GPU-based Monte Carlo Research Articles

Adaptive assessment based on fractional CBCT images for cervical cancer.

Anatomical and other changes during radiotherapy will cause inaccuracy of dose distributions, therefore the expectation for online adaptive radiation therapy (ART) is high in effectively reducing uncertainties due to intra-variation. However, ART requires extensive time and effort. This study investigated an adaptive assessment workflow based on fractional cone-beam computed tomography (CBCT) images. Image registration, synthetic CT (sCT) generation, auto-segmentation, and dose calculation were implemented and integrated into ArcherQA Adaptive Check. The rigid registration was based on ITK open source. The deformable image registration (DIR) method was based on a 3D multistage registration network, and the sCT generation method was performed based on a 2D cycle-consistent adversarial network (CycleGAN). The auto-segmentation of organs at risk (OARs) on sCT images was finished by a deep learning-based auto-segmentation software, DeepViewer. The contours of targets were obtained by the structure-guided registration. Finally, the dose calculation was based on a GPU-based Monte Carlo (MC) dose code, ArcherQA. The dice similarity coefficient (DSCs) were over 0.86 for target volumes and over 0.79 for OARs. The gamma pass rate of ArcherQA versus Eclipse treatment planning system was more than 99% at the 2%/2mm criterion with a low-dose threshold of 10%. The time for the whole process was less than 3 min. The dosimetric results of ArcherQA Adaptive Check were consistent with the Ethos scheduled plan, which can effectively identify the fractions that need the implementation of the Ethos adaptive plan. This study integrated AI-based technologies and GPU-based MC technology to evaluate the dose distributions using fractional CBCT images, demonstrating remarkably high efficiency and precision to support future ART processes.

Technical note: A GPU-based shared Monte Carlo method for fast photon transport in multi-energy x-ray exposures.

The Monte Carlo (MC) method is an accurate technique for particle transport calculation due to the precise modeling of physical interactions. Nevertheless, the MC method still suffers from the problem of expensive computational cost, even with graphics processing unit (GPU) acceleration. Our previous works have investigated the acceleration strategies of photon transport simulation for single-energy CT. But for multi-energy CT, conventional individual simulation leads to unnecessary redundant calculation, consuming more time. This work proposes a novel GPU-based shared MC scheme (gSMC) to reduce unnecessary repeated simulations of similar photons between different spectra, thereby enhancing the efficiency of scatter estimation in multi-energy x-ray exposures. The shared MC method selects shared photons between different spectra using two strategies. Specifically, we introduce spectral region classification strategy to select photons with the same initial energy from different spectra, thus generating energy-shared photon groups. Subsequently, the multi-directional sampling strategy is utilized to select energy-and-direction-shared photons, which have the same initial direction, from energy-shared photon groups. Energy-and-direction-shared photons perform shared simulations, while others are simulated individually. Finally, all results are integrated to obtain scatter distribution estimations for different spectral cases. The efficiency and accuracy of the proposed gSMC are evaluated on the digital phantom and clinical case. The experimental results demonstrate that gSMC can speed up the simulation in the digital case by ∼37.8% and the one in the clinical case by ∼20.6%, while keeping the differences in total scatter results within 0.09%, compared to the conventional MC package, which performs an individual simulation. The proposed GPU-based shared MC simulation method can achieve fast photon transport calculation for multi-energy x-ray exposures.

A GPU-based fast Monte Carlo code that supports proton transport in magnetic field for radiation therapy.

This paper presents the effort to extend a previously reported code ARCHER, a GPU-based Monte Carlo (MC) code for coupled photon and electron transport, into protons including the consideration of magnetic fields. The proton transport is modeled using a Class-II condensed-history algorithm with continuous slowing-down approximation. The model includes ionization, multiple scattering, energy straggling, elastic and inelastic nuclear interactions, as well as deflection due to the Lorentz force in magnetic fields. An additional direction change is added for protons at the end of each step in the presence of the magnetic field. Secondary charge particles, except for protons, are terminated depositing kinetic energies locally, whereas secondary neutral particles are ignored. Each proton is transported step by step until its energy drops to below 0.5 MeV or when the proton leaves the phantom. The code is implemented using the compute unified device architecture (CUDA) platform for optimized GPU thread-level parallelism and efficiency. The code is validated by comparing it against TOPAS. Comparisons of dose distributions between our code and TOPAS for several exposure scenarios, ranging from single square beams in water to patient plan with magnetic fields, show good agreement. The 3D-gamma pass rate with a 2mm/2% criterion in the region with dose greater than 10% of the maximum dose is computed to be over 99% for all tested cases. Using a single NVIDIA TITAN V GPU card, the computational time of ARCHER is found to range from 0.82 to 4.54 seconds for 1×107 proton histories. Compared to a few hours running on TOPAS, this speed improvement is significant. This work presents, for the first time, the performance of a GPU-based MC code to simulate proton transportation magnetic fields, demonstrating the feasibility of accurate and efficient dose calculations in potential magnetic resonance imaging (MRI)-guided proton therapy.

GPU-Accelerated Monte Carlo Simulation for a Single-Photon Underwater Lidar

The Monte Carlo (MC) simulation, due to its ability to accurately simulate the backscattered signal of lidar, plays a crucial role in the design, optimization, and interpretation of the backscattered signal in lidar systems. Despite the development of several MC models for lidars, a suitable MC simulation model for underwater single-photon lidar, which is a vital ocean remote sensing technique utilized in underwater scientific investigations, obstacle avoidance for underwater platforms, and deep-sea environmental exploration, is still lacking. There are two main challenges in underwater lidar simulation. Firstly, the simulation results are significantly affected by near-field abnormal signals. Secondly, the simulation process is time-consuming due to the requirement of a high number of random processes to obtain reliable results. To address these issues, an algorithm is proposed to minimize the impacts of abnormal simulation signals. Additionally, a graphics processing unit (GPU)-accelerated semi-analytic MC simulation with a compute unified device architecture is proposed. The performance of the GPU-based program was validated using 109 photons and compared to a central processing unit (CPU)-based program. The GPU-based program achieved up to 68 times higher efficiency and a maximum relative deviation of less than 1.5%. Subsequently, the MC model was employed to simulate the backscattered signal in inhomogeneous water using the Henyey–Greenstein phase functions. By utilizing the look-up table method, simulations of backscattered signals were achieved using different scattering phase functions. Finally, a comparison between the simulation results and measurements derived from an underwater single-photon lidar demonstrated the reliability and robustness of our GPU-based MC simulation model.

A fast GPU-accelerated Monte Carlo engine for calculation of MLC-collimated electron fields.

Although intensity-modulated radiation therapy and volumetric arc therapy have revolutionized photon external beam therapies, the technological advances associated with electron beam therapy have fallen behind. Modern linear accelerators contain technologies that would allow for more advanced forms of electron treatments, such as beam collimation, using the conventional photon multi-leaf collimator (MLC); however, no commercial solutions exist that calculate dose from such beam delivery modes. Additionally, for clinical adoption to occur, dose calculation times would need to be on par with that of modern dose calculation algorithms. This work developed a graphics processing unit (GPU)-accelerated Monte Carlo (MC) engine incorporating the Varian TrueBeam linac head geometry for a rapid calculation of electron beams collimated using the conventional photon MLC. A compute unified device architecture framework was created for the following: (1) transport of electrons and photons through the linac head geometry, considering multiple scattering, Bremsstrahlung, Møller, Compton, and pair production interactions; (2) electron and photon propagation through the CT geometry, considering all interactions plus the photoelectric effect; and (3) secondary particle cascades through the linac head and within the CT geometry. The linac head collimating geometry was modeled according to the specifications provided by the vendor, who also provided phase-space files. The MC was benchmarked against EGSnrc/DOSXYZnrc/GEANT by simulating individual interactions with simple geometries, pencil, and square beam dose calculations in various phantoms. MC-calculated dose distributions for MLC and jaw-collimated electron fields were compared to measurements in a water phantom and with radiochromic film. Pencil and square beam dose distributions are in good agreement with DOSXYZnrc. Angular and spatial distributions for multiple scattering and secondary particle production in thin slab geometries are in good agreement with EGSnrc and GEANT. Dose profiles for MLC and jaw-collimated 6-20-MeV electron beams showed an average absolute difference of 1.1 and 1.9mm for the FWHM and 80%-20% penumbra from measured profiles. Percent depth doses showed differences of <5% for as compared to measurement. The computation time on an NVIDIA Tesla V100 card was 2.5min to achieve a dose uncertainty of <1%, which is ∼300 times faster than published results in a similar geometry using a single-CPU core. The GPU-based MC can quickly calculate dose for electron fields collimated using the conventional photon MLC. The fast calculation times will allow for a rapid calculation of electron fields for mixed photon and electron particle therapy.

MOQUI: an open-source GPU-based Monte Carlo code for proton dose calculation with efficient data structure

Objective. Monte Carlo (MC) codes are increasingly used for accurate radiotherapy dose calculation. In proton therapy, the accuracy of the dose calculation algorithm is expected to have a more significant impact than in photon therapy due to the depth-dose characteristics of proton beams. However, MC simulations come at a considerable computational cost to achieve statistically sufficient accuracy. There have been efforts to improve computational efficiency while maintaining sufficient accuracy. Among those, parallelizing particle transportation using graphic processing units (GPU) achieved significant improvements. Contrary to the central processing unit, a GPU has limited memory capacity and is not expandable. It is therefore challenging to score quantities with large dimensions requiring extensive memory. The objective of this study is to develop an open-source GPU-based MC package capable of scoring those quantities. Approach. We employed a hash-table, one of the key-value pair data structures, to efficiently utilize the limited memory of the GPU and score the quantities requiring a large amount of memory. With the hash table, only voxels interacting with particles will occupy memory, and we can search the data efficiently to determine their address. The hash-table was integrated with a novel GPU-based MC code, moqui. Main results. The developed code was validated against an MC code widely used in proton therapy, TOPAS, with homogeneous and heterogeneous phantoms. We also compared the dose calculation results of clinical treatment plans. The developed code agreed with TOPAS within 2%, except for the fall-off and regions, and the gamma pass rates of the results were >99% for all cases with a 2 mm/2% criteria. Significance. We can score dose-influence matrix and dose-rate on a GPU for a 3-field H&N case with 10 GB of memory using moqui, which would require more than 100 GB of memory with the conventionally used array data structure.

Cone Beam CT-Based Online Evaluation in Two Minutes Using a Commercial Treatment Planning Software for Proton Therapy

Daily online treatment evaluation is essential for proton therapy, which is sensitive to daily anatomy and setup uncertainties. We have developed a program based on a commercial treatment planning system (TPS) to streamline the online evaluation process using pre-treatment cone-beam CT (CBCT) images. Herein, we evaluate the speed and accuracy of the tool based on clinical proton plans.Data from 25 previously treated proton patients (7 HN, 11 lung, and 7 prostate) at our institution were evaluated. Corrected CBCT (cCBCT) images were generated using a research version of the TPS, which removes artifacts and calibrates HU for proton dose calculation. A quality assurance simulation CT (QACT) scanned on the same day as the CBCT is deformed to the cCBCT and used as a reference (dQACT). The cCBCT is deformed to the treatment planning CT (TPCT), and all contours on the initial TPCT were deformed to the cCBCT and then rigidly copied to the dQACT. Original clinical treatment plans were applied to both the cCBCT and dQACT, and the doses were calculated with the GPU-based Monte-Carlo dose calculation engine at 0.5% statistical uncertainty. The entire evaluation time (Eval_time) from importing CBCT image to completing final dose calculation for cCBCT was recorded. Plan parameters, including the number of beams (N_bm), proton spot number (N_sp), dose grid voxel numbers (N_voxel), were collected. Pearson correlation coefficient between the Eval_time and the N_bm, N_sp, and N_vosel were calculated. Dosimetric parameters were calculated for the cCBCT and compared to those calculated from the reference dQACT. Dosimetric parameters of interest included the following: for all, CTV D99, D95, and V100, and plan maximum dose (Dmax); for H&N cases, parotid mean dose (P_Dmean) and V30Gy (P_V30), and oral cavity mean dose (C_Dmean); and for H&N and lung cases, spinal cord max dose (SC_Dmax).Mean online Eval_time is 106.6 ± 24.9s for all patients, with HN as the fastest site 87.9 ± 17.5s for HN, 104.5 ± 15.9s for lung, 128.5 ± 28.0s for prostate, P < 0.01. The corresponding (N_bm, N_sp, N_voxel) were (3.9, 7781, 2.6E6) for HN, (3.3, 11080, 2.4E6) for lung, and (3.0, 10484, 3.8E6) for prostate. Eval_time was significantly correlated to N_sp (P = 0.02), but not to N_bm and N_voxel. The absolute differences for CTV D99, D95, V100, plan Dmax, HN P_Dmean, P_V30, C_Dmean, and SC_Dmax are 0.85 ± 0.60%, 0.39 ± 0.22%, 0.48 ± 0.41%, 0.46 ± 0.48%, 0.08 ± 0.05Gy, 0.05 ± 0.06%, 0.21 ± 0.20 Gy, and 0.57 ± 0.53Gy, respectively.Online evaluation can be achieved within 2 minutes for most clinical proton cases (80% in this study) with the commercial TPS. The speed can be further increased with reduced OAR mapping, fine-tuned deformable registration, optimized and reduced spot number in the initial plans, and upgraded computer server. This proposed method may optimize the efficiency and quality of care for proton radiotherapy.

Quasi-Monte Carlo method for calculating X-ray scatter in CT

In this paper we transform the trajectories of X-ray as it interacts with a phantom into a high-dimensional integration problem and give the integral formula for the probability of photons emitted from the X-ray source through the phantom to reach the detector. We propose a superior algorithm called gQMCFRD, which combines GPU-based quasi-Monte Carlo (gQMC) method with forced random detection (FRD) technique to simulate this integral. QMC simulation is deterministic versions of Monte Carlo (MC) simulation, which uses deterministic low discrepancy points (such as Sobol' points) instead of the random points. By using the QMC and FRD technique, the gQMCFRD greatly increases the simulation convergence rate and efficiency. We benchmark gQMCFRD, GPU based MC tool (gMCDRR), which performs conventional simulations, a GPU-based Metropolis MC tool (gMMC), which uses the Metropolis-Hasting algorithm to sample the entire photon path from the X-ray source to the detector and gMCFRD, that uses random points for sampling against PENELOPE subroutines: MC-GPU. The results are in excellent agreement and the Efficiency Improvement Factor range 27 ∼ 37 (or 1.09 ∼ 1.16, or 0.12 ∼ 0.15, or 3.62 ∼ 3.70) by gQMCFRD (or gMCDRR, or gMMC, or gMCFRD) with comparison to MC-GPU in all cases. It shows that gQMCFRD is more effective in these cases.

Deep dose plugin: towards real-time Monte Carlo dose calculation through a deep learning-based denoising algorithm

Monte Carlo (MC) simulation is considered the gold standard method for radiotherapy dose calculation. However, achieving high precision requires a large number of simulation histories, which is time-consuming. The use of computer graphics processing units (GPUs) has greatly accelerated MC simulation and allows dose calculation within a few minutes for a typical radiotherapy treatment plan. However, some clinical applications demand real-time efficiency for MC dose calculation. To tackle this problem, we have developed a real-time, deep learning (DL)-based dose denoiser that can be plugged into a current GPU-based MC dose engine to enable real-time MC dose calculation. We used two different acceleration strategies to achieve this goal: (1) we applied voxel unshuffle and voxel shuffle operators to decrease the input and output sizes without any information loss, and (2) we decoupled the 3D volumetric convolution into a 2D axial convolution and a 1D slice convolution. In addition, we used a weakly supervised learning framework to train the network, which greatly reduces the size of the required training dataset and thus enables fast fine-tuning-based adaptation of the trained model to different radiation beams. Experimental results show that the proposed denoiser can run in as little as 39 ms, which is 11.6 times faster than the baseline model. As a result, the whole MC dose calculation pipeline can be finished within ∼ 0.15 s, including both GPU MC dose calculation and DL-based denoising, achieving the real-time efficiency needed for some radiotherapy applications, such as online adaptive radiotherapy.

Experimental and numerical studies on kV scattered x-ray imaging for real-time image guidance in radiation therapy

Motion management is a critical component of image guided radiotherapy for lung cancer. We previously proposed a scheme using kV scattered x-ray photons for marker-less real-time image guidance in lung cancer radiotherapy. This study reports our recent progress using the photon counting detection technique to demonstrate potential feasibility of this method and using Monte Carlo (MC) simulations and ray-tracing calculations to characterize the performance. In our scheme, a thin slice of x-ray beam was directed to the target and we measured the outgoing scattered photons using a photon counting detector with a parallel-hole collimator to establish the correspondence between detector pixels and scatter positions. Image corrections of geometry, beam attenuation and scattering angle were performed to convert the raw image to the actual image of Compton attenuation coefficient. We set up a MC simulation system using an in-house developed GPU-based MC package modeling the image formation process. We also performed ray-tracing calculations to investigate the impacts of imaging system geometry on resulting image resolution. The experiment demonstrated feasibility of using a photon counting detector to measure scattered x-ray photons and generate the proposed scattered x-ray image. After correction, x-ray scattering image intensity and Compton scattering attenuation coefficient were linearly related, with R 2 greater than 0.9. Contrast to noise ratios of different objects were improved and the values in experimental results and MC simulation results agreed with each other. Ray-tracing calculations revealed the dependence of image resolution on imaging geometry. The image resolution increases with reduced source to object distance and increased collimator height. The study demonstrated potential feasibility of using scattered x-ray imaging as a real-time image guidance method in radiation therapy.

Monte Carlo simulation fused with target distribution modeling via deep reinforcement learning for automatic high-efficiency photon distribution estimation

Particle distribution estimation is an important issue in medical diagnosis. In particular, photon scattering in some medical devices extremely degrades image quality and causes measurement inaccuracy. The Monte Carlo (MC) algorithm is regarded as the most accurate particle estimation approach but is still time-consuming, even with graphic processing unit (GPU) acceleration. The goal of this work is to develop an automatic scatter estimation framework for high-efficiency photon distribution estimation. Specifically, a GPU-based MC simulation initially yields a raw scatter signal with a low photon number to hasten scatter generation. In the proposed method, assume that the scatter signal follows Poisson distribution, where an optimization objective function fused with sparse feature penalty is modeled. Then, an over-relaxation algorithm is deduced mathematically to solve this objective function. For optimizing the parameters in the over-relaxation algorithm, the deep Q -network in the deep reinforcement learning scheme is built to intelligently interact with the over-relaxation algorithm to accurately and rapidly estimate a scatter signal with the large range of photon numbers. Experimental results demonstrated that our proposed framework can achieve superior performance with structural similarity &gt; 0.94 , peak signal-to-noise ratio &gt; 26.55 dB , and relative absolute error &lt; 5.62 % , and the lowest computation time for one scatter image generation can be within 2 s.

Scatter correction based on adaptive photon path-based Monte Carlo simulation method in Multi-GPU platform

Monte Carlo (MC)-based simulation is the most precise method in scatter correction for Cone-beam CT (CBCT). Nonetheless, the existing MC methods cannot be fully applied in clinical due to its low efficiency. The traditional MC simulations perform calculations via a particle-by-particle scheme, which leads to high computation costs because abundant photons do not reach the X-ray detector in transport. The conventional approaches cannot control where the particle ends. Hence, it unavoidably waste lots of time in transporting numerous photons that have no contribution to the signal at the detector, yielding a low computational efficiency. To solve the problem, an innovative GPU-based Metropolis MC (gMMC) method was proposed. Compared with the traditional ones, the Metropolis based algorithm utilizes a path-by-path sampling method. The method can automatically control each particle path and eventually accelerate the convergence. In this paper, we firstly take planning CT image as prior information because of its precise CT value, and utilize gMMC to estimate scatter signal. Then the scatter signals are removed from the raw CBCT projections. Afterwards, FDK reconstruction is performed to obtain the corrected image,some accelerating strategies including reducing photon history number, pixels sampling, projection angles sampling and reconstructed image down-sampling achieve adaptive fast CBCT image reconstruction. For having high computational efficiency, we implemented the whole workflow on a 4-GPU workstation. In order to verify the feasibility of the the method, the experiment of several cases are conducted including simulation, phantom, and real patient cases. Results indicate that the image contrast becomes better, the scatter artifacts are eliminated. The maximum error (emax), the minimum error (emin), the 95th percentile error (e95%), average error (¯e) are reduced from 264, 56, 14 and 21 HU to 28, 10, 3 and 7 HU in full-fan case, and from 387, 5, 19 and 95 HU to 39, 2, 2 and 6 HU in the half-fan case. In terms of computation time, the MC simulation time of all cases is within 2.5 seconds, and the total time is within 15 seconds.

Sensitivity of DNA Damage to Variance of Simulation Parameters in Microscopic Monte Carlo Simulation

Monte Carlo (MC) simulation of radiation-induced DNA damage involves the usage of many physical/biological parameters, which are often of a large uncertainty. It may hinder the key interpretation of the underlying physical-biological mechanism, yet the quantification process is quite time consuming using the current CPU-based MC packages. Recently, we developed and validated a GPU-based fast microscopic MC simulation tool, goMicroMC. Based on it, we quantified the impacts of DNA single strand breaks (SSBs) and double strand breaks (DSBs) from ten controllable parameters. In goMicroMC, we simulated the physical energy depositions and chemical hydroxyl radicals introduced by the ionizing-radiation via physical, physiochemical and chemical stages. Based on their superpositions with a pre-developed multi-scale nucleus lymphocyte DNA geometrical model, we computed SSBs and DSBs. Both processes were CUDA-GPU-accelerated and validated via comparison to ICRU measurements and Geant4-DNA simulation. As for the parameter tests, we focused on the simulation of mono-energetic electrons (initial kinetic energy of 1/4.5 keV) with a dose deposition of 2 Gy to the cellular nuclear. The ten parameters studied were: 1) physical cross section, 2) electron cut-off energy, 3)-5) three branch-ratios for hydroxyl generations in physicochemical stage, 6) chemical diffusion time, 7)-8) searching radii for direct/indirect damages, 9) energy range for direct damage and 10) probability for indirect damage. We quantified the impacts with “sensitivity” defined as the ratio between the percent change of SSBs/DSBs and that of the parameter. Simulation results from goMicroMC agree with ICRUs and Geant4-DNA within 10% difference. For the parameter tests, taking a sensitivity threshold of 33%, DSBs were especially sensitive to the physical cross section (>1), electron cut-off energy (>0.54) and direct damage radius (>0.5), with both DSBs and SSBs sensitive to the energy range triggering direct damages (>1.1).

Hybrid 3D analytical linear energy transfer calculation algorithm based on precalculated data from Monte Carlo simulations

The dose-averaged linear energy transfer (LETd ) for intensity-modulated proton therapy (IMPT) calculated by one-dimensional (1D) analytical models deviates from more accurate but time-consuming Monte Carlo (MC) simulations. We developed a fast hybrid three-dimensional (3D) analytical LETd calculation that is more accurate than 1D analytical model. We used the Geant4 MC code to generate 3D LETd distributions of monoenergetic proton beams in water for all energies and used a customized error function to fit the LETd lateral profiles at various depths to the MC simulation. The 3D LETd calculation kernel was a lookup table of these fitted coefficients, and LETd was determined directly from spot energies and voxel coordinates during analytical dose calculations. We validated our new method by comparing the calculated LETd distributions to MC results using 3D Gamma index analysis with 3%/2mm criteria in 12 patient geometries. The significance of the improvement in Gamma index analysis passing rates over the 1D analytical model was determined using the Wilcoxon rank-sum test. The passing rate of 3D Gamma analysis comparing LETd distributions from the hybrid 3D method and the 1D method to MC simulations was significantly improved from 94.0%±2.5% to 98.0%±1.0% (P=0.0003). The typical time to calculate dose and LETd simultaneously using an Intel Xeon E5-2680 2.50GHz workstation was approximately 2.5min. Our new method significantly improved the LETd calculation accuracy compared to the 1D method while maintaining significantly shorter calculation time even comparing with the GPU-based fast MC code.

A real-time Monte Carlo tool for individualized dose estimations in clinical CT

The increasing awareness of the adverse effects associated with radiation exposure in computed tomography (CT) has necessesitated the quantification of dose delivered to patients for better risk assessment in the clinic. The current methods for dose quantification used in the clinic are approximations, lacking realistic models for the irradiation conditions utilized in the scan and the anatomy of the patient being imaged, which limits their relevance for a particular patient. The established gold-standard technique for individualized dose quantification uses Monte Carlo (MC) simulations to obtain patient-specific estimates of organ dose in anatomically realistic computational phantoms to provide patient-specific estimates of organ dose. Although accurate, MC simulations are computationally expensive, which limits their utility for time-constrained applications in the clinic. To overcome these shortcomings, a real-time GPU-based MC tool based on FDA’s MC-GPU framework was developed for patient and scanner-specific dosimetry in the clinic. The tool was validated against (1) AAPM’s TG-195 reference datasets and (2) physical measurements of dose acquired using TLD chips in adult and pediatric anthropomorphic phantoms. To demonstrate its utility towards providing individualized dose estimates, it was integrated with an automatic segmentation method for generating patient-specific models, which were then used to estimate patient- and scanner-specific organ doses for a select population of 50 adult patients using a clinically relevant CT protocol. The organ dose estimates were compared to corresponding dose estimates from a previously validated MC method based on Penelope. The dose estimates from our MC tool agreed within 5% for all organs (except thyroid) tabulated by TG-195 and within 10% for all TLD locations in the adult and pediactric phantoms, across all validation cases. Compared against Penelope, the organ dose estimates agreed within 3% on average for all organs in the patient population study. The average run duration for each patient was estimated at 23.79 s, representing a significant speedup (~700×) over existing non-parallelized MC methods. The accuracy of dose estimates combined with a significant improvement in execution times suggests a feasible solution utilizing the proposed MC tool for real-time individualized dosimetry in the clinic.

Metropolis Monte Carlo simulation scheme for fast scattered X-ray photon calculation in CT.

Monte Carlo (MC) method is commonly considered as the most accurate approach for particle transport simulation because of its capability to precisely model physics interactions and simulation geometry. Conventionally, MC simulation is performed in a particle-by-particle fashion. In certain problems such as computing scattered X-ray photon signal at a detector of CT, the conventional simulation scheme suffers from low efficiency mainly due to the fact that abundant photons are simulated but do not reach the detector. The computational resources spent on those photons are therefore wasted. To solve this problem, this study develops a novel GPU-based Metropolis MC (gMMC) with a novel path-by-path simulation scheme and demonstrates its effectiveness in an example problem of scattered X-ray photon calculation in CT. In contrast to the conventional MC approach, gMMC samples an entire photon path extending from the X-ray source to the detector using Metropolis-Hasting algorithm. The path-by-path simulation scheme ensures contribution of every sampled event to the signal of interest, improving overall efficiency. We benchmark gMMC against an in-house developed GPU-based MC tool, gMCDRR, which performs simulations in the conventional particle-by-particle fashion. gMMC reaches speed up factors of 37~48 times in simple phantom cases and 20-34 times in real patient cases. The results calculated by gMCDRR and gMMC agree well with average differences < 3%.

MCDNet – A Denoising Convolutional Neural Network to Accelerate Monte Carlo Radiation Transport Simulations: A Proof of Principle With Patient Dose From X-Ray CT Imaging

X-ray computed tomography (CT) is a popular diagnostic imaging tool that has caused public concern over potential radiation risks to the patient. Monte Carlo (MC) simulations are the most accurate methods to calculate x-ray interactions with the patient's body and voxel-wise dose distributions, but the statistical methods suffer from extremely long computing time that is required to achieve necessary statistical precision. In this paper, we propose and demonstrate the Monte Carlo Denoising Net (MCDNet), a convolutional encoder-decoder neural network, for the purpose of accelerating the MC radiation transport simulations for patient CT dosimetry. A unique set of full-body anatomically realistic adult voxel phantoms of various sizes and a GPU-based parallel MC code were used to produce adequate training and testing data for supervised learning. Gamma index passing rate (GIPR) was used to evaluate the performance of predicted dose maps. For CT scan protocols considered in this study, MCDNet is found to have the ability of predicting dose maps of $9.9\times 10 ^{\mathbf {7}}$ photons from corresponding dose maps of $1.3\times 10^{\mathbf {6}}$ photons, yielding $76\times $ speed-up in terms of photon numbers used in the MC simulations. MCDNet is the first CNN-based method to speed-up MC radiation transport simulations involving 3D and heterogeneous patient anatomies for x-ray CT. Future studies will test the feasibility of applying the deep-learning based denoising strategy to other MC radiation transport applications.

Efficient GPU-based Monte-Carlo simulation of diffusion in real astrocytes reconstructed from confocal microscopy

The primary goal of this work is to develop an efficient Monte-Carlo simulation of diffusion-weighted signal in complex cellular structures, such as astrocytes, directly derived from confocal microscopy. In this study, we first use an octree structure for spatial decomposition of surface meshes. Octree structure and radius-search algorithm help to quickly identify the faces that particles can possibly encounter during the next time step, thus speeding up the Monte-Carlo simulation. Furthermore, we propose to use a three-dimensional binary marker to describe the complex cellular structure and optimize the particle trajectory simulation. Finally, a GPU-based version of these two approaches is implemented for more efficient modeling. It is shown that the GPU-based binary marker approach yields unparalleled performance, opening up new possibilities to better understand intracellular diffusion, validate diffusion models, and create dictionaries of intracellular diffusion signatures.

Fast GPU-based Monte Carlo code for SPECT/CT reconstructions generates improved 177Lu images

BackgroundFull Monte Carlo (MC)-based SPECT reconstructions have a strong potential for correcting for image degrading factors, but the reconstruction times are long. The objective of this study was to develop a highly parallel Monte Carlo code for fast, ordered subset expectation maximum (OSEM) reconstructions of SPECT/CT images. The MC code was written in the Compute Unified Device Architecture language for a computer with four graphics processing units (GPUs) (GeForce GTX Titan X, Nvidia, USA). This enabled simulations of parallel photon emissions from the voxels matrix (1283 or 2563). Each computed tomography (CT) number was converted to attenuation coefficients for photo absorption, coherent scattering, and incoherent scattering. For photon scattering, the deflection angle was determined by the differential scattering cross sections. An angular response function was developed and used to model the accepted angles for photon interaction with the crystal, and a detector scattering kernel was used for modeling the photon scattering in the detector. Predefined energy and spatial resolution kernels for the crystal were used. The MC code was implemented in the OSEM reconstruction of clinical and phantom 177Lu SPECT/CT images. The Jaszczak image quality phantom was used to evaluate the performance of the MC reconstruction in comparison with attenuated corrected (AC) OSEM reconstructions and attenuated corrected OSEM reconstructions with resolution recovery corrections (RRC).ResultThe performance of the MC code was 3200 million photons/s. The required number of photons emitted per voxel to obtain a sufficiently low noise level in the simulated image was 200 for a 1283 voxel matrix. With this number of emitted photons/voxel, the MC-based OSEM reconstruction with ten subsets was performed within 20 s/iteration. The images converged after around six iterations. Therefore, the reconstruction time was around 3 min. The activity recovery for the spheres in the Jaszczak phantom was clearly improved with MC-based OSEM reconstruction, e.g., the activity recovery was 88% for the largest sphere, while it was 66% for AC-OSEM and 79% for RRC-OSEM.ConclusionThe GPU-based MC code generated an MC-based SPECT/CT reconstruction within a few minutes, and reconstructed patient images of 177Lu-DOTATATE treatments revealed clearly improved resolution and contrast.

A new approach to integrate GPU-based Monte Carlo simulation into inverse treatment plan optimization for proton therapy

Monte Carlo (MC)-based spot dose calculation is highly desired for inverse treatment planning in proton therapy because of its accuracy. Recent studies on biological optimization have also indicated the use of MC methods to compute relevant quantities of interest, e.g. linear energy transfer. Although GPU-based MC engines have been developed to address inverse optimization problems, their efficiency still needs to be improved. Also, the use of a large number of GPUs in MC calculation is not favorable for clinical applications. The previously proposed adaptive particle sampling (APS) method can improve the efficiency of MC-based inverse optimization by using the computationally expensive MC simulation more effectively. This method is more efficient than the conventional approach that performs spot dose calculation and optimization in two sequential steps. In this paper, we propose a computational library to perform MC-based spot dose calculation on GPU with the APS scheme. The implemented APS method performs a non-uniform sampling of the particles from pencil beam spots during the optimization process, favoring those from the high intensity spots. The library also conducts two computationally intensive matrix-vector operations frequently used when solving an optimization problem. This library design allows a streamlined integration of the MC-based spot dose calculation into an existing proton therapy inverse planning process. We tested the developed library in a typical inverse optimization system with four patient cases. The library achieved the targeted functions by supporting inverse planning in various proton therapy schemes, e.g. single field uniform dose, 3D intensity modulated proton therapy, and distal edge tracking. The efficiency was 41.6 ± 15.3% higher than the use of a GPU-based MC package in a conventional calculation scheme. The total computation time ranged between 2 and 50 min on a single GPU card depending on the problem size.