STIR: software for tomographic image reconstruction release 2.

Abstract:

:We present a new version of STIR (Software for Tomographic Image Reconstruction), an open source object-oriented library implemented in C++ for 3D positron emission tomography reconstruction. This library has been designed such that it can be used for many algorithms and scanner geometries, while being portable to various computing platforms. This second release enhances its flexibility and modular design and includes additional features such as Compton scatter simulation, an additional iterative reconstruction algorithm and parametric image reconstruction (both indirect and direct). We discuss the new features in this release and present example results. STIR can be downloaded from http://stir.sourceforge.net.

journal_name

Phys Med Biol

authors

Thielemans K,Tsoumpas C,Mustafovic S,Beisel T,Aguiar P,Dikaios N,Jacobson MW

doi

10.1088/0031-9155/57/4/867

subject

Has Abstract

pub_date

2012-02-21 00:00:00

pages

867-83

issue

4

eissn

0031-9155

issn

1361-6560

journal_volume

57

pub_type

杂志文章
  • Modifying proton fluence spectra to generate spread-out Bragg peaks with laser accelerated proton beams.

    abstract::Currently, energy spectra of laser accelerated proton beams are far from being monoenergetic. For their application in radiation therapy, energy selection systems using magnetic fields have been proposed to single out particles with the desired energy. These systems allow the choice of protons between a lowest and a h...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/54/19/N04

    authors: Schell S,Wilkens JJ

    更新日期:2009-10-07 00:00:00

  • Fundamental study on diffuse reflective optical tomography.

    abstract::We report a simulation study on diffuse reflective optical computed tomography, in which continuous-wave sources and detectors are placed on the plane surface of a semi-infinite body. We adopted a simple Tikhonov regularization in the inverse problem and demonstrated the feasibility of three-dimensional reconstruction...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/49/10/004

    authors: Endoh R,Suzuki A,Fujii M,Nakayama K

    更新日期:2004-05-21 00:00:00

  • A Fourier rebinning algorithm incorporating spectral transfer efficiency for 3D PET.

    abstract::This paper presents a Fourier rebinning algorithm for three-dimensional image reconstruction in PET that incorporates the concept of spectral transfer function. It suggests the need for discarding low-frequency components in the rebinning. It also includes the correction for rebinning efficiency which was evaluated by...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/43/4/004

    authors: Tanaka E,Amo Y

    更新日期:1998-04-01 00:00:00

  • Robust treatment planning with 4D intensity modulated carbon ion therapy for multiple targets in stage IV non-small cell lung cancer.

    abstract::Intensity modulated particle therapy (IMPT) with carbon ions can generate highly conformal treatment plans; however, IMPT is limited in robustness against range and positioning uncertainty. This is particularly true for moving targets, even though all motion states of a 4DCT are considered in 4D-IMPT. Here, we expand ...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/1361-6560/aba1a3

    authors: Wolf M,Anderle K,Durante M,Graeff C

    更新日期:2020-11-06 00:00:00

  • The consequences of fixed-pattern noise and image movement on electronic portal images.

    abstract::Fixed-pattern noise in electronic portal images (EPIs) is normally eliminated by dividing raw image data by an open-field calibration image (OFCI). However, for successful elimination, there must be exact registration between the two image sets. Any movement within the imaging system, such as that which occurs with ga...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/41/11/007

    authors: Kirby MC

    更新日期:1996-11-01 00:00:00

  • Brachytherapy technology and physics practice since 1950: a half-century of progress.

    abstract::The 50-year tenure of Physics in Medicine and Biology has coincided with some of the most important developments in radiological science, including the introduction of artificial radioactivity, computers and 3D imaging into medicine. These events have profoundly influenced the development of brachytherapy. Although it...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章,评审

    doi:10.1088/0031-9155/51/13/R18

    authors: Williamson JF

    更新日期:2006-07-07 00:00:00

  • Monitoring the irradiation field of 12C and 16O SOBP beams using positron emitters produced through projectile fragmentation reactions.

    abstract::In order to effectively utilize the prominent properties of heavy ions in radiotherapy, it is important to evaluate both the position of the field irradiated with incident ions and the absorbed dose distribution in a patient's body. One of the methods for this purpose is the utilization of the positron emitters produc...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/53/3/002

    authors: Inaniwa T,Kohno T,Tomitani T,Sato S

    更新日期:2008-02-07 00:00:00

  • A 3D point-kernel multiple scatter model for parallel-beam SPECT based on a gamma-ray buildup factor.

    abstract::A three-dimensional (3D) point-kernel multiple scatter model for point spread function (PSF) determination in parallel-beam single-photon emission computed tomography (SPECT), based on a dose gamma-ray buildup factor, is proposed. This model embraces nonuniform attenuation in a voxelized object of imaging (patient bod...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/52/19/004

    authors: Marinkovic P,Ilic R,Spaic R

    更新日期:2007-10-07 00:00:00

  • 4D Monte Carlo simulation of proton beam scanning: modelling of variations in time and space to study the interplay between scanning pattern and time-dependent patient geometry.

    abstract::When dosimetric effects in time-dependent geometries are studied, usually either the results of individual three-dimensional (3D) calculations are combined or probability-based approaches are applied. These methods may become cumbersome and time-consuming if high time resolution is required or if the geometry is compl...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/50/5/020

    authors: Paganetti H,Jiang H,Trofimov A

    更新日期:2005-03-07 00:00:00

  • The modelling of biological systems in three dimensions using the time domain finite-difference method: I. The implementation of the model.

    abstract::A computer method has been developed which uses the time domain finite-difference (TDFD) algorithm to calculate the deposition of the electromagnetic (EM) field in three-dimensional biological models. This, the first of two papers, describes the algorithm and the computer programs developed. The method is demonstrated...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/31/11/006

    authors: Lau RW,Sheppard RJ

    更新日期:1986-11-01 00:00:00

  • Influence of beam characteristics and detector size in negative-pion dose studies.

    abstract::Dose calculations were performed for a tissue phantom irradiated by uniform circular beams of negative pions with an assumed gaussian momentum distribution. The mean momentum of the pions was varied from 104.4 to 171.5 MeV/c (mean range 5-20 cm in unit-density tissue) and the momentum spread from 0 to 5% of the mean. ...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/24/3/012

    authors: Hamm RN,Wright HA,Turner JE

    更新日期:1979-05-01 00:00:00

  • Dosimetric accuracy of planning and delivering small proton therapy fields.

    abstract::A detailed Monte Carlo model of a proton therapy treatment head was commissioned to simulate the delivery of small field proton treatments. Small fields are challenging in the planning and quality assurance process because of aperture scattering and dosimetric disequilibrium. Four patients with small fields used in al...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/55/24/003

    authors: Bednarz B,Daartz J,Paganetti H

    更新日期:2010-12-21 00:00:00

  • Learning image based surrogate relevance criterion for atlas selection in segmentation.

    abstract::Picking geometrically relevant atlases from the whole training set is crucial to multi-atlas based image segmentation, especially with extensive data of heterogeneous quality in the Big Data era. Unfortunately, there is very limited understanding of how currently used image similarity criteria reveal geometric relevan...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/61/11/4223

    authors: Zhao T,Ruan D

    更新日期:2016-06-07 00:00:00

  • Reconstructing uniformly attenuated rotating slant-hole SPECT projection data using the DBH method.

    abstract::This work applies a previously developed analytical algorithm to the reconstruction problem in a rotating multi-segment slant-hole (RMSSH) SPECT system. The RMSSH collimator has greater detection efficiency than the parallel-hole collimator with comparable spatial resolution at the expense of limited common volume-of-...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/54/13/024

    authors: Huang Q,Xu J,Tsui BM,Gullberg GT

    更新日期:2009-07-07 00:00:00

  • A mathematical model for predicting the changes of non-small cell lung cancer based on tumor mass during radiotherapy.

    abstract::This study aims to build a feasible mathematical model to analyze the mass evolution of NSCLC during standard fractionated radiotherapy. Seventy-three cases of NSCLC who were received radiotherapy with prescription dose of 2 Gy  ×  30 fx were selected retrospectively and divided into adenocarcinoma (ADC) group and squ...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/1361-6560/ab47c0

    authors: Chen J,Wang K,Jian J,Zhang W

    更新日期:2019-11-26 00:00:00

  • Response of x-ray intensifying screens to scattered and primary radiation.

    abstract::The energy dependence of the luminance ratio due to scattered and primary radiation has been determined for four types of X-ray intensifying screens. A water phantom of 30 cm X 30 cm X 20 cm was used as the scattering medium. Ten narrow band X-ray spectra were used as incident radiation: the mean energies of these spe...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/29/10/007

    authors: Koedooder K,Venema HW

    更新日期:1984-10-01 00:00:00

  • Comparison between the lateral penumbra of a collimated double-scattered beam and uncollimated scanning beam in proton radiotherapy.

    abstract::Intensity modulated proton radiotherapy (IMPT) can reduce the dose to critical structures by optimizing the distribution and intensity of individual pencil beams. The IMPT can be delivered by dynamically scanning a pencil beam with variable intensity and energy across the tumor target volume. The lateral penumbra of a...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/53/6/016

    authors: Safai S,Bortfeld T,Engelsman M

    更新日期:2008-03-21 00:00:00

  • An absorptiometry method for the determination of arterial blood concentration of injected iodinated contrast agent.

    abstract::A single photon absorptiometry method to measure the arterial concentration of injected iodinated contrast agent was developed. A prototype absorptiometry unit was built which consists of either a square or circular cross section acrylic (polymethylmethacrylate) cuvette connected to an arterial catheter at one end and...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/37/9/002

    authors: Yeung WT,Lee TY,Del Maestro RF,Kozak R,Bennett JD,Brown T

    更新日期:1992-09-01 00:00:00

  • Fast dose calculation in magnetic fields with GPUMCD.

    abstract::A new hybrid imaging-treatment modality, the MRI-Linac, involves the irradiation of the patient in the presence of a strong magnetic field. This field acts on the charged particles, responsible for depositing dose, through the Lorentz force. These conditions require a dose calculation engine capable of taking into con...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/56/16/003

    authors: Hissoiny S,Raaijmakers AJ,Ozell B,Després P,Raaymakers BW

    更新日期:2011-08-21 00:00:00

  • Evaluation of deformable image registration and a motion model in CT images with limited features.

    abstract::Deformable image registration (DIR) is increasingly used in radiotherapy applications and provides the basis for a previously described model of patient-specific respiratory motion. We examine the accuracy of a DIR algorithm and a motion model with respiration-correlated CT (RCCT) images of software phantom with known...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/57/9/2539

    authors: Liu F,Hu Y,Zhang Q,Kincaid R,Goodman KA,Mageras GS

    更新日期:2012-05-07 00:00:00

  • Phase contrast image guidance for synchrotron microbeam radiotherapy.

    abstract::Recent image guidance developments for preclinical synchrotron microbeam radiotherapy represent a necessary step for future clinical translation of the technique. Image quality can be further improved using x-ray phase contrast, which is readily available at synchrotron facilities. We here describe a methodology for p...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/61/16/5942

    authors: Pelliccia D,Crosbie JC,Larkin KG

    更新日期:2016-08-21 00:00:00

  • Near real-time automated dose restoration in IMPT to compensate for daily tissue density variations in prostate cancer.

    abstract::Proton therapy is very sensitive to daily density changes along the pencil beam paths. The purpose of this study is to develop and evaluate an automated method for adaptation of IMPT plans to compensate for these daily tissue density variations. A two-step restoration method for 'densities-of-the-day' was created: (1)...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/1361-6560/aa5c12

    authors: Jagt T,Breedveld S,van de Water S,Heijmen B,Hoogeman M

    更新日期:2017-06-07 00:00:00

  • Dielectric property measurement of ocular tissues up to 110 GHz using 1 mm coaxial sensor.

    abstract::Measurement of the dielectric properties of ocular tissues up to 110 GHz was performed by the coaxial probe method. A coaxial sensor was fabricated to allow the measurement of small amounts of biological tissues. Four-standard calibration was applied in the dielectric property measurement to obtain more accurate data ...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/60/16/6273

    authors: Sasaki K,Isimura Y,Fujii K,Wake K,Watanabe S,Kojima M,Suga R,Hashimoto O

    更新日期:2015-08-21 00:00:00

  • Denoising of multi b-value diffusion-weighted MR images using deep image prior.

    abstract::The clinical value of multiple b-value diffusion-weighted (DW) magnetic resonance imaging (MRI) has been shown in many studies. However, DW-MRI often suffers from low signal-to-noise ratio, especially at high b-values. To address this limitation, we present an image denoising method based on the concept of deep image ...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/1361-6560/ab8105

    authors: Lin YC,Huang HM

    更新日期:2020-05-11 00:00:00

  • Implementation of biologically conformal radiation therapy (BCRT) in an algorithmic segmentation-based inverse planning approach.

    abstract::The development of new biological imaging technologies offers the opportunity to further individualize radiotherapy. Biologically conformal radiation therapy (BCRT) implies the use of the spatial distribution of one or more radiobiological parameters to guide the IMRT dose prescription. Our aim was to implement BCRT i...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/51/16/N02

    authors: Vanderstraeten B,De Gersem W,Duthoy W,De Neve W,Thierens H

    更新日期:2006-08-21 00:00:00

  • Carbon dioxide reactivity of computed tomography functional parameters in rabbit VX2 soft tissue tumour.

    abstract::Tumour blood flow is one of the important factors limiting the efficacy of radiation therapy (hypoxic radioresistance), chemotherapy (drug delivery) and thermal therapy (heat dissipation) in treating cancer. The modification of tumour blood flow has been an area of intense investigation. In the current study, the arte...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/48/7/303

    authors: Purdie TG,Lee TY

    更新日期:2003-04-07 00:00:00

  • Numerical model of heat transfer in the human eye with consideration of fluid dynamics of the aqueous humour.

    abstract::In this work we present a new 3D numerical model for heat transfer in the human eye, which takes into account the aqueous humour flow in the anterior chamber. We show that consideration of this phenomenon in the calculations alters the temperature distribution on the corneal and lens surfaces, without, however, notice...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/55/19/003

    authors: Karampatzakis A,Samaras T

    更新日期:2010-10-07 00:00:00

  • Monte Carlo aided room scatter studies in the primary air kerma strength standardization of a remote afterloading 192Ir HDR source.

    abstract::Corrections for room scatter, [ksc(d, H)]RM, were derived using Monte Carlo methods for rooms of various sizes, including the brachytherapy treatment room, in which primary air kerma strength standardization of a remote afterloading microSelectron 192Ir HDR source was carried out, using a 60 cm3 spherical graphite ion...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/46/9/303

    authors: Selvam TP,Rajan KN,Nagarajan PS,Sethulakshmi P,Bhatt BC

    更新日期:2001-09-01 00:00:00

  • Exploration and application of phenomenological RBE models for proton therapy.

    abstract::The relative biological effectiveness (RBE) of protons varies with multiple physical and biological factors. Phenomenological RBE models have been developed to include such factors in the estimation of a variable RBE, in contrast to the clinically applied constant RBE of 1.1. In this study, eleven published phenomenol...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/1361-6560/aad9db

    authors: Rørvik E,Fjæra LF,Dahle TJ,Dale JE,Engeseth GM,Stokkevåg CH,Thörnqvist S,Ytre-Hauge KS

    更新日期:2018-09-13 00:00:00

  • Dead time correction and counting statistics for positron tomography.

    abstract::A correction for loss of events due to dead time in dynamic positron emission tomography (PET) is presented. The model employs a paralysing dead time to describe the behaviour of a tomograph over the range of event rates normally encountered in patient studies (up to 200 000 events/s per detector layer). The Donner 28...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/30/5/002

    authors: Mazoyer BM,Roos MS,Huesman RH

    更新日期:1985-05-01 00:00:00