodes clàssics utilitzats habitualment per estimar la dosimetria interna. Es van utilitzar estudis de biodistribució per comparar aquests mètodes. Els principals aspectes d'estudi incloïen mètodes de delimitació de la regió d'interès (ROI), algoritmes de reconstrucció, correcció de dispersió i biocinètiques de radiofàrmacs. L'optimització de la dosimetria interna en aquesta tesi es va completar amb el desenvolupament d'una tècnica de Monte Carlo (MC) per a estimar la dosimetria PET / TC específica del pacient. El desenvolupament d'un model matemàtic amb tècniques de MC ens va permetre tenir una referència amb la que comparar les tècniques clàssiques i estudiar els aspectes descrits anteriorment. Es va observar que les estimacions de la dosi efectiva (DE) eren sensibles a qualsevol mètode de delimitació de la ROI aplicada. A més a més, es va percebre que la biocinètica del radiolligand també influeix en l'estimació de la DE. D'altra banda, es va trobar una exactitud quantitativament similar pel que fa a la reconstrucció d'imatges (FBP i OSEM) i els mètodes de correcció de dispersió estudiats (FSC i SSC). L'anàlisi de l'impacte de la variabilitat entre operadors i intra-operadors en les estimacions de dosis va mostrar una major reproductibilitat en els mètodes 3D en comparació amb el mètode planar 2D. Aquest últim, va mostrar la màxima variabilitat entre operadors, la qual cosa implica una sobreestimació de la DE. En aquesta tesi, es van desenvolupar rutines específiques per aplicar-les amb el codi MC PENELOPE / penEasy per a realitzar estimacions de dosimetria interna individualitzades. Es van generar mapes de dosis absorbida a nivell de voxel que incloïen dosis d? autoirradiació i irradiació creuada a partir de les imatges morfològiques i funcionals del pacient. Es van reportar altres paràmetres d?interès com la dosi d'òrgan acumulada, els valors màxims i mínims de l'òrgan i del vòxel, el volum de l'òrgan i els histogrames de dosi-volum. El model implementat es va aplicar a un estudi teòric mitjançant imatges simulades de PET d'un maniquí de Zubal voxelitzat. Els resultats es van comparar amb els obtinguts mitjançant el programa OLINDA / EXM. Es va observar un bon acord per a aquells òrgans semblants entre el maniquí de Zubal i el maniquí de referència del software OLINDA/EXM. Sens dubte, la implementació d'un mètode de dosimetria interna específic per al pacient no només condueix a una millora en les exploracions de diagnòstic on es pot quantificar el risc d?irradiació, sinó que la teràpia amb medicina nuclear podria ser més eficaç en termes que els pacients rebin un tractament òptim.Postprint (published version

Automation of the Monte Carlo simulation of medical linear accelerators

La consulta íntegra de la tesi, inclosos els articles no comunicats públicament per drets d'autor, es pot realitzar prèvia petició a l'Arxiu de la UPCThe main result of this thesis is a software system, called PRIMO, which simulates clinical linear accelerators and the subsequent dose distributions using the Monte Carlo method. PRIMO has the following features: (i) it is self- contained, that is, it does not require additional software libraries or coding; (ii) it includes a geometry library with most Varian and Elekta linacs; (iii) it is based on the general-purpose Monte Carlo code PENELOPE; (iv) it provides a suite of variance-reduction techniques and distributed parallel computing to enhance the simulation efficiency; (v) it is graphical user interfaced; and (vi) it is freely distributed through the website http://www.primoproject.net In order to endow PRIMO with these features the following tasks were conducted: - PRIMO was conceived with a layered structure. The topmost layer, named the GLASS, was developed in this thesis. The GLASS implements the GUI, drives all the functions of the system and performs the analysis of results. Lower layers generate geometry files, provide input data and execute the Monte Carlo simulation. - The geometry of Elekta linacs from series SU and MLCi were coded in the PRIMO system. - A geometrical model of the Varian True Beam linear accelerator was developed and validated. This model was created to surmount the limitations of the Varian distributed phase-space files and the absence of released information about the actual geometry of that machine. This geometry model was incorporated into PRIMO. - Two new variance-reduction techniques, named splitting roulette and selective splitting, were developed and validated. In a test made with an Elekta linac it was found that when both techniques are used in conjunction the simulation efficiency improves by a factor of up to 45. - A method to automatically distribute the simulation among the available CPU cores of a computer was implemented. The following investigations were done using PRIMO as a research tool : - The configu ration of the condensed history transport algorithm for charged particles in PENELOPE was optimized for linac simulation. Dose distributions in the patient were found to be particularly sensitive to the values of the transport parameters in the linac target. Use of inadequate values of these parameters may lead to an incorrect determination of the initial beam configuration or to biased dose distributions. - PRIMO was used to simulate phase-space files distributed by Varian for the True Beam linac. The results were compared with experimental data provided by five European radiotherapycenters. It was concluded thatthe latent variance and the accuracy of the phase-space files were adequate for the routine clinical practice. However, for research purposes where low statistical uncertainties are required the phase-space files are not large enough. To the best of our knowledge PRIMO is the only fully Monte Carlo-based linac and dose simulation system , addressed to research and dose verification, that does not require coding tasks from end users and is publicly available.El principal resultado de esta tesis es un sistema informático llamado PRIMO el cual simula aceleradores lineales médicos y las subsecuentes distribuciones de dosis empleando el método de Monte Carlo. PRIMO tiene las siguiente características: (i) es auto contenido, o sea no requiere de librerías de código ni de programación adicional ; (ii) incluye las geometrías de los principales modelos de aceleradores Varían y Elekta; (iii) está basado en el código Monte Carlo de propósitos generales PENELOPE; (iv) contiene un conjunto de técnicas de reducción de varianza y computación paralela distribuida para mejorar la eficiencia de simulación; (v) tiene una interfaz gráfica de usuario; y (vi) se distribuye gratis en el sitio web http://vvww.primoproject.net. Para dotar a PRIMO de esas características, se realizaron las tareas siguientes: - PRIMO se concibió con una estructura de capas. La capa superior, nombrada GLASS, fue desarrollada en esta tesis. GLASS implementa la interfazgráfica de usuario, controla todas las funciones del sistema y realiza el análisis de resultados. Las capas inferiores generan los archivos de geometría y otros datos de entrada y ejecutan la simulación Monte Carlo. - Se codificó en el sistema PRIMO la geometría de los aceleradores Elekta de las series SLi y MLC. - Se desarrolló y validó un modelo geométrico del acelerador TrueBeam de Varian. Este modelo fue creado para superar las limitaciones de los archivos de espacio de fase distribuidos por Varian, así como la ausencia de información sobre la geometría real de esta máquina. Este modelo geométrico fue incorporado en PRIMO. - Fueron desarrolladas y validadas dos nuevas técnicas de reducción de varianza nombradas splitting roulette y selective splitting. En pruebas hechas en un acelerador Elekta se encontró que cuando ambas técnicas se usan en combinación, la eficiencia de simulación mejora 45 veces. - Se implementó un método para distribuir la simulación entre los procesadores disponibles en un ordenador. Las siguientes investigaciones fueron realizadas usando PRIMO como herramienta: - Fue optimizada la configuración del algoritmo de PENELOPE para el transporte de partículas cargadas con historia condensada en la simulación del linac. Se encontró que las distribuciones de dosis en el paciente son particularmente sensibles a los valores de los parámetros de transporte usados para el target del linac. El uso de va lores inadecuados para esos parámetros puede conducir a una incorrecta determinación de la configuración del haz inicial o producir sesgos en las distribuciones de dosis. - Se utilizó PRIMO para simular archivos de espacios de fase distribuidos por Varian para el linac TrueBeam. Los resultados se compararon con datos experimentales aportados por cinco centros de radioterapia europeos. Se concluyó que la varianza latente y la exactitud de estos espacios de fase son adecuadas para la práctica clínica de rutina. Sin embargo estos espacios de fase no son suficientemente grandes para emplearse en investigaciones que requieren alcanzar una baja incertidumbre estadística. Hasta donde conocemos, PRIMO es el único sistema Monte Carlo que simula completamente el acelerador lineal y calcula la dosis absorbida, dirigido a la investigación y la verificación de dosis que no requiere del usuario tareas de codificación y está disponible públicamentePostprint (published version

Dose assessment and reconstruction algorithm optimization in simultaneous breast and lung CT imaging

Cancer is the second leading cause of death in the world, and therefore, there is an undeniable need to ensure early screening and detection systems worldwide. The aim of this project is to study the feasibility of a Cone Beam Computed Tomography (CBCT) scanner for simultaneous breast and lung imaging. Additionally, the development of reconstruction algorithms and the study of their impact to the image quality was considered. Monte Carlo (MC) simulations were performed using the PENELOPE code system. A MC geometry model of a CBCT scanner was implemented for energies of 30 keV and 80 keV for hypothetical scanning protocols. Microcalcifications were inserted into the breast and lung of the computational phantom (ICRP Adult Female Reference), used in the simulations for dose assessment and projection acquisition. Reconstructed images were analyzed in terms of the Contrast-to-Noise Ratio (CNR) and dose calculations were performed for two protocols, one with a normalization factor of 2 mGy in the breast and another with 5 mGy in the lungs. Both, MC geometry model and reconstruction algorithm were validated by means of on-field measurements and data acquisition in a clinical center. Dosimetric and imaging performances were evaluated through Quality Assurance phantoms (Computed Tomography Dose Index and Catphan, respectively). Results indicate that the best implementation of the reconstruction algorithm was achieved with 80 keV, using the Hanning filter and linear interpolation. More specifically, for a spherical lung lesion with a radius of 7 mm a 30% CNR gain was found when the number of projections varied from 12 to 36 (corresponding to a dose increase of a factor of 3). This research suggests the possibility of developing a CBCT modulated beam scanner for simultaneous breast and lung imaging while ensuring dose reduction. However further investigation regarding the number of projections needed for image reconstruction is required

Development of Human Body CAD Models and Related Mesh Processing Algorithms with Applications in Bioelectromagnetics

Simulation of the electromagnetic response of the human body relies heavily upon efficient computational CAD models or phantoms. The Visible Human Project (VHP)-Female v. 3.1 - a new platform-independent full-body electromagnetic computational model is revealed. This is a part of a significant international initiative to develop powerful computational models representing the human body. This model’s unique feature is full compatibility both with MATLAB and specialized FEM computational software packages such as ANSYS HFSS/Maxwell 3D and CST MWS. Various mesh processing algorithms such as automatic intersection resolver, Boolean operation on meshes, etc. used for the development of the Visible Human Project (VHP)-Female are presented. The VHP - Female CAD Model is applied to two specific low frequency applications: Transcranial Magnetic Stimulation (TMS) and Transcranial Direct Current Stimulation (tDCS). TMS and tDCS are increasingly used as diagnostic and therapeutic tools for numerous neuropsychiatric disorders. The development of a CAD model based on an existing voxel model of a Japanese pregnant woman is also presented. TMS for treatment of depression is an appealing alternative to drugs which are teratogenic for pregnant women. This CAD model was used to study fetal wellbeing during induced peak currents by TMS in two possible scenarios: (i) pregnant woman as a patient; and (ii) pregnant woman as an operator. An insight into future work and potential areas of research such as a deformable phantom, implants, and RF applications will be presented

Brain and Human Body Modeling

This open access book describes modern applications of computational human modeling with specific emphasis in the areas of neurology and neuroelectromagnetics, depression and cancer treatments, radio-frequency studies and wireless communications. Special consideration is also given to the use of human modeling to the computational assessment of relevant regulatory and safety requirements. Readers working on applications that may expose human subjects to electromagnetic radiation will benefit from this book’s coverage of the latest developments in computational modelling and human phantom development to assess a given technology’s safety and efficacy in a timely manner. Describes construction and application of computational human models including anatomically detailed and subject specific models; Explains new practices in computational human modeling for neuroelectromagnetics, electromagnetic safety, and exposure evaluations; Includes a survey of modern applications for which computational human models are critical; Describes cellular-level interactions between the human body and electromagnetic fields

Full-body Shell Creation for CAD Virtual Humans including Tightly-Spaced, Enclosed Shells

Computational human models have become essential in several different biomedical and electrical engineering research areas. They enable scientists to study, model, and solve complex problems of human body responses to various external stimuli including electromagnetic and radio-frequency signals. This study describes the algorithms and procedures of creating multi-tissue full-body Computer-Aided Design (CAD) human models. An emphasis is made on full-body shells of variable thicknesses, e.g. skin, fat, and average body container shells. Such shells, along with internal organs, are useful for multiple high- and low-frequency simulations in a variety of applications. Along with the creation of full-body models, an automatic algorithm to selectively decimate the meshes based on average surface curvature is developed. The algorithm will significantly reduce model size while keeping the same interpolation accuracy

Brain and Human Body Modeling

This open access book describes modern applications of computational human modeling with specific emphasis in the areas of neurology and neuroelectromagnetics, depression and cancer treatments, radio-frequency studies and wireless communications. Special consideration is also given to the use of human modeling to the computational assessment of relevant regulatory and safety requirements. Readers working on applications that may expose human subjects to electromagnetic radiation will benefit from this book’s coverage of the latest developments in computational modelling and human phantom development to assess a given technology’s safety and efficacy in a timely manner. Describes construction and application of computational human models including anatomically detailed and subject specific models; Explains new practices in computational human modeling for neuroelectromagnetics, electromagnetic safety, and exposure evaluations; Includes a survey of modern applications for which computational human models are critical; Describes cellular-level interactions between the human body and electromagnetic fields