Journal ArticleDOI
CERR: A computational environment for radiotherapy research
TLDR
CERR provides a powerful, convenient, and common framework which allows researchers to use common patient data sets, and compare and share research results.Abstract:
A software environment is described, called the computational environment for radiotherapy research (CERR, pronounced "sir"). CERR partially addresses four broad needs in treatment planning research: (a) it provides a convenient and powerful software environment to develop and prototype treatment planning concepts, (b) it serves as a software integration environment to combine treatment planning software written in multiple languages (MATLAB, FORTRAN, C/C++, JAVA, etc.), together with treatment plan information (computed tomography scans, outlined structures, dose distributions, digital films, etc.), (c) it provides the ability to extract treatment plans from disparate planning systems using the widely available AAPM/RTOG archiving mechanism, and (d) it provides a convenient and powerful tool for sharing and reproducing treatment planning research results. The functional components currently being distributed, including source code, include: (1) an import program which converts the widely available AAPM/RTOG treatment planning format into a MATLAB cell-array data object, facilitating manipulation; (2) viewers which display axial, coronal, and sagittal computed tomography images, structure contours, digital films, and isodose lines or dose colorwash, (3) a suite of contouring tools to edit and/or create anatomical structures, (4) dose-volume and dose-surface histogram calculation and display tools, and (5) various predefined commands. CERR allows the user to retrieve any AAPM/RTOG key word information about the treatment plan archive. The code is relatively self-describing, because it relies on MATLAB structure field name definitions based on the AAPM/RTOG standard. New structure field names can be added dynamically or permanently. New components of arbitrary data type can be stored and accessed without disturbing system operation. CERR has been applied to aid research in dose-volume-outcome modeling, Monte Carlo dose calculation, and treatment planning optimization. In summary, CERR provides a powerful, convenient, and common framework which allows researchers to use common patient data sets, and compare and share research results.read more
Citations
More filters
Journal ArticleDOI
Monte Carlo proton dose calculations using a radiotherapy specific dual-energy CT scanner for tissue segmentation and range assessment.
Isabel P. Almeida,Lotte E J R Schyns,Ana Vaniqui,Brent van der Heyden,George Dedes,A. Resch,A. Resch,Florian Kamp,Jaap D. Zindler,Katia Parodi,Guillaume Landry,Frank Verhaegen +11 more
TL;DR: Proton beam ranges derived from dual-energy computed tomography (DECT) images from a dual-spiral radiotherapy (RT)-specific CT scanner were assessed using Monte Carlo (MC) dose calculations, and differences in proton range for the different image-based simulations were assessed.
Journal ArticleDOI
Feasibility of In Situ, High-Resolution Correlation of Tracer Uptake with Histopathology by Quantitative Autoradiography of Biopsy Specimens Obtained Under 18F-FDG PET/CT Guidance
Louise M. Fanchon,Louise M. Fanchon,Snjezana Dogan,Andre L. Moreira,Sean A. Carlin,C. Ross Schmidtlein,Ellen Yorke,Aditya Apte,Irene A. Burger,Jeremy C. Durack,Joseph P. Erinjeri,Majid Maybody,Heiko Schöder,R.H. Siegelbaum,Constantinos T. Sofocleous,Joseph O. Deasy,Stephen B. Solomon,John L. Humm,Assen S. Kirov +18 more
TL;DR: Performing QABS on core-biopsy specimens obtained using PET/CT guidance enables in situ correlation of 18F-FDG tracer uptake and histopathology on a millimeter scale.
Journal ArticleDOI
OpenKBP: The open-access knowledge-based planning grand challenge.
Aaron Babier,Binghao Zhang,Rafid Mahmood,Kevin L. Moore,Thomas G. Purdie,Andrea McNiven,Timothy C. Y. Chan +6 more
TL;DR: OpenKBP is the first platform that enables researchers to compare KBP prediction methods fairly and consistently using a large open-source dataset and standardized metrics and should help accelerate the progress of KBP research.
Journal ArticleDOI
Reconstruction of organ dose for external radiotherapy patients in retrospective epidemiologic studies
TL;DR: Methods to reconstruct organ doses for radiotherapy patients by using a series of computational human phantoms coupled with a commercial treatment planning system and a radiotherapy-dedicated Monte Carlo transport code are developed and performed illustrative dose calculations.
Journal ArticleDOI
PETSTEP: Generation of synthetic PET lesions for fast evaluation of segmentation methods.
Beatrice Berthon,Ida Häggström,Aditya Apte,Bradley J. Beattie,Assen S. Kirov,John L. Humm,Christopher Marshall,Emiliano Spezi,Anne Larsson,C. Ross Schmidtlein +9 more
TL;DR: PETSTEP allows fast simulation of synthetic images reproducing scanner-acquired PET data and shows great promise for the evaluation of PET segmentation methods.
References
More filters
Book ChapterDOI
WaveLab and Reproducible Research
TL;DR: Wavelab is a library of wavelet-packet analysis, cosine- Packet analysis and matching pursuit, available free of charge over the Internet.
Journal ArticleDOI
A DICOM-RT-based toolbox for the evaluation and verification of radiotherapy plans
TL;DR: A DICOM (Digital Imaging and Communication in Medicine) based toolbox, developed for the evaluation and the verification of radiotherapy treatment plans, offers the possibility of importing treatment plans generated with different calculation algorithms and/or different optimization engines and evaluating dose distributions on an independent platform.
Journal ArticleDOI
Integrated software tools for the evaluation of radiotherapy treatment plans
Robert E. Drzymala,Michael D. Holman,Di Yan,William B. Harms,Nilesh L. Jain,Michael G. Kahn,Bahman Emami,James A. Purdy +7 more
TL;DR: Within the constraints of the X Window System environment, this assemblage of software tools provides a portable, flexible, and convenient method for the quantitative evaluation of several radiotherapy treatment plans.
Journal ArticleDOI
Extending Python with Fortran
Paul F. Dubois,T.-Y. Yang +1 more
TL;DR: The authors have created a tool, Pyfort, for connecting Fortran routines to Python, which produces one or more Python extension modules which you then compile and load into Python, either statically or dynamically, as desired.
Journal Article
Extending python with Fortran
Paul F. Dubois,T.-Y. Yang +1 more
TL;DR: Pyfort as mentioned in this paper is a tool for connecting Fortran routines to Python, using a syntax that is close to a subset of the Fortran 95 interface syntax, which can produce one or more Python extension modules which can then be loaded into Python, either statically or dynamically, as desired.