Joseph Perl
Current Organizations / Institutes
The organizations/institutes from the scholar's latest article
Previous Organizations / Institutes
The organizations / institutes from the scholar's other articles in the past ten years
Research Subjects
Research Interests
Joseph Perl has a total of 28 co-authors. Here are the top co-authors by number of shared publications:
B Faddegon
University of California San Francisco, San Francisco, CA
8 shared publicationsH Paganetti
University of California San Francisco, San Francisco, CA
7 shared publicationsJ Shin
University of California San Francisco, San Francisco, CA
5 shared publications- Jan Schuemann
Massachusetts General Hospital
3 shared publications B. Faddegon
2 shared publicationsH. Paganetti
2 shared publications
Latest Publications
- 29 June 2015
- Published by Wiley in Medical Physics
- Vol. 42 (6Part19) , 3441-3442
SU‐E‐T‐466: Implementation of An Extension Module for Dose Response Models in the TOPAS Monte Carlo Toolkit
- 29 June 2015
- Published by Wiley in Medical Physics
- Vol. 42 (6Part19) , 3441-3442
SU‐E‐T‐466: Implementation of An Extension Module for Dose Response Models in the TOPAS Monte Carlo Toolkit
- Open Access
- 1 January 2014
- Published by Elsevier in Medicina e Investigación
- Vol. 2 (1) , 61
16O: Parámetros óptimos para reducción de varianza en simulaciones Monte Carlo para terapia de protones en modo de dispersión pasiva
- 1 January 2014
- Published by Elsevier in Medicina e Investigación
- Vol. 2 (1) , 61
Open Access16O: Parámetros óptimos para reducción de varianza en simulaciones Monte Carlo para terapia de protones en modo de dispersión pasiva
- 6 June 2013
- Published by Wiley in Medical Physics
- Vol. 40 (6Part28) , 475
WE-C-108-07: Optimal Parameters for Variance Reduction in Monte Carlo Simulations for Proton Therapy
- 6 June 2013
- Published by Wiley in Medical Physics
- Vol. 40 (6Part28) , 475
WE-C-108-07: Optimal Parameters for Variance Reduction in Monte Carlo Simulations for Proton Therapy
- 6 June 2013
- Published by Wiley in Medical Physics
- Vol. 40 (6Part25) , 419
TU-A-108-01: Four-Dimensional Monte Carlo Using the TOPAS TOol for PArticle Simulation
- 6 June 2013
- Published by Wiley in Medical Physics
- Vol. 40 (6Part25) , 419
TU-A-108-01: Four-Dimensional Monte Carlo Using the TOPAS TOol for PArticle Simulation
- Open Access
The Geant4 Visualisation System - a multi-driver graphics system
From the beginning the Geant4 Visualisation System was designed to support several simultaneous graphics systems written to common abstract interfaces. Today it has matured into a powerful diagnostic and presentational tool. It comes with a library of models that may be added to the current scene and which include the representation of the Geant4 geometry hierarchy, simulated trajectories and user-written hits and digitisations. The workhorse is the OpenGL suite of drivers for X, Xm, Qt and Win32. There is an Open Inventor driver. Scenes can be exported in special graphics formats for offline viewing in the DAWN, VRML, HepRApp and gMocren browsers. PostScript can be generated through OpenGL, Open Inventor, DAWN and HepRApp. Geant4's own tracking algorithms are used by the Ray Tracer. Not all drivers support all features but all drivers bring added functionality of some sort. This paper describes the interfaces and details the individual drivers.
Open AccessThe Geant4 Visualisation System - a multi-driver graphics system
From the beginning the Geant4 Visualisation System was designed to support several simultaneous graphics systems written to common abstract interfaces. Today it has matured into a powerful diagnostic and presentational tool. It comes with a library of models that may be added to the current scene and which include the representation of the Geant4 geometry hierarchy, simulated trajectories and user-written hits and digitisations. The workhorse is the OpenGL suite of drivers for X, Xm, Qt and Win32. There is an Open Inventor driver. Scenes can be exported in special graphics formats for offline viewing in the DAWN, VRML, HepRApp and gMocren browsers. PostScript can be generated through OpenGL, Open Inventor, DAWN and HepRApp. Geant4's own tracking algorithms are used by the Ray Tracer. Not all drivers support all features but all drivers bring added functionality of some sort. This paper describes the interfaces and details the individual drivers.
- Top Cited Papers
- 19 October 2012
- Published by Wiley in Medical Physics
- Vol. 39 (11) , 6818-6837
TOPAS: An innovative proton Monte Carlo platform for research and clinical applications
Purpose: While Monte Carlo particle transport has proven useful in many areas (treatment head design, dose calculation, shielding design, and imaging studies) and has been particularly important for proton therapy (due to the conformal dose distributions and a finite beam range in the patient), the available general purpose Monte Carlo codes in proton therapy have been overly complex for most clinical medical physicists. The learning process has large costs not only in time but also in reliability. To address this issue, we developed an innovative proton Monte Carlo platform and tested the tool in a variety of proton therapy applications.Methods: Our approach was to take one of the already‐established general purpose Monte Carlo codes and wrap and extend it to create a specialized user‐friendly tool for proton therapy. The resulting tool, TOol for PArticle Simulation (TOPAS), should make Monte Carlo simulation more readily available for research and clinical physicists. TOPAS can model a passive scattering or scanning beam treatment head, model a patient geometry based on computed tomography (CT) images, score dose, fluence, etc., save and restart a phase space, provides advanced graphics, and is fully four‐dimensional (4D) to handle variations in beam delivery and patient geometry during treatment. A custom‐designed TOPAS parameter control system was placed at the heart of the code to meet requirements for ease of use, reliability, and repeatability without sacrificing flexibility.Results: We built and tested the TOPAS code. We have shown that the TOPAS parameter system provides easy yet flexible control over all key simulation areas such as geometry setup, particle source setup, scoring setup, etc. Through design consistency, we have insured that user experience gained in configuring one component, scorer or filter applies equally well to configuring any other component, scorer or filter. We have incorporated key lessons from safety management, proactively removing possible sources of user error such as line‐ordering mistakes. We have modeled proton therapy treatment examples including the UCSF eye treatment head, the MGH stereotactic alignment in radiosurgery treatment head and the MGH gantry treatment heads in passive scattering and scanning modes, and we have demonstrated dose calculation based on patient‐specific CT data. Initial validation results show agreement with measured data and demonstrate the capabilities of TOPAS in simulating beam delivery in 3D and 4D.Conclusions: We have demonstrated TOPAS accuracy and usability in a variety of proton therapy setups. As we are preparing to make this tool freely available for researchers in medical physics, we anticipate widespread use of this tool in the growing proton therapy community.
- 19 October 2012
- Published by Wiley in Medical Physics
- Vol. 39 (11) , 6818-6837
Top Cited PapersTOPAS: An innovative proton Monte Carlo platform for research and clinical applications
Purpose: While Monte Carlo particle transport has proven useful in many areas (treatment head design, dose calculation, shielding design, and imaging studies) and has been particularly important for proton therapy (due to the conformal dose distributions and a finite beam range in the patient), the available general purpose Monte Carlo codes in proton therapy have been overly complex for most clinical medical physicists. The learning process has large costs not only in time but also in reliability. To address this issue, we developed an innovative proton Monte Carlo platform and tested the tool in a variety of proton therapy applications.Methods: Our approach was to take one of the already‐established general purpose Monte Carlo codes and wrap and extend it to create a specialized user‐friendly tool for proton therapy. The resulting tool, TOol for PArticle Simulation (TOPAS), should make Monte Carlo simulation more readily available for research and clinical physicists. TOPAS can model a passive scattering or scanning beam treatment head, model a patient geometry based on computed tomography (CT) images, score dose, fluence, etc., save and restart a phase space, provides advanced graphics, and is fully four‐dimensional (4D) to handle variations in beam delivery and patient geometry during treatment. A custom‐designed TOPAS parameter control system was placed at the heart of the code to meet requirements for ease of use, reliability, and repeatability without sacrificing flexibility.Results: We built and tested the TOPAS code. We have shown that the TOPAS parameter system provides easy yet flexible control over all key simulation areas such as geometry setup, particle source setup, scoring setup, etc. Through design consistency, we have insured that user experience gained in configuring one component, scorer or filter applies equally well to configuring any other component, scorer or filter. We have incorporated key lessons from safety management, proactively removing possible sources of user error such as line‐ordering mistakes. We have modeled proton therapy treatment examples including the UCSF eye treatment head, the MGH stereotactic alignment in radiosurgery treatment head and the MGH gantry treatment heads in passive scattering and scanning modes, and we have demonstrated dose calculation based on patient‐specific CT data. Initial validation results show agreement with measured data and demonstrate the capabilities of TOPAS in simulating beam delivery in 3D and 4D.Conclusions: We have demonstrated TOPAS accuracy and usability in a variety of proton therapy setups. As we are preparing to make this tool freely available for researchers in medical physics, we anticipate widespread use of this tool in the growing proton therapy community.
- 28 June 2012
- Published by Wiley in Medical Physics
- Vol. 39 (6Part18) , 3820
SU‐E‐T‐500: Pencil‐Beam versus Monte Carlo Based Dose Calculation for Proton Therapy Patients with Complex Geometries. Clinical Use of the TOPAS Monte Carlo System
Pencil beam algorithms provide an accurate description of dose in the target volume. However, we conclude that the differences between MC simulations and pencil beam algorithms in regions outside the target for complex geometries, such as present in head and neck patients, support the necessity of routine use of MC simulations for treatment verifications before treatment. TOPAS is aiming to make such routine simulations available to all researchers and clinics. An automated interface utilizing TOPAS to enable such simulations has been developed at MGH and should become routinely used in the near future for patients with complex geometries. NIH/NCI R01 CA140735.
- 28 June 2012
- Published by Wiley in Medical Physics
- Vol. 39 (6Part18) , 3820
SU‐E‐T‐500: Pencil‐Beam versus Monte Carlo Based Dose Calculation for Proton Therapy Patients with Complex Geometries. Clinical Use of the TOPAS Monte Carlo System
Pencil beam algorithms provide an accurate description of dose in the target volume. However, we conclude that the differences between MC simulations and pencil beam algorithms in regions outside the target for complex geometries, such as present in head and neck patients, support the necessity of routine use of MC simulations for treatment verifications before treatment. TOPAS is aiming to make such routine simulations available to all researchers and clinics. An automated interface utilizing TOPAS to enable such simulations has been developed at MGH and should become routinely used in the near future for patients with complex geometries. NIH/NCI R01 CA140735.
- 1 June 2011
- Published by Wiley in Medical Physics
- Vol. 38 (6Part28) , 3754-3755
TU-C-BRB-08: TOPAS: A Fast and Easy to Use Tool for Particle Simulation
- 1 June 2011
- Published by Wiley in Medical Physics
- Vol. 38 (6Part28) , 3754-3755
TU-C-BRB-08: TOPAS: A Fast and Easy to Use Tool for Particle Simulation
- 2 June 2010
- Published by Wiley in Medical Physics
- Vol. 37 (6) , 3286
SU-GG-T-432: Implementation of Modular Phase Space IO in Geant4 with Enhanced Latch Capability
- 2 June 2010
- Published by Wiley in Medical Physics
- Vol. 37 (6) , 3286
SU-GG-T-432: Implementation of Modular Phase Space IO in Geant4 with Enhanced Latch Capability
- 24 September 2009
- Published by IOP Publishing in Physics in Medicine & Biology
- Vol. 54 (20) , 6151-6163
The accuracy of EGSnrc, Geant4 and PENELOPE Monte Carlo systems for the simulation of electron scatter in external beam radiotherapy
Three widely used Monte Carlo systems were benchmarked against recently published measurements of the angular distribution of 13 MeV and 20 MeV electrons scattered from foils of different atomic numbers and thicknesses. Source and geometry were simulated in detail to calculate electron fluence profiles 118.2 cm from the exit window. Results were compared to the measured fluence profiles and the characteristic angle where the fluence drops to 1/e of its maximum value. EGSnrc and PENELOPE results, on average, agreed with measurement within 1 standard deviation experimental uncertainty, with EGSnrc estimating slightly lower scatter than measurement and PENELOPE slightly higher scatter. Geant4.9.2 overestimated the characteristic angle for the lower atomic number foils by as much as 10%. Retuning of the scatter distributions in Geant4 led to a much better agreement with measurement, close to that achieved with the other codes. The 3% differences from measurement seen with all codes for at least some of the foils would result in clinically significant errors in the fluence profiles (2%/4 mm), given accurate knowledge of the electron source and treatment head geometry used in radiotherapy. Further improvement in simulation accuracy is needed to achieve 1%/1 mm agreement with measurement for the full range of beam energies, foil atomic number and thickness used in radiotherapy. EGSnrc would achieve this accuracy with an increase in thickness of the mylar sheets in the monitor chamber, PENELOPE with a decrease in thickness.
- 24 September 2009
- Published by IOP Publishing in Physics in Medicine & Biology
- Vol. 54 (20) , 6151-6163
The accuracy of EGSnrc, Geant4 and PENELOPE Monte Carlo systems for the simulation of electron scatter in external beam radiotherapy
Three widely used Monte Carlo systems were benchmarked against recently published measurements of the angular distribution of 13 MeV and 20 MeV electrons scattered from foils of different atomic numbers and thicknesses. Source and geometry were simulated in detail to calculate electron fluence profiles 118.2 cm from the exit window. Results were compared to the measured fluence profiles and the characteristic angle where the fluence drops to 1/e of its maximum value. EGSnrc and PENELOPE results, on average, agreed with measurement within 1 standard deviation experimental uncertainty, with EGSnrc estimating slightly lower scatter than measurement and PENELOPE slightly higher scatter. Geant4.9.2 overestimated the characteristic angle for the lower atomic number foils by as much as 10%. Retuning of the scatter distributions in Geant4 led to a much better agreement with measurement, close to that achieved with the other codes. The 3% differences from measurement seen with all codes for at least some of the foils would result in clinically significant errors in the fluence profiles (2%/4 mm), given accurate knowledge of the electron source and treatment head geometry used in radiotherapy. Further improvement in simulation accuracy is needed to achieve 1%/1 mm agreement with measurement for the full range of beam energies, foil atomic number and thickness used in radiotherapy. EGSnrc would achieve this accuracy with an increase in thickness of the mylar sheets in the monitor chamber, PENELOPE with a decrease in thickness.