Hardware acceleration using FPGAs for adaptive radiotherapy

Adaptive radiotherapy (ART) seeks to improve the accuracy of radiotherapy by adapting the treatment based on up-to-date images of the patient's anatomy captured at the time of treatment delivery. The amount of image data, combined with the clinical time requirements for ART, necessitates automatic image analysis to adapt the treatment plan. Currently, the computational effort of the image processing and plan adaptation means they cannot be completed in a clinically acceptable timeframe. This thesis aims to investigate the use of hardware acceleration on Field Programmable Gate Arrays (FPGAs) to accelerate algorithms for segmenting bony anatomy in Computed Tomography (CT) scans, to reduce the plan adaptation time for ART. An assessment was made of the overhead incurred by transferring image data to an FPGA-based hardware accelerator using the industry-standard DICOM protocol over an Ethernet connection. The rate was found to be likely to limit the performanceof hardware accelerators for ART, highlighting the need for an alternative method of integrating hardware accelerators with existing radiotherapy equipment. A clinically-validated segmentation algorithm was adapted for implementation in hardware. This was shown to process three-dimensional CT images up to 13.81 times faster than the original software implementation. The segmentations produced by the two implementations showed strong agreement. Modifications to the hardware implementation were proposed for segmenting fourdimensional CT scans. This was shown to process image volumes 14.96 times faster than the original software implementation, and the segmentations produced by the two implementations showed strong agreement in most cases.A second, novel, method for segmenting four-dimensional CT data was also proposed. The hardware implementation executed 1.95 times faster than the software implementation. However, the algorithm was found to be unsuitable for the global segmentation task examined here, although it may be suitable as a refining segmentation in the context of a larger ART algorithm.Adaptive radiotherapy (ART) seeks to improve the accuracy of radiotherapy by adapting the treatment based on up-to-date images of the patient's anatomy captured at the time of treatment delivery. The amount of image data, combined with the clinical time requirements for ART, necessitates automatic image analysis to adapt the treatment plan. Currently, the computational effort of the image processing and plan adaptation means they cannot be completed in a clinically acceptable timeframe. This thesis aims to investigate the use of hardware acceleration on Field Programmable Gate Arrays (FPGAs) to accelerate algorithms for segmenting bony anatomy in Computed Tomography (CT) scans, to reduce the plan adaptation time for ART. An assessment was made of the overhead incurred by transferring image data to an FPGA-based hardware accelerator using the industry-standard DICOM protocol over an Ethernet connection. The rate was found to be likely to limit the performanceof hardware accelerators for ART, highlighting the need for an alternative method of integrating hardware accelerators with existing radiotherapy equipment. A clinically-validated segmentation algorithm was adapted for implementation in hardware. This was shown to process three-dimensional CT images up to 13.81 times faster than the original software implementation. The segmentations produced by the two implementations showed strong agreement. Modifications to the hardware implementation were proposed for segmenting fourdimensional CT scans. This was shown to process image volumes 14.96 times faster than the original software implementation, and the segmentations produced by the two implementations showed strong agreement in most cases.A second, novel, method for segmenting four-dimensional CT data was also proposed. The hardware implementation executed 1.95 times faster than the software implementation. However, the algorithm was found to be unsuitable for the global segmentation task examined here, although it may be suitable as a refining segmentation in the context of a larger ART algorithm

Dosimetry of Photon and Proton MRI Guided Radiotherapy Beams using Silicon Array Dosimeters

The integration of online magnetic resonance imaging (MRI) with photon and pro-ton radiotherapy has potential to overcome the soft tissue contrast limitations of the current standard of care kV-image guided radiotherapy in some challenging treat-ment sites. By directly visualising soft tissue targets and organs at risk, removing the dependence on surrogates for image guidance, it is expected there will be a decrease in the geometric uncertainties related to daily patient setup. This new approach to image guided radiotherapy presents unique challenges due to the permanent mag-netic field of the integrated MRI unit. The trajectory of charged particles including dose depositing secondary electrons are perturbed by the magnetic field, adding to the challenge of calculating the patient dosimetry and validating the calculation with measurement as is standard practice in radiotherapy. The magnetic field may also effect the operation and response of radiation detectors and a method of accurately characterising the influence of the magnetic field on detector response and operation is required. This thesis reports progress made towards real time high spatial resolution dosime-try of photon and proton MRI guided radiotherapy beams using novel monolithic silicon detectors designed at the Centre for Medical Radiation Physics (CMRP). One challenge in experimentally characterising the magnetic field effects on a radiation detectors operation is how to perform dosimetry measurements with and without a magnetic field of varying strength and orientation from a single radiation source as this is not feasible on existing MRI linacs with a permanent magnetic field of fixed strength. A bespoke semi-portable magnet device was developed to meet this need. The device employs an adjustable iron yoke and focusing cones to vary the magnetic field of the central volume, a 0.3 T field can be achieved for volume to 10 x 10 x 10 cm3 and up to a 1.2 T for a volume of at least 3 x 3 x 3 cm3. The device is de-signed to be used with a clinical linear accelerator in both inline and perpendicular magnetic field orientations to meet the challenge of detector characterisation. The performance of the magnetic field generated by the device was within ±2 % of finite element modelling predictions of all configurations tested

Development and experimental validation of adaptive conformal particle therapy

In radiotherapy, conforming the high dose to the tumor is of special importance to avoid toxicity in critical organs. Scanned ion beam therapy has shown its potential to reduce the dose in the healthy tissue. However, its application is limited for thoracic and abdominal tumors like lung, liver or pancreatic cancer. In those organs, respiratory motion induces considerable changes in tumor position and beam range to the tumor. In current clinical practice, this causes severe dose degradations and necessitates large safety margins that invalidate the conformity gain of ion beam therapy. In order to minimize target margins, the motion has to be compensated by real-time adaptive beam delivery. A major challenge are the irregularities of realistic tumor motion that are unknown during treatment planning. To study the impact of irregular motion, an extension of an RBE-weighted dose calculation algorithm enabling the computation on arbitrarily long series of CT images was experimentally validated. A workflow for simulation studies with irregular motion data for the assessment of plan robustness and treatment quality was presented. A new motion mitigation technique denoted as multi-phase 4D dose delivery with residual tracking (MP4DRT) was implemented into the research version of a clinical dose delivery system. It combines the earlier proposed multi-phase 4D dose delivery (MP4D) technique with lateral beam tracking. MP4D synchronizes the delivery of phase specific treatment plans with the observed motion. It therefore enables conformal, time-resolved 4D treatment planning for periodic motion. It considers range changes and deformations during the optimization process and therefore removes the need for real-time range adjustments. In the new technique, additional lateral beam tracking adapts beam positions in real-time to the unexpected residual component of the observed irregular motion. The potential of MP4DRT was evaluated in a comparative experimental study that included also the other free breathing motion mitigation techniques MP4D, lateral beam tracking and ITV rescanning. Treatment plans were optimized for a digital anthropomorphic lung phantom with a nominal tumor motion amplitude of 20 mm. The plans were delivered at a clinical carbon ion therapy facility to a quality assurance like setup performing regular and irregular motion scenarios including 25 % amplitude variations with and without baseline drift. Treatment quality was assessed using detector measurements and log-file based dose reconstructions. The robustness of the delivery was tested by adding artificial errors to the motion signal during the delivery and rotational tumor motion up to 30° during dose reconstruction. It was demonstrated that MP4DRT is able to deliver highly conformal dose distributions. A target coverage of D95>95 % was achieved irrespective of the motion scenario and rotation amplitude, and for clinically relevant mean absolute tracking errors of the motion monitoring up to 1.9 mm. MP4DRT synergized the complementary strengths of its predecessors and outperformed all other compared motion mitigation techniques in target coverage, dose conformity and homogeneity, organ at risk sparing, and robustness against rotational motion. MP4DRT can deliver conformal and homogeneous dose distributions to moving tumors in a single fraction. After clinical implementation, it therefore might improve treatment quality and enable the treatment of tumors so far unavailable for particle therapy

Methodology for complex dataflow application development

This thesis addresses problems inherent to the development of complex applications for reconfig- urable systems. Many projects fail to complete or take much longer than originally estimated by relying on traditional iterative software development processes typically used with conventional computers. Even though designer productivity can be increased by abstract programming and execution models, e.g., dataflow, development methodologies considering the specific properties of reconfigurable systems do not exist. The first contribution of this thesis is a design methodology to facilitate systematic develop- ment of complex applications using reconfigurable hardware in the context of High-Performance Computing (HPC). The proposed methodology is built upon a careful analysis of the original application, a software model of the intended hardware system, an analytical prediction of performance and on-chip area usage, and an iterative architectural refinement to resolve identi- fied bottlenecks before writing a single line of code targeting the reconfigurable hardware. It is successfully validated using two real applications and both achieve state-of-the-art performance. The second contribution extends this methodology to provide portability between devices in two steps. First, additional tool support for contemporary multi-die Field-Programmable Gate Arrays (FPGAs) is developed. An algorithm to automatically map logical memories to hetero- geneous physical memories with special attention to die boundaries is proposed. As a result, only the proposed algorithm managed to successfully place and route all designs used in the evaluation while the second-best algorithm failed on one third of all large applications. Second, best practices for performance portability between different FPGA devices are collected and evaluated on a financial use case, showing efficient resource usage on five different platforms. The third contribution applies the extended methodology to a real, highly demanding emerging application from the radiotherapy domain. A Monte-Carlo based simulation of dose accumu- lation in human tissue is accelerated using the proposed methodology to meet the real time requirements of adaptive radiotherapy.Open Acces

High Spatial Resolution Silicon Detectors for Independent Quality Assurance in Motion Adaptive Radiotherapy and Charged Particle Radiotherapy Energy Verification

Accurate empirical modelling of the treatment beam is necessary to ensure accurate delivery of dose to the intended target site. Dose calculations within the treatment planning system (TPS) for Stereotactic Radiosurgery (SRS) and Stereotactic Radiotherapy (SRT) treatment rely upon accurate beam data. Inaccuracies within the empirical measurements will propagate as errors throughout calculated patient dose distributions (Tyler, 2013). The necessary empirical measurements for beam commissioning include: percentage depth dose (PDD), output factor (OF) and beam profiles. Thus, especially for the consideration of the afore mentioned small radiation fields, it is important to ensure the most appropriate detector is chosen to conduct measurements of the treatment beams to achieve the highest possible accuracy in measurement of beam parameters. Stereotactic Body Radiation Therapy (SBRT) requires precise delineation of the target using modern imaging modalities (MRI, CT etc.), accurate dosimetry to ensure the planned dose is delivered correctly and effective patient immobilisation. For extracranial sites the treatment accuracy is affected by tumour delineation which identifies the extent of the tumour volume and tumour motion resulting from the physical, biological and physiological processes of the human body. Delivery of radiation using highly conformal and small radiation beams presents challenges for dosimetry and quality assurance (Heydarian, 1996), (Das, 2008). To correctly measure dose in a small field an ideal dosimeter must exhibit properties including: small sensitive volume, near water equivalence, minimal beam perturbation and no dose-rate, energy or directional dependence (Pappas, 2008). Also, treatment planning for dose calculation must be conducted using algorithms which can account for the impact of the heterogeneities found in the abdomen and thoracic cavities to ensure calculation of the dose to tissue in regions with complex scattering conditions is accurate (Rubio, 2013)

Power and Monitor Solution for the Proton Computed Tomography Project

The ProtonCT project is an academic endeavor carried out by the University of Bergen in collaboration with several universities and entities across the world. The end goal of the project is to improve dosage plans by directly measuring the relative stopping power of protons using a digital tracking calorimeter. Directly measuring relative stopping power as opposed to approximating it using CT numbers can provide a more accurate dosage plan. The digital tracking calorimeter will be able to do computed tomography scans of head-sized objects. The digital tracking calorimeter will utilize pixel detector sensors developed by CERN for the ALICE project. 43 pixel arrays, segmented into layers, measure the angle and energy of proton particles traversing through the layers. With 108 chips per layer, 4644 ALPIDE chips build up all the layers. At full load, the expected power draw is close to 2.5kW. This thesis explores the design of a user-controllable power delivery and monitoring system. Each layer consists of 12 ALPIDE strings, with 9 ALPIDE chips making up one string. A power delivery system capable of supplying one layer is realized by using a small form factor switch mode power supply unit. An FPGA design created by peer students connects the 43 power delivery systems to a graphical interface. A filter, monitor, and control solution is designed with a newly released AVR microcontroller unit. A custom PCB, named the Monitor Board, is designed to host the filter and the MCU with all its support circuitry. Using differential signaling, the 43 monitorboards communicate with a Xilinx Kintex UltraScale FPGA responsible for storing and relaying information over IPbus to the user. Each monitor board can switch the strings of its designated layer on or off. Diagnostics and soft startups/shutdowns can be executed through software. The back-biasing of an entire layer is customizable by using the microcontroller DAC and an onboard negative voltage supply. A temperature monitoring solution is designed with the use of a PT1000 element mounted close to the ALPIDE chips.Master's Thesis in PhysicsPHYS399MAMN-PHY

Experiments with RADFET dosimeter in electron-beams irradiation and numerical computation of the physical shielding factor

MOSFET electronic components are already the subject of several decades of research in various fields of dosimetry and radiation protection. Special interest appeared when these components are started to be used as dosimeters in radiotherapy with electron beams. However, if one looks much more serious in the wider scientific research horizon, all the results obtained in experiments with precisely defined energies of incident electrons can be used in other disciplines which consider the impacts spectra of cosmic radiation on electronic devices, which is especially importance for cosmic science and space research instrumentation. In this paper, one of the objectives was to examine the electrical characteristics specially designed ESAPMOS RADFET dosimeters in the experiments that were conducted on a linear accelerator installations. RADFET components are bombarded electron beams energy of 6 MeV and 8 MeV, and then are followed by changes in threshold voltage shift mean values depending on the change of absorbed dose is referred to as D(cGy) was determined in water. Conclusions performance RADFET components are more than encouraging in terms of further research to improve the linearity of the energy dependence as widely energy electrons. In the second part of the test complex structure of packaging components RADFET focus is placed on the determination of the energy deposited in layers that are of interest for the analysis of microscopic processes related to the recombination of radiation-induced electron-hole pairs. Transport incident electrons through all the layers of structure RADFET component type ESAPMOS was carried out numerical simulations of the Monte Carlo method using the software package FOTELP-2K12. On this occasion, were taken into account all the physical processes of interaction of electrons with materials given structure. When he conquered the numerical application of mathematical and physical model for determining the value of the absorbed energy as the energy deposited per unit mass in a given layers with different materials, it could be accessed defining physical shielding factor (PSF) for a given structure RADFET components. Physical shielding factor (PSF) is defined as the ratio of absorbed dose values, which in fact means that it is equal to the energy deposited when the RADFET is shielded with protection, and the RADFET without lid. When we know the energy dependence factor for PSF of RADFET with and without armour, can be carried out and the analysis of whether and to what extent the energy required compensating the electronic components. Monte Carlo simulations were performed for the transport of incident electrons from 4 MeV, 6 MeV, 8 MeV and 12 MeV. It can be concluded that the different energy of incident electrons there is a significant influence of material Kovar on the absorbed energy in SiO2 and Si layers structure RADFET, in cases where Kovar used among other things as physical protection.Third International Conference on Radiation and Applications in Various Fields of Research, RAD 2015, June 8-12, 2015, Budva, Montenegr