Phantom Scatter and the A-SI EPID

Introduction: The use of amorphous-silicon electronic portal imaging devices (a-Si EPIDs) for dosimetry is complicated by the effects of scattered radiation. In photon radiotherapy, primary signal at the detector can be accompanied by photons scattered from linear accelerator components, detector materials, intervening air, treatment room surfaces (floor, walls, etc) and from the patient/phantom being irradiated. Consequently, EPID measurements which presume to take scatter into account are highly sensitive to the identification of these contributions. One example of this susceptibility is the process of calibrating an EPID for use as a gauge of (radiological) thickness, where specific allowance must be made for the effect of phantom-scatter on the intensity of radiation measured through different thicknesses of phantom. This is usually done via a theoretical calculation which assumes that phantom scatter is linearly related to thickness and field-size. We have, however, undertaken a more detailed study of the scattering effects of fields of different dimensions when applied to phantoms of various thicknesses in order to derive scattered-primary ratios (SPRs) directly from simulation results. This allows us to make a more-accurate calibration of the EPID, and to qualify the appositeness of the theoretical SPR calculations. Methods: This study uses a full MC model of the entire linac-phantom-detector system simulated using EGSnrc/BEAMnrc codes. The Elekta linac and EPID are modelled according to specifications from the manufacturer and the intervening phantoms are modelled as rectilinear blocks of water or plastic, with their densities set to a range of physically realistic and unrealistic values. Transmissions through these various phantoms are calculated using the dose detected in the model EPID and used in an evaluation of the field-size-dependence of SPR, in different media, applying a method suggested for experimental systems by Swindell and Evans [1]. These results are compared firstly with SPRs calculated using the theoretical, linear relationship between SPR and irradiated volume, and secondly with SPRs evaluated from our own experimental data. An alternate evaluation of the SPR in each simulated system is also made by modifying the BEAMnrc user code READPHSP, to identify and count those particles in a given plane of the system that have undergone a scattering event. In addition to these simulations, which are designed to closely replicate the experimental setup, we also used MC models to examine the effects of varying the setup in experimentally challenging ways (changing the size of the air gap between the phantom and the EPID, changing the longitudinal position of the EPID itself). Experimental measurements used in this study were made using an Elekta Precise linear accelerator, operating at 6MV, with an Elekta iView GT a-Si EPID. Results and Discussion: 1. Comparison with theory: With the Elekta iView EPID fixed at 160 cm from the photon source, the phantoms, when positioned isocentrically, are located 41 to 55 cm from the surface of the panel. At this geometry, a close but imperfect agreement (differing by up to 5%) can be identified between the results of the simulations and the theoretical calculations. However, this agreement can be totally disrupted by shifting the phantom out of the isocentric position. Evidently, the allowance made for source-phantom-detector geometry by the theoretical expression for SPR is inadequate to describe the effect that phantom proximity can have on measurements made using an (infamously low-energy sensitive) a-Si EPID. 2. Comparison with experiment: For various square field sizes and across the range of phantom thicknesses, there is good agreement between simulation data and experimental measurements of the transmissions and the derived values of the primary intensities. However, the values of SPR obtained through these simulations and measurements seem to be much more sensitive to slight differences between the simulated and real systems, leading to difficulties in producing a simulated system which adequately replicates the experimental data. (For instance, small changes to simulated phantom density make large differences to resulting SPR.) 3. Comparison with direct calculation: By developing a method for directly counting the number scattered particles reaching the detector after passing through the various isocentric phantom thicknesses, we show that the experimental method discussed above is providing a good measure of the actual degree of scattering produced by the phantom. This calculation also permits the analysis of the scattering sources/sinks within the linac and EPID, as well as the phantom and intervening air. Conclusions: This work challenges the assumption that scatter to and within an EPID can be accounted for using a simple, linear model. Simulations discussed here are intended to contribute to a fuller understanding of the contribution of scattered radiation to the EPID images that are used in dosimetry calculations. Acknowledgements: This work is funded by the NHMRC, through a project grant, and supported by the Queensland University of Technology (QUT) and the Royal Brisbane and Women's Hospital, Brisbane, Australia. The authors are also grateful to Elekta for the provision of manufacturing specifications which permitted the detailed simulation of their linear accelerators and amorphous-silicon electronic portal imaging devices. Computational resources and services used in this work were provided by the HPC and Research Support Group, QUT, Brisbane, Australia.

The development of Monte Carlo techniques for the verification of radiotherapy treatments

Introduction: Recent advances in the planning and delivery of radiotherapy treatments have resulted in improvements in the accuracy and precision with which therapeutic radiation can be administered. As the complexity of the treatments increases it becomes more difficult to predict the dose distribution in the patient accurately. Monte Carlo (MC) methods have the potential to improve the accuracy of the dose calculations and are increasingly being recognised as the ‘gold standard’ for predicting dose deposition in the patient [1]. This project has three main aims: 1. To develop tools that enable the transfer of treatment plan information from the treatment planning system (TPS) to a MC dose calculation engine. 2. To develop tools for comparing the 3D dose distributions calculated by the TPS and the MC dose engine. 3. To investigate the radiobiological significance of any errors between the TPS patient dose distribution and the MC dose distribution in terms of Tumour Control Probability (TCP) and Normal Tissue Complication Probabilities (NTCP). The work presented here addresses the first two aims. Methods: (1a) Plan Importing: A database of commissioned accelerator models (Elekta Precise and Varian 2100CD) has been developed for treatment simulations in the MC system (EGSnrc/BEAMnrc). Beam descriptions can be exported from the TPS using the widespread DICOM framework, and the resultant files are parsed with the assistance of a software library (PixelMed Java DICOM Toolkit). The information in these files (such as the monitor units, the jaw positions and gantry orientation) is used to construct a plan-specific accelerator model which allows an accurate simulation of the patient treatment field. (1b) Dose Simulation: The calculation of a dose distribution requires patient CT images which are prepared for the MC simulation using a tool (CTCREATE) packaged with the system. Beam simulation results are converted to absolute dose per- MU using calibration factors recorded during the commissioning process and treatment simulation. These distributions are combined according to the MU meter settings stored in the exported plan to produce an accurate description of the prescribed dose to the patient. (2) Dose Comparison: TPS dose calculations can be obtained using either a DICOM export or by direct retrieval of binary dose files from the file system. Dose difference, gamma evaluation and normalised dose difference algorithms [2] were employed for the comparison of the TPS dose distribution and the MC dose distribution. These implementations are spatial resolution independent and able to interpolate for comparisons. Results and Discussion: The tools successfully produced Monte Carlo input files for a variety of plans exported from the Eclipse (Varian Medical Systems) and Pinnacle (Philips Medical Systems) planning systems: ranging in complexity from a single uniform square field to a five-field step and shoot IMRT treatment. The simulation of collimated beams has been verified geometrically, and validation of dose distributions in a simple body phantom (QUASAR) will follow. The developed dose comparison algorithms have also been tested with controlled dose distribution changes. Conclusion: The capability of the developed code to independently process treatment plans has been demonstrated. A number of limitations exist: only static fields are currently supported (dynamic wedges and dynamic IMRT will require further development), and the process has not been tested for planning systems other than Eclipse and Pinnacle. The tools will be used to independently assess the accuracy of the current treatment planning system dose calculation algorithms for complex treatment deliveries such as IMRT in treatment sites where patient inhomogeneities are expected to be significant. Acknowledgements: Computational resources and services used in this work were provided by the HPC and Research Support Group, Queensland University of Technology, Brisbane, Australia. Pinnacle dose parsing made possible with the help of Paul Reich, North Coast Cancer Institute, North Coast, New South Wales.

Assessing testamentary and decision-making competence/capacity in the Australian context

Australia lacks a satisfactory, national paradigm for assessing competence and capacity in the context of testamentary, enduring power of attorney and advance care directive documents. Competence/capacity assessments are currently conducted on an ad hoc basis by legal and/or medical professionals. The reliability of the assessment process is subject to the skill set and mutual understanding of the legal and/or medical professional conducting the assessment. There is a growth in the prevalence of diseases such as dementia. Such diseases impact upon cognition which increasingly necessitates collaboration between the legal and medical professions when assessing the effect of mentally disabling conditions upon competency/capacity. Miscommunication and lack of understanding between legal and medical professionals involved could impede the development of a satisfactory paradigm. A qualitative study seeking the views of legal and medical professionals who practise in this area has been conducted. This incorporated surveys and interviews of 10 legal and 20 medical practitioners. Some of the results are discussed here. Practitioners were asked whether there is a standard approach and whether national guidelines were desirable. There was general agreement that uniform guidelines for the assessment of competence/capacity would be desirable. The interviews also canvassed views as to the state of the relationship between the professions. The results of the empirical research support the hypothesis that relations between the professions could be improved. The development of a national paradigm would promote consistency and transparency of process, helping to improve the professional relationship and maximising the principles of autonomy, participation and dignity.

An efficient algorithm for the detection of Eden

In this paper, a polynomial time algorithm is presented for solving the Eden problem for graph cellular automata. The algorithm is based on our neighborhood elimination operation which removes local neighborhood configurations which cannot be used in a pre-image of a given configuration. This paper presents a detailed derivation of our algorithm from first principles, and a detailed complexity and accuracy analysis is also given. In the case of time complexity, it is shown that the average case time complexity of the algorithm is \Theta(n^2), and the best and worst cases are \Omega(n) and O(n^3) respectively. This represents a vast improvement in the upper bound over current methods, without compromising average case performance.

Get real : the development, implementation and evaluation of an intervention for primary aged children with High Functioning Autism

Children with Autism Spectrum Disorder experience difficulty in communication and in understanding the social world which can have negative consequences for their relationships, in managing emotions, and generally dealing with the challenges of everyday life. This thesis examines the effectiveness of the Active and Reflective components of the Get REAL program through the assessment of the detailed coding of video-recorded observations and longitudinal quantitative analysis. The aim of Get REAL is to increase the social, emotional, and cognitive learning of children with High Functioning Autism (HFA). Get REAL is a group program designed specifically for use in inclusive primary school settings. The Get REAL program was designed in response to the mixed success of generalisation of learning to new contexts of existing social skills programs. The theoretical foundation of Get REAL is based upon pedagogical theory and learning theory to facilitate transfer of learning, combined with experiential, individualised, evaluative and organisational approaches. This thesis is by publication and consists of four refereed journal papers; 1 accepted for publication and 3 that are under review. Paper 1 describes the development and theoretical basis of the Get REAL program and provides detail of the program structure and learning cycle. The focus of Paper 1 reflects the first question of interest in the thesis which is about the extent to which learning derived from participation in the program can be generalised to other contexts. Participants are 16 children with HFA ranging in age from 8-13 years. Results provided support for the generalisability of learning from Get REAL to home and school evidenced by parent and teacher data collected pre and post participation in Get REAL. Following establishment of the generalisation of learning from Get REAL, Papers 2 and 3 focus on the Active and Reflective components of the program in order to examine how individual and group learning takes place. Participants (N = 12) in the program are video-taped during the Active and Reflective Sessions. Using identical coding protocols of video data, improvements in prosocial behaviour and diminishing of inappropriate behaviours were apparent with the exception of perspective taking. Data also revealed that 2 of the participants had atypical trajectories. An in-depth case study analysis was then conducted with these 2 participants in Paper 4. Data included reports from health care and education professionals within the school and externally (e.g., paediatrician) and identified the multi-faceted nature of care needed for children with comorbid diagnoses and extremely challenging family circumstances as a complex task to effect change. Results of this research support the effectiveness of the Get REAL program in promoting pro social behaviours such as improvements in engaging with others and emotional regulation, and in diminishing unwanted behaviours such as conduct problems. Further, the gains made by the participating children were found to be generalisable beyond Get REAL to home and other school settings. The research contained in the thesis adds to current knowledge about how learning can take place for children with HFA. Results show that an experiential learning framework with a focus on social cognition, together with explicit teaching, scaffolded with video feedback, are key ingredients for the generalisation of social learning to broader contexts.

Visualising experimental flow fields through a stormwater gross pollutant trap

Abstract An experimental dataset representing a typical flow field in a stormwater gross pollutant trap (GPT) was visualised. A technique was developed to apply the image-based flow visualisation (IBFV) algorithm to the raw dataset. Particle image velocimetry (PIV) software was previously used to capture the flow field data by tracking neutrally buoyant particles with a high speed camera. The dataset consisted of scattered 2D point velocity vectors and the IBFV visualisation facilitates flow feature characterisation within the GPT. The flow features played a pivotal role in understanding stormwater pollutant capture and retention behaviour within the GPT. It was found that the IBFV animations revealed otherwise unnoticed flow features and experimental artefacts. For example, a circular tracer marker in the IBFV program visually highlighted streamlines to investigate the possible flow paths of pollutants entering the GPT. The investigated flow paths were compared with the behaviour of pollutants monitored during experiments.

Computational fluid dynamic analysis of intracranial aneurysmal bleb formation

Background The management of unruptured aneurysms is controversial with the decision to treat influenced by aneurysm characteristics including size and morphology. Aneurysmal bleb formation is thought to be associated with an increased risk of rupture. Objective To correlate computational fluid dynamic (CFD) indices with bleb formation. Methods Anatomical models were constructed from three-dimensional rotational angiogram (3DRA) data in 27 patients with cerebral aneurysms harbouring single blebs. Additional models representing the aneurysm before bleb formation were constructed by digitally removing the bleb. We characterised haemodynamic features of models both with and without the bleb using CFDs. Flow structure, wall shear stress (WSS), pressure and oscillatory shear index (OSI) were analysed. Results There was a statistically significant association between bleb location at or adjacent to the point of maximal WSS (74.1%, p=0.019), irrespective of rupture status. Aneurysmal blebs were related to the inflow or outflow jet in 88.9% of cases (p<0.001) whilst 11.1% were unrelated. Maximal wall pressure and OSI were not significantly related to bleb location. The bleb region attained a lower WSS following its formation in 96.3% of cases (p<0.001) and was also lower than the average aneurysm WSS in 86% of cases (p<0.001). Conclusion Cerebral aneurysm blebs generally form at or adjacent to the point of maximal WSS and are aligned with major flow structures. Wall pressure and OSI do not contribute to determining bleb location. The measurement of WSS using CFD models may potentially predict bleb formation and thus improve the assessment of rupture risk in unruptured aneurysms.

Pulse-coupled neural network performance for real-time identification of vegetation during forced landing

Safety concerns in the operation of autonomous aerial systems require safe-landing protocols be followed during situations where the a mission should be aborted due to mechanical or other failure. On-board cameras provide information that can be used in the determination of potential landing sites, which are continually updated and ranked to prevent injury and minimize damage. Pulse Coupled Neural Networks have been used for the detection of features in images that assist in the classification of vegetation and can be used to minimize damage to the aerial vehicle. However, a significant drawback in the use of PCNNs is that they are computationally expensive and have been more suited to off-line applications on conventional computing architectures. As heterogeneous computing architectures are becoming more common, an OpenCL implementation of a PCNN feature generator is presented and its performance is compared across OpenCL kernels designed for CPU, GPU and FPGA platforms. This comparison examines the compute times required for network convergence under a variety of images obtained during unmanned aerial vehicle trials to determine the plausibility for real-time feature detection.

Introducing standardized protocols for anthropological measurement of virtual subadult crania using computed tomography

Objectives This study introduces and assesses the precision of a standardized protocol for anthropometric measurement of the juvenile cranium using three-dimensional surface rendered models, for implementation in forensic investigation or paleodemographic research. Materials and methods A subset of multi-slice computed tomography (MSCT) DICOM datasets (n=10) of modern Australian subadults (birth—10 years) was accessed from the “Skeletal Biology and Forensic Anthropology Virtual Osteological Database” (n>1200), obtained from retrospective clinical scans taken at Brisbane children hospitals (2009–2013). The capabilities of Geomagic Design X™ form the basis of this study; introducing standardized protocols using triangle surface mesh models to (i) ascertain linear dimensions using reference plane networks and (ii) calculate the area of complex regions of interest on the cranium. Results The protocols described in this paper demonstrate high levels of repeatability between five observers of varying anatomical expertise and software experience. Intra- and inter-observer error was indiscernible with total technical error of measurement (TEM) values ≤0.56 mm, constituting <0.33% relative error (rTEM) for linear measurements; and a TEM value of ≤12.89 mm2, equating to <1.18% (rTEM) of the total area of the anterior fontanelle and contiguous sutures. Conclusions Exploiting the advances of MSCT in routine clinical assessment, this paper assesses the application of this virtual approach to acquire highly reproducible morphometric data in a non-invasive manner for human identification and population studies in growth and development. The protocols and precision testing presented are imperative for the advancement of “virtual anthropology” into routine Australian medico-legal death investigation.

Comparison of high level FPGA hardware design for solving tri-diagonal linear systems

Reconfigurable computing devices can increase the performance of compute intensive algorithms by implementing application specific co-processor architectures. The power cost for this performance gain is often an order of magnitude less than that of modern CPUs and GPUs. Exploiting the potential of reconfigurable devices such as Field-Programmable Gate Arrays (FPGAs) is typically a complex and tedious hardware engineering task. Re- cently the major FPGA vendors (Altera, and Xilinx) have released their own high-level design tools, which have great potential for rapid development of FPGA based custom accelerators. In this paper, we will evaluate Altera’s OpenCL Software Development Kit, and Xilinx’s Vivado High Level Sythesis tool. These tools will be compared for their per- formance, logic utilisation, and ease of development for the test case of a Tri-diagonal linear system solver.

Pulse-coupled neural network performance for real-time identification of vegetation during forced landing

Safety concerns in the operation of autonomous aerial systems require safe-landing protocols be followed during situations where the mission should be aborted due to mechanical or other failure. This article presents a pulse-coupled neural network (PCNN) to assist in the vegetation classification in a vision-based landing site detection system for an unmanned aircraft. We propose a heterogeneous computing architecture and an OpenCL implementation of a PCNN feature generator. Its performance is compared across OpenCL kernels designed for CPU, GPU, and FPGA platforms. This comparison examines the compute times required for network convergence under a variety of images to determine the plausibility for real-time feature detection.

Characterising an ECG signal using statistical modelling : a feasibility study

For clinical use, in electrocardiogram (ECG) signal analysis it is important to detect not only the centre of the P wave, the QRS complex and the T wave, but also the time intervals, such as the ST segment. Much research focused entirely on qrs complex detection, via methods such as wavelet transforms, spline fitting and neural networks. However, drawbacks include the false classification of a severe noise spike as a QRS complex, possibly requiring manual editing, or the omission of information contained in other regions of the ECG signal. While some attempts were made to develop algorithms to detect additional signal characteristics, such as P and T waves, the reported success rates are subject to change from person-to-person and beat-to-beat. To address this variability we propose the use of Markov-chain Monte Carlo statistical modelling to extract the key features of an ECG signal and we report on a feasibility study to investigate the utility of the approach. The modelling approach is examined with reference to a realistic computer generated ECG signal, where details such as wave morphology and noise levels are variable.

CTCombine : rotating and combining CT data with an accurate detector model to simulate radiotherapy portal imaging at non-zero beam angles

Established Monte Carlo user codes BEAMnrc and DOSXYZnrc permit the accurate and straightforward simulation of radiotherapy experiments and treatments delivered from multiple beam angles. However, when an electronic portal imaging detector (EPID) is included in these simulations, treatment delivery from non-zero beam angles becomes problematic. This study introduces CTCombine, a purpose-built code for rotating selected CT data volumes, converting CT numbers to mass densities, combining the results with model EPIDs and writing output in a form which can easily be read and used by the dose calculation code DOSXYZnrc...

Computation of ECG signal features using MCMC modelling in software and FPGA reconfigurable hardware

Computational optimisation of clinically important electrocardiogram signal features, within a single heart beat, using a Markov-chain Monte Carlo (MCMC) method is undertaken. A detailed, efficient data-driven software implementation of an MCMC algorithm has been shown. Initially software parallelisation is explored and has been shown that despite the large amount of model parameter inter-dependency that parallelisation is possible. Also, an initial reconfigurable hardware approach is explored for future applicability to real-time computation on a portable ECG device, under continuous extended use.

Three dimensional digitisation of plant leaves

Realistic plant models are important for leaf area and plant volume estimation, reconstruction of growth canopies, structure generation of the plant, reconstruction of leaf surfaces and agrichemical spray droplet modelling. This article investigates several different scanning devices for obtaining a three dimensional digitisation of plant leaves with a point cloud resolution of 200-500μm. The devices tested were a Roland mdx-20, Microsoft Kinect, Roland lpx-250, Picoscan and Artec S. The applicability of each of these devices for scanning plant leaves is discussed. The most suitable tested digitisation device for scanning plant leaves is the Artec S scanner.