HeinzelCluster: accelerated reconstruction for FORE and OSEM3D.

Abstract:

:Using iterative three-dimensional (3D) reconstruction techniques for reconstruction of positron emission tomography (PET) is not feasible on most single-processor machines due to the excessive computing time needed, especially so for the large sinogram sizes of our high-resolution research tomograph (HRRT). In our first approach to speed up reconstruction time we transform the 3D scan into the format of a two-dimensional (2D) scan with sinograms that can be reconstructed independently using Fourier rebinning (FORE) and a fast 2D reconstruction method. On our dedicated reconstruction cluster (seven four-processor systems, Intel PIII@700 MHz, switched fast ethernet and Myrinet, Windows NT Server), we process these 2D sinograms in parallel. We have achieved a speedup > 23 using 26 processors and also compared results for different communication methods (RPC, Syngo, Myrinet GM). The other approach is to parallelize OSEM3D (implementation of C Michel), which has produced the best results for HRRT data so far and is more suitable for an adequate treatment of the sinogram gaps that result from the detector geometry of the HRRT. We have implemented two levels of parallelization for four dedicated cluster (a shared memory fine-grain level on each node utilizing all four processors and a coarse-grain level allowing for 15 nodes) reducing the time for one core iteration from over 7 h to about 35 min.

journal_name

Phys Med Biol

authors

Vollmar S,Michel C,Treffert JT,Newport DF,Casey M,Knöss C,Wienhard K,Liu X,Defrise M,Heiss WD

doi

10.1088/0031-9155/47/15/307

subject

Has Abstract

pub_date

2002-08-07 00:00:00

pages

2651-8

issue

15

eissn

0031-9155

issn

1361-6560

journal_volume

47

pub_type

杂志文章
  • Application of the Monte Carlo integration (MCI) method for calculation of the anisotropy of 192Ir brachytherapy sources.

    abstract::Source anisotropy is a very important factor in the brachytherapy quality assurance of high-dose rate (HDR) 192Ir afterloading stepping sources. If anisotropy is not taken into account then doses received by a brachytherapy patient in certain directions can be in error by a clinically significant amount. Experimental ...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/43/6/029

    authors: Baltas D,Giannouli S,Garbi A,Diakonos F,Geramani K,Ioannidis GT,Tsalpatouros A,Uzunoglu N,Kolotas C,Zamboglou N

    更新日期:1998-06-01 00:00:00

  • Viscoelastic characterization of thin tissues using acoustic radiation force and model-based inversion.

    abstract::By means of the viscoelastodynamic model for a two-layer solid-fluid system and a detailed account of the locally induced acoustic radiation force, a rational analytical and computational framework is established for the viscoelastic characterization of thin tissues from high-frequency ultrasound (HFUS) measurements. ...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/54/13/009

    authors: Guzina BB,Tuleubekov K,Liu D,Ebbini ES

    更新日期:2009-07-07 00:00:00

  • A new extended-length parallel-plate ionization chamber.

    abstract::A special parallel-plate ionization chamber was developed. The motivation for the construction of this new chamber was mainly to fulfil the need of a reference system for computed tomography standard beams in the Calibration Laboratory of IPEN. However, the chamber was tested also in standard radiation beams of mammog...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/50/16/012

    authors: Maia AF,Caldas LV

    更新日期:2005-08-21 00:00:00

  • Feasibility of replacing patient specific cutouts with a computer-controlled electron multileaf collimator.

    abstract::A motorized electron multileaf collimator (eMLC) was developed as an add-on device to the Varian linac for delivery of advanced electron beam therapy. It has previously been shown that electron beams collimated by an eMLC have very similar penumbra to those collimated by applicators and cutouts. Thus, manufacturing pa...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/58/16/5653

    authors: Eldib A,Jin L,Li J,Ma CM

    更新日期:2013-08-21 00:00:00

  • Substituting gelatine with Pluronic F-127 matrix in 3D polymer gel dosimeters can improve nuclear magnetic resonance, thermal and optical properties.

    abstract::This work discusses the substitution of a gelatine physical gel matrix with a matrix made of poly(ethylene oxide)-block-poly(propylene oxide)-block-poly(ethylene oxide) (Pluronic F-127) in five 3D radiotherapy polymer gel dosimeters: MAGAT, PAGAT, NIPAM, VIPARnd (VIP) and VIPARCT (VIC). The current research outcomes s...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/1361-6560/aad9d5

    authors: Jaszczak M,Wach R,Maras P,Dudek M,Kozicki M

    更新日期:2018-09-06 00:00:00

  • Estimation of tissue resistivities from multiple-electrode impedance measurements.

    abstract::In order to measure in vivo resistivity of tissues in the thorax, the possibility of combining anatomical data extracted from high-resolution images with multiple-electrode impedance measurements, a priori knowledge of the range of tissue resistivities, and a priori data on the instrumentation noise is assessed in thi...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/39/1/001

    authors: Eyüboğlu BM,Pilkington TC,Wolf PD

    更新日期:1994-01-01 00:00:00

  • Role of skin tissue layers and ultra-structure in transcutaneous electrical stimulation including tDCS.

    abstract:BACKGROUND:During transcranial electrical stimulation (tES), including transcranial direct current stimulation (tDCS) and transcranial alternating current stimulation (tACS), current density concentration around the electrode edges that is predicted by simplistic skin models does not match experimental observations of ...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/1361-6560/abb7c1

    authors: Khadka N,Bikson M

    更新日期:2020-09-11 00:00:00

  • A new approach to account for the medium-dependent effect in model-based dose calculations for kilovoltage x-rays.

    abstract::This study presents a new approach to accurately account for the medium-dependent effect in model-based dose calculations for kilovoltage (kV) x-rays. This approach is based on the hypothesis that the correction factors needed to convert dose from model-based dose calculations to absorbed dose-to-medium depend on both...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/56/13/011

    authors: Pawlowski JM,Ding GX

    更新日期:2011-07-07 00:00:00

  • Including robustness in multi-criteria optimization for intensity-modulated proton therapy.

    abstract::We present a method to include robustness in a multi-criteria optimization (MCO) framework for intensity-modulated proton therapy (IMPT). The approach allows one to simultaneously explore the trade-off between different objectives as well as the trade-off between robustness and nominal plan quality. In MCO, a database...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/57/3/591

    authors: Chen W,Unkelbach J,Trofimov A,Madden T,Kooy H,Bortfeld T,Craft D

    更新日期:2012-02-07 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 comparison of rotation- and blob-based system models for 3D SPECT with depth-dependent detector response.

    abstract::We compare two different implementations of a 3D SPECT system model for iterative reconstruction, both of which compensate for non-uniform photon attenuation and depth-dependent system response. One implementation performs fast rotation of images represented using a basis of rectangular voxels, whereas the other repre...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/49/11/003

    authors: Yendiki A,Fessler JA

    更新日期:2004-06-07 00:00:00

  • Performance measurements of a high-spatial-resolution YAP camera.

    abstract::Physical properties of a position-sensitive camera for the analysis of biodistributions of gamma- and beta-emitting radiopharmaceuticals in small animals have been studied, in order to achieve optimal operating conditions. The camera consisted of a highly segmented yttrium-aluminate perovskite (YAP) scintillator, coup...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/50/3/n01

    authors: Uzunov N,Bello M,Boccaccio P,Moschini G,Baldazzi G,Bollini D,de Notaristefani F,Mazzi U,Riondato M

    更新日期:2005-02-07 00:00:00

  • Optimization of multiply acquired magnetic flux density B(z) using ICNE-Multiecho train in MREIT.

    abstract::The aim of magnetic resonance electrical impedance tomography (MREIT) is to visualize the electrical properties, conductivity or current density of an object by injection of current. Recently, the prolonged data acquisition time when using the injected current nonlinear encoding (ICNE) method has been advantageous for...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/55/9/021

    authors: Nam HS,Kwon OI

    更新日期:2010-05-07 00:00:00

  • Three-dimensional performance of a small-diameter positron emission tomograph.

    abstract::Recently, the initial 2D physical characterization of a small-diameter positron emission tomograph, designed specifically for scanning of small laboratory animals, was reported. The physical characteristics of the tomograph operating in 3D mode have now been measured and compared to those obtained in 2D mode. In 3D, t...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/42/2/010

    authors: Bloomfield PM,Myers R,Hume SP,Spinks TJ,Lammertsma AA,Jones T

    更新日期:1997-02-01 00:00:00

  • Accurate Monte Carlo calculations of the combined attenuation and build-up factors, for energies (20-1500 keV) and distances (0-10 cm) relevant in brachytherapy.

    abstract::The combined build-up and attenuation factor, B exp (-mu r), of point isotropic photon sources in a water medium has been calculated using the Monte Carlo method, for energies (20-1500 keV) and distances (1-10 cm) relevant in brachytherapy. For the transport of photons and electrons, up-to-date and self-consistent tot...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/36/6/005

    authors: Angelopoulos A,Perris A,Sakellariou K,Sakelliou L,Sarigiannis K,Zarris G

    更新日期:1991-06-01 00:00:00

  • Photothermal effects of laser tissue soldering.

    abstract::Low-strength anastomoses and thermal damage of tissue are major concerns in laser tissue welding techniques where laser energy is used to induce thermal changes in the molecular structure of the tissues being joined, hence allowing them to bond together. Laser tissue soldering, on the other hand, is a bonding techniqu...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/44/4/013

    authors: McNally KM,Sorg BS,Welch AJ,Dawes JM,Owen ER

    更新日期:1999-04-01 00:00:00

  • Dose evaluation of boron neutron capture synovectomy using the THOR epithermal neutron beam: a feasibility study.

    abstract::Rheumatoid arthritis is one of the most common epidemic diseases in the world. For some patients, the treatment with steroids or nonsteroidal anti-inflammatory drugs is not effective, thus necessitating physical removal of the inflamed synovium. Alternative approaches other than surgery will provide appropriate diseas...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/52/6/014

    authors: Wu J,Chang SJ,Chuang KS,Hsueh YW,Yeh KC,Wang JN,Tsai WP

    更新日期:2007-03-21 00:00:00

  • Calculation of radiation exposures from patients to whom radioactive materials have been administered.

    abstract::Spreadsheet templates which calculate cumulative exposures to other persons from patients to whom radioactive materials have been administered have been developed by the authors. Calculations can be based on any specified single-, bi- or tri-exponential whole-body clearance rate and a diurnal (or any other periodic) c...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/43/3/003

    authors: Cormack J,Shearer J

    更新日期:1998-03-01 00:00:00

  • The Hug-Kellerer equation as the universal cell survival curve.

    abstract::The Hug-Kellerer (H-K) equation is one of the earliest proposed radiation cell survival curves. We examine this equation in view of the recent perceived need for a universal cell survival curve which would be applicable to single radiation fractions at high doses. We derive relationships between the three parameters o...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/55/10/N01

    authors: Ekstrand KE

    更新日期:2010-05-21 00:00:00

  • Imaging placental function: current technology, clinical needs, and emerging modalities.

    abstract::The function of the placenta is challenging to characterize and as a result is understudied, despite the growing awareness of the impact of the placental environment on human health and development. Medical imaging has the potential to improve our ability to screen for diseases associated with placental insufficiency,...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章,评审

    doi:10.1088/1361-6560/aaccd9

    authors: Wu C,Bayer CL

    更新日期:2018-07-09 00:00:00

  • Introducing the Jacobian-volume-histogram of deforming organs: application to parotid shrinkage evaluation.

    abstract::The Jacobian of the deformation field of elastic registration between images taken during radiotherapy is a measure of inter-fraction local deformation. The histogram of the Jacobian values (Jac) within an organ was introduced (JVH-Jacobian-volume-histogram) and first applied in quantifying parotid shrinkage. MVCTs of...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/56/11/008

    authors: Fiorino C,Maggiulli E,Broggi S,Liberini S,Cattaneo GM,Dell'oca I,Faggiano E,Di Muzio N,Calandrino R,Rizzo G

    更新日期:2011-06-07 00:00:00

  • An automatic algorithm for detecting stent endothelialization from volumetric optical coherence tomography datasets.

    abstract::Recent research has suggested that endothelialization of vascular stents is crucial to reducing the risk of late stent thrombosis. With a resolution of approximately 10 microm, optical coherence tomography (OCT) may be an appropriate imaging modality for visualizing the vascular response to a stent and measuring the p...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/53/12/001

    authors: Bonnema GT,Cardinal KO,Williams SK,Barton JK

    更新日期:2008-06-21 00:00:00

  • Effects of body habitus on internal radiation dose calculations using the 5-year-old anthropomorphic male models.

    abstract::Computational phantoms are commonly used in internal radiation dosimetry to assess the amount and distribution pattern of energy deposited in various parts of the human body from different internal radiation sources. Radiation dose assessments are commonly performed on predetermined reference computational phantoms wh...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/1361-6560/aa75b4

    authors: Xie T,Kuster N,Zaidi H

    更新日期:2017-07-13 00:00:00

  • Online prediction of respiratory motion: multidimensional processing with low-dimensional feature learning.

    abstract::Accurate real-time prediction of respiratory motion is desirable for effective motion management in radiotherapy for lung tumor targets. Recently, nonparametric methods have been developed and their efficacy in predicting one-dimensional respiratory-type motion has been demonstrated. To exploit the correlation among v...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/55/11/002

    authors: Ruan D,Keall P

    更新日期:2010-06-07 00:00:00

  • Additional factors for the estimation of mean glandular breast dose using the UK mammography dosimetry protocol.

    abstract::The UK and European protocols for mammographic dosimetry use conversion factors that relate incident air kerma to the mean glandular dose (MGD) within the breast. The conversion factors currently used were obtained by computer simulation of a model breast with a composition of 50% adipose and 50% glandular tissues by ...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/45/11/308

    authors: Dance DR,Skinner CL,Young KC,Beckett JR,Kotre CJ

    更新日期:2000-11-01 00:00:00

  • Recovering the triple coincidence of non-pure positron emitters in preclinical PET.

    abstract::Non-pure positron emitters, with their long half-lives, allow for the tracing of slow biochemical processes which cannot be adequately examined by the commonly used short-lived positron emitters. Most of these isotopes emit high-energy cascade gamma rays in addition to positron decay that can be detected and create a ...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/61/5/1904

    authors: Lin HH,Chuang KS,Chen SY,Jan ML

    更新日期:2016-03-07 00:00:00

  • Measurement of the dielectric properties of the epidermis and dermis at frequencies from 0.5 GHz to 110 GHz.

    abstract::Numerous studies have reported the measurements of the dielectric properties of the skin. Clarifying the manner in which the human body interacts with electromagnetic waves is essential for medical research and development, as well as for the safety assessment of electromagnetic wave exposure. The skin comprises sever...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/59/16/4739

    authors: Sasaki K,Wake K,Watanabe S

    更新日期:2014-08-21 00:00:00

  • Use of an amorphous silicon electronic portal imaging device for multileaf collimator quality control and calibration.

    abstract::Multileaf collimator (MLC) calibration and quality control is a time-consuming procedure typically involving the processing, scanning and analysis of films to measure leaf and collimator positions. Faster and more reliable calibration procedures are required for these tasks, especially with the introduction of intensi...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/50/7/003

    authors: Baker SJ,Budgell GJ,MacKay RI

    更新日期:2005-04-07 00:00:00

  • 3D radiotherapy dose prediction on head and neck cancer patients with a hierarchically densely connected U-net deep learning architecture.

    abstract::The treatment planning process for patients with head and neck (H&N) cancer is regarded as one of the most complicated due to large target volume, multiple prescription dose levels, and many radiation-sensitive critical structures near the target. Treatment planning for this site requires a high level of human experti...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/1361-6560/ab039b

    authors: Nguyen D,Jia X,Sher D,Lin MH,Iqbal Z,Liu H,Jiang S

    更新日期:2019-03-18 00:00:00

  • The electromagnetic response of human skin in the millimetre and submillimetre wave range.

    abstract::Recent studies of the minute morphology of the skin by optical coherence tomography revealed that the sweat ducts in human skin are helically shaped tubes, filled with a conductive aqueous solution. This, together with the fact that the dielectric permittivity of the dermis is higher than that of the epidermis, brings...

    journal_title:Physics in medicine and biology

    pub_type: 杂志文章

    doi:10.1088/0031-9155/54/11/005

    authors: Feldman Y,Puzenko A,Ben Ishai P,Caduff A,Davidovich I,Sakran F,Agranat AJ

    更新日期:2009-06-07 00:00:00