Keegan McNamara

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McNamara

First Name

Keegan

ORCID

0000-0002-1926-2444

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Publications 1 - 8 of 8

Iterative reconstruction with a rotating open-ring PET scanner for proton therapy range verification
McNamara, Keegan; Béguin, Marina; Dissertori, Günther; et al. (2025)
Physics in Medicine and Biology
Objective. In-beam positron emission tomography (PET) is a leading contender for non-invasive monitoring of proton therapy. The design constraints for in-beam PET have led to the development of an open-ring scanner as part of the PETITION project, which provides the unique opportunity to image immediately following the delivery of each treatment field. This study introduces computational techniques for the reconstruction of data recorded between delivery of each treatment field by a clinically implementable rotating open-ring design. Our proposed design enables fully-3D imaging of activity induced during proton therapy for verification on a field-by-field basis. Approach. We introduce a modification of the maximum likelihood expectation maximisation (MLEM) algorithm which accounts for imaging a source consisting of multiple isotopes with a rotating open-ring PET system. Pre-calculated system matrices are used to perform timely reconstructions for inter-field and post irradiation imaging for verification. We show the capabilities of our system by simulating a Derenzo-like phantom, as well as the treatment of a superatentorial neoplasm with 3 fields. We also show a proof of principle experimental measurement of a single field delivered to a CIRS 731-HN phantom. Main results. We show an increase in image quality when compared to fixed position imaging with an open-ring scanner, making the rotating open-ring design comparable to a similar full-ring design. The normalised root mean square error (NRMSE) was a factor of 1.6-2.2 better in comparison to imaging in a fixed position with an open-ring scanner. The new MLEM implementation was capable of assigning range to within an average of 0.6 mm along the beam direction for all fields, allowing for range verification of multiple fields. Significance. We have introduced a novel MLEM algorithm for imaging with a rotating open-ring PET device, opening the way for a clinically feasible implementation of fully-3D PET imaging of all treatment fields for verification of proton therapy.
Rayleigh and Raman scattering from alkali atoms
Singor, Adam; Fursa, Dmitry; McNamara, Keegan; et al. (2020)
Atoms
Two computational methods developed recently [McNamara, Fursa, and Bray, Phys. Rev. A 98, 043435 (2018)] for calculating Rayleigh and Raman scattering cross sections for atomic hydrogen have been extended to quasi one-electron systems. A comprehensive set of cross sections have been obtained for the alkali atoms: lithium, sodium, potassium, rubidium, and cesium. These cross sections are accurate for incident photon energies above and below the ionization threshold, but they are limited to energies below the excitation threshold of core electrons. The effect of spin-orbit interaction, importance of accounting for core polarization, and convergence of the cross sections have been investigated. © 2020 by the authors.
Are you absolutely positive? Verification of proton therapy using positron emission tomography
McNamara, Keegan (2024)
Proton therapy is a highly targeted form of radiotherapy which can maximise dose to the tumour while sparing the surrounding healthy tissue. The benefits of the high conformality of the dose are limited by sensitivity to uncertainties. In-vivo verification is therefore highly desired, and can be performed using positron emission tomography (PET) imaging of isotopes induced by the treatment, indirectly verifying the delivered dose. This work focuses on the simulation, implementation, and testing of an open-ring PET scanner built for use in Gantry 2 at the Center for Proton Therapy (CPT) of PSI as part of the PETITION (PET for InTensive care units and Innovative protON therapy) project. A variety of computational tools which enable the fast and accurate simulation of on-line imaging with an open-ring PET scanner are implemented. And an experimental showcase of the clinically feasible operation of the scanner is presented. It is shown that 3D on-line PET imaging with a rotating open-ring design can be used for validation of each treatment field in multi-field proton treatment plans, and can detect and quantify anatomical changes in complex regions of the patient. Verification of delivered dose using PET imaging requires a full understanding, and therefore simulation, of the expected dose and isotope distributions in the patient. In part II of the thesis the simulation workflow, including patient irradiation, isotope production, positron decay, and PET imaging, is presented. The scoring of positron emitting isotopes is included in the GPU accelerated Monte Carlo code FRED, and validated against a full physics Monte Carlo code, GATE. The inclusion of isotope scoring on the GPU allows for calculation of dose and seven common isotopes in the patient geometry within less than 3 minutes on average, representing a 50 fold speed up when compared to similar simulations on large compute clusters. This is then used as part of a simulation workflow for modelling the patient treatment and subsequent imaging. The various details which must be accounted for in the modelling of the patient treatment, as well as imaging of the patient with the PET scanner, are discussed. In part III, the development and implementation of several iterative reconstruction techniques are presented. First the methods used for calculating and storing the system matrix of the PETITION PET scanner are shown. It is shown that the system matrices for an open-ring scanner rotated at all angles about the axial axis can be accessed through the calculation of the system matrix of a related full-ring scanner, giving a compression factor of 1122. The high compression and ability to access the system matrix at any rotation angle is then used to propose an extension of the standard iterative reconstruction methods for reconstruction of images acquired with a rotating open-ring PET scanner. Reconstruction using a rotating open-ring PET scanner is shown to achieve comparable quality to imaging with a full-ring scanner, enabling high-quality PET imaging of multiple treatment fields delivered to the patient without interruption to the treatment workflow. Following this, two further extensions of the iterative reconstruction algorithm are presented. First, an algorithm for disentangling the activity induced by each field in a typical multi-field proton treatment plan is given, allowing validation of the dose delivered by each field in such a plan. Both the rotating and multi-field reconstruction algorithms perform well in assignment of the range when compared to the expected ground truth activity distributions. A method for determining the isotope specific distribution induced within the patient is also proposed. The iterative reconstruction algorithms are implemented in the SIONARA code, which can perform reconstructions of the induced activity within seconds, opening the door for prompt clinical feedback. In part IV the work of parts II and III are applied to the simulation of seven patients previously treated at the Center for Proton Therapy. The use of magnetic resonance imaging (MRI) for tissue assignment is implemented, and the impact of tumour tissue assignment on the estimation of the range within the patient is investigated. It is found that the proposed rotating open-ring PETITION scanner has varying success at reproducing the ground truth activity distributions within the patient, dependent on the tumour location and size. Modeling of the detector effects and image reconstruction is therefore necessary when comparing to future clinical measurements. It is also found that the inclusion of tumour tissue assignment has an impact on the assigned range of up to 10 mm. Finally, in part V, the first fully 3D inter-field PET imaging of a head phantom in a clinical like setting is presented. The proposed use of a rotating open-ring scanner is emulated by attaching the anthropomorphic head phantom to a rotatable jig, and rotating the head within the scanner field of view. Anatomical changes are induced in the phantom, which lead to under-dosage in the tumour. The PETITION scanner is shown to be capable of localising the anatomical changes, and shows good correlation between the measured shift in range of the activity and the recalculated dose. It is also shown that the simulation workflow of the previous parts is in good agreement with the measured activity, achieving, on average, sub millimetre agreement in the range, with the caveat that we are limited on a spot by spot basis to standard deviations of up to 3.3 mm. The proposed rotating open-ring design is therefore shown to open the door to non-invasive and prompt feedback on the delivered dose in clinical settings, with range verification capabilities comparable or better than currently existing designs, with the added benefit of full 3D information. This is the first work (as far as we are aware) on PET range verification using an open-ring geometry allowing for direct on-line treatment verification.
ProTheRaMon—a GATE simulation framework for proton therapy range monitoring using PET imaging
Borys, Damian; Baran, Jakub; Brzeziński, Karol; et al. (2022)
Physics in Medicine and Biology
Objective. This paper reports on the implementation and shows examples of the use of the ProTheRaMon framework for simulating the delivery of proton therapy treatment plans and range monitoring using positron emission tomography (PET). ProTheRaMon offers complete processing of proton therapy treatment plans, patient CT geometries, and intra-treatment PET imaging, taking into account therapy and imaging coordinate systems and activity decay during the PET imaging protocol specific to a given proton therapy facility. We present the ProTheRaMon framework and illustrate its potential use case and data processing steps for a patient treated at the Cyclotron Centre Bronowice (CCB) proton therapy center in Krakow, Poland. Approach. The ProTheRaMon framework is based on GATE Monte Carlo software, the CASToR reconstruction package and in-house developed Python and bash scripts. The framework consists of five separated simulation and data processing steps, that can be further optimized according to the user’s needs and specific settings of a given proton therapy facility and PET scanner design. Main results. ProTheRaMon is presented using example data from a patient treated at CCB and the J-PET scanner to demonstrate the application of the framework for proton therapy range monitoring. The output of each simulation and data processing stage is described and visualized. Significance. We demonstrate that the ProTheRaMon simulation platform is a high-performance tool, capable of running on a computational cluster and suitable for multi-parameter studies, with databases consisting of large number of patients, as well as different PET scanner geometries and settings for range monitoring in a clinical environment. Due to its modular structure, the ProTheRaMon framework can be adjusted for different proton therapy centers and/or different PET detector geometries. It is available to the community via github (Borys et al 2022).
Feasibility of the J-PET to monitor the range of therapeutic proton beams
Baran, Jakub; Borys, Damian; Brzeziński, Karol; et al. (2024)
Physica Medica
Purpose: The aim of this work is to investigate the feasibility of the Jagiellonian Positron Emission Tomography (J-PET) scanner for intra-treatment proton beam range monitoring. Methods: The Monte Carlo simulation studies with GATE and PET image reconstruction with CASToR were performed in order to compare six J-PET scanner geometries. We simulated proton irradiation of a PMMA phantom with a Single Pencil Beam (SPB) and Spread-Out Bragg Peak (SOBP) of various ranges. The sensitivity and precision of each scanner were calculated, and considering the setup's cost-effectiveness, we indicated potentially optimal geometries for the J-PET scanner prototype dedicated to the proton beam range assessment. Results: The investigations indicate that the double-layer cylindrical and triple-layer double-head configurations are the most promising for clinical application. We found that the scanner sensitivity is of the order of 10-5 coincidences per primary proton, while the precision of the range assessment for both SPB and SOBP irradiation plans was found below 1 mm. Among the scanners with the same number of detector modules, the best results are found for the triple-layer dual-head geometry. The results indicate that the double-layer cylindrical and triple-layer double-head configurations are the most promising for the clinical application, Conclusions: We performed simulation studies demonstrating that the feasibility of the J-PET detector for PET-based proton beam therapy range monitoring is possible with reasonable sensitivity and precision enabling its pre-clinical tests in the clinical proton therapy environment. Considering the sensitivity, precision and cost-effectiveness, the double-layer cylindrical and triple-layer dual-head J-PET geometry configurations seem promising for future clinical application.
GPU accelerated Monte Carlo scoring of positron emitting isotopes produced during proton therapy for PET verification
McNamara, Keegan; Schiavi, Angelo; Borys, Damian; et al. (2022)
Physics in Medicine and Biology
Objective. Verification of delivered proton therapy treatments is essential for reaping the many benefits of the modality, with the most widely proposed in vivo verification technique being the imaging of positron emitting isotopes generated in the patient during treatment using positron emission tomography (PET). The purpose of this work is to reduce the computational resources and time required for simulation of patient activation during proton therapy using the GPU accelerated Monte Carlo code FRED, and to validate the predicted activity against the widely used Monte Carlo code GATE. Approach. We implement a continuous scoring approach for the production of positron emitting isotopes within FRED version 5.59.9. We simulate treatment plans delivered to 95 head and neck patients at Centrum Cyklotronowe Bronowice using this GPU implementation, and verify the accuracy using the Monte Carlo toolkit GATE version 9.0. Main results. We report an average reduction in computational time by a factor of 50 when using a local system with 2 GPUs as opposed to a large compute cluster utilising between 200 to 700 CPU threads, enabling simulation of patient activity within an average of 2.9 min as opposed to 146 min. All simulated plans are in good agreement across the two Monte Carlo codes. The two codes agree within a maximum of 0.95σ on a voxel-by-voxel basis for the prediction of 7 different isotopes across 472 simulated fields delivered to 95 patients, with the average deviation over all fields being 6.4 × 10−3 σ. Significance. The implementation of activation calculations in the GPU accelerated Monte Carlo code FRED provides fast and reliable simulation of patient activation following proton therapy, allowing for research and development of clinical applications of range verification for this treatment modality using PET to proceed at a rapid pace.
Detection of range shifts in proton beam therapy using the J-PET scanner: a patient simulation study
Brzeziński, Karol; Baran, Jakub; Borys, Damian; et al. (2023)
Physics in Medicine and Biology
Objective. The Jagiellonian positron emission tomography (J-PET) technology, based on plastic scintillators, has been proposed as a cost effective tool for detecting range deviations during proton therapy. This study investigates the feasibility of using J-PET for range monitoring by means of a detailed Monte Carlo simulation study of 95 patients who underwent proton therapy at the Cyclotron Centre Bronowice (CCB) in Krakow, Poland. Approach. Discrepancies between prescribed and delivered treatments were artificially introduced in the simulations by means of shifts in patient positioning and in the Hounsfield unit to the relative proton stopping power calibration curve. A dual-layer, cylindrical J-PET geometry was simulated in an in-room monitoring scenario and a triple-layer, dual-head geometry in an in-beam protocol. The distribution of range shifts in reconstructed PET activity was visualized in the beam’s eye view. Linear prediction models were constructed from all patients in the cohort, using the mean shift in reconstructed PET activity as a predictor of the mean proton range deviation. Main results. Maps of deviations in the range of reconstructed PET distributions showed agreement with those of deviations in dose range in most patients. The linear prediction model showed a good fit, with coefficient of determination r 2 = 0.84 (in-room) and 0.75 (in-beam). Residual standard error was below 1 mm: 0.33 mm (in-room) and 0.23 mm (in-beam). Significance. The precision of the proposed prediction models shows the sensitivity of the proposed J-PET scanners to shifts in proton range for a wide range of clinical treatment plans. Furthermore, it motivates the use of such models as a tool for predicting proton range deviations and opens up new prospects for investigations into the use of intra-treatment PET images for predicting clinical metrics that aid in the assessment of the quality of delivered treatment.
Design of a Mobile and Electromagnetic Emissions-Compliant Brain Positron Emission Tomography (PET) Scanner
Fuentes, Cristian; Béguin, Marina; Commichau, Volker; et al. (2025)
Sensors
This paper presents the development of two mobile brain Positron Emission Tomography (PET) scanners under the PETITION project, designed for Intensive Care Units (ICUs) and Proton Beam Therapy (PBT) applications. The ICU scanner facilitates bedside imaging for critically ill patients, while the PBT scanner enables undisturbed proton beam irradiation during imaging. Key aspects of the hardware design, including modular detectors and electromagnetic interference considerations, are discussed along with preliminary performance evaluations. Operational testing, employing a ²²Na source and a hot-rod phantom, was conducted to determine the timing resolution (548 (Formula presented.) (Formula presented.)), energy resolution (11.4%) and a qualitative spatial resolution (around 2.2 (Formula presented.) (Formula presented.)). Our study presents findings on the ICU PET scanner’s electromagnetic emissions measured in a controlled EMC testing facility, where all the emissions tests performed comply with the standard EN 60601-1-2 (radiated emissions 15 dB below regulatory limits in the frequency range of 30 (Formula presented.) (Formula presented.) to 1 G (Formula presented.)).

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