GATE指的是Geant4 Application for Emission Tomography. 这里是几个学习GATE的中国人的博客兼邮件列表。欢迎加入我们的学习团队！
如果repeat number是奇数（53、55）的时候就没有这个错误，而偶数时（52、54）就出现这个错误。
在模拟mosaic的过程中，使用了linear repeater来重复axial方向上的52个crystal，但是有时候（不总是）出现Overlapping daughter volumes
/gate/crystal/repeaters/insert linear
/gate/crystal/linear/setRepeatNumber 52
/gate/crystal/linear/setRepeatVector 0. 0. 2.3 mm
/gate/crystal/linear/autoCenter true
在模拟mosaic的过程中，使用了linear repeater来重复axial方向上的52个crystal，但是有时候（不总是）出现Overlapping daughter volumes
手册里说：
下面定义collimator的方法在recursive test时出现SolidProblem错误：
/gate/world/daughters/name Collimator
/gate/world/daughters/insert cylinder
#- Define the dimensions of the Collimator volume
/gate/Collimator/geometry/setRmax 42 mm
/gate/Collimator/geometry/setRmin 28 mm
/gate/Collimator/geometry/setHeight 120 mm
/gate/Collimator/setMaterial Air
#- CollimatorLead is the real Lead part
/gate/Collimator/daughters/name CollimatorLead
/gate/Collimator/daughters/insert cylinder
#- Define the dimensions of the Lead volume
/gate/CollimatorLead/geometry/setRmax 37 mm
/gate/CollimatorLead/geometry/setRmin 30 mm
/gate/CollimatorLead/geometry/setHeight 120 mm
#- Set the material of the collimator volume
/gate/CollimatorLead/setMaterial Lead
出现很多下面的错误：
GeomTest Error: SolidProblem
Spurious exiting intersection point
Solid name = Collimator_S
Local position = 2.8 0 5.6 cm
如果Collimator和CollimatorLead定义的大小一样的话：
/gate/Collimator/geometry/setRmax 37 mm
/gate/Collimator/geometry/setRmin 30 mm
就没有错误。
The default rotation axis is the Z axis. Note that the default ring
如果想让它顺时针转，我用的是下面的方法：
/gate/rsector/repeaters/insert ring
/gate/rsector/ring/setFirstAngle 0 deg
/gate/rsector/ring/setAngularSpan -360 deg
/gate/rsector/ring/setRepeatNumber 4
但是上面运行结果只重复了3个，而不是4。 原因是：最后一个的位置和第一个完全重复了。
修改成：/gate/rsector/ring/setAngularSpan -270 deg 就可以了
对于mosaic系统，可以用：
/gate/rsector/ring/setFirstAngle -0.6475 deg
/gate/rsector/ring/setAngularSpan -359.3525 deg
/gate/rsector/ring/setRepeatNumber 278
第一个crystal的角度在 -360/278/2= -0.6475 degree
最后一个(277)个crystal的角度在 -(360-0.6475)= -359.3525 degree
1. 什么是voxels.dat文件？
Initial seed = 9876
你好！
Dr. Shawn,
您好！
谢谢您的分析，我现在得想法是这样：我用一台 Linux PC ，其他的PC 机我想安装cygwin（ Linux虚拟机）来构建 cluster, 在平台上我准备用的是openmosix . 我之所以要构建一个标准的cluster,正如您所说，我是想把所有的任务送到一台 PC上，而每个任务都各占用自己 PC机上的 CPU。这样不就能提高运行速度了吗？
我觉得要是用 ssh将自己写的script 发送到不同机器上的话，这应该要求每台机器上都要安装上GATE软件，要是这样的话，假如要用 100台 PC机同时运算的话，安装软件的工作量就会很大了。不知我的理解是否正确，请您指点！
祝好！
吴
Gate输出里有一个 /gate/output/root/setRootNtupleFlag 1
# SENSITIVE DETECTORS
Dr. Shawn
在您的博客中提到用 clutter进行联机模拟，我现在也正朝这个方向做，因为要的得到一个完整的模拟数据用一台 PC实在是太慢了。正如您所说的，现在 GATE方面的资料非常少，因此，在实现联机的过程中也遇到了难题。
我现在已经用 job splitter所提供的 gjs 将一个完整的scripts 分割后得到：几个 subscripts, 以及submit file 、split file ，具体的如下：
my1.mac my3.mac my5.mac seed1.rndm seed3.rndm seed5.rndm
my2.mac my4.mac my. split seed2.rndm seed4.rndm
想请教您的问题是：在得到这些 subscripts后，接下来该如何实现联机？也就是说该怎样才能让其他的 PC 机也能运行我的subscript 。
因为我曾试着执行 .submit命令结果不能产生任何的数据。
谢谢！
祝您生活开心、顺利！！！
吴
任务1:
先用 gjs 产生random seed文件
Dear Martin,
I guess the random number generation in GATE can be somewhat
confusing. I better explain everything in detail.
-------------------------------------------------------------
The default behaviour:
Without any
/gate/output/root/setSaveRndmFlag n
/random/resetEngineFrom xxx
command GATE will create 2 random seed files:
beginOfRun.rndm and endOfRun.rndm.
If you do not change these files the next run will be initialized from the
endOfRun.rndm file (the beginOfRun.rndm will not change anyhow). So by
default each run will be different.
The random number engine will be initialized from the endOfRun.rndm.
If there is no endOfRun.rndm GATE will create a beginOfRun.rndm and will
start from this file. The beginOfRun.rndm will _always_ be the same! The
endOfRun.rndm will change after each run.
------------------------------------------------------------
Rerunning with the same random numbers:
If you want to re-run the same events you can set
/gate/output/root/setSaveRndmFlag 0
GATE will be initialized internally and each run will be the same.
----------------------------------------------------------------
Continuning an existing simulation to increase the number of events:
In the case where you already run a simulation and want to continue to get
better statistics you need the endOfRun.rndm from your first simulation.
/gate/output/root/setSaveRndmFlag 1
GATE will automatically look for the endOfRun.rndm file in directory where it
runs.
--------------------------------------------------------------------------------------
BTW
When the SaveRndmFlag is set you can observe the status of the random
generator at run end. There are some lines before GATE stops:
----- HepJamesRandom engine status -----
Initial seed = 9876
u[] = 0.207714 ...
I skip the 103 numbers describing the state of the random number engine. If
(at least 1 of) these 103 numbers are different your events will be
statistically independent.
--------------------------------------------------------------------------------------
Continuning an existing simulation to increase the number of events in the
case where you did not save the endOfRun.rndm from the first simulation:
Here the safest method is to use a seed which is totally different from what
GATE creates. I have included a zip file with a few seeds to create
independent random number streams.
/gate/output/root/setSaveRndmFlag 0
/random/resetEngineFrom StartSeq(n).rndm
Just giving the filename without /gate/output/root/setSaveRndmFlag 0 will not be sufficient since GATE will still look for the endOfRun.rndm file.
I hope this helps
Dirk
-------------------------------------------------------------------
我的GATE运行环境：Apple G5 Server Dual 2GHz 2GRAM
Laboratoire de Physique Corpusculaire, CNRS/IN2P3, Université de Clermont-Ferrand, 24 avenue des Landais, 63177 Aubière, France. lazaro@clermont.in2p3.fr
Monte Carlo simulations are increasingly used in scintigraphic imaging to model imaging systems and to develop and assess tomographic reconstruction algorithms and correction methods for improved image quantitation. GATE (GEANT4 application for tomographic emission) is a new Monte Carlo simulation platform based on GEANT4 dedicated to nuclear imaging applications. This paper describes the GATE simulation of a prototype of scintillation camera dedicated to small-animal imaging and consisting of a CsI(Tl) crystal array coupled to a position-sensitive photomultiplier tube. The relevance of GATE to model the camera prototype was assessed by comparing simulated 99mTc point spread functions, energy spectra, sensitivities, scatter fractions and image of a capillary phantom with the corresponding experimental measurements. Results showed an excellent agreement between simulated and experimental data: experimental spatial resolutions were predicted with an error less than 100 microns. The difference between experimental and simulated system sensitivities for different source-to-collimator distances was within 2%. Simulated and experimental scatter fractions in a [98-182 keV] energy window differed by less than 2% for sources located in water. Simulated and experimental energy spectra agreed very well between 40 and 180 keV. These results demonstrate the ability and flexibility of GATE for simulating original detector designs. The main weakness of GATE concerns the long computation time it requires: this issue is currently under investigation by the GEANT4 and the GATE collaborations.
UMR 678 INSERM/UPMC, CHU Pitié Salpêtrière, 91 boulevard de l'Hôpital, 75634 Paris Cedex 13, France.
Monte Carlo simulations are useful for optimizing and assessing single photon emission computed tomography (SPECT) protocols, especially when aiming at measuring quantitative parameters from SPECT images. Before Monte Carlo simulated data can be trusted, the simulation model must be validated. The purpose of this work was to validate the use of GATE, a new Monte Carlo simulation platform based on GEANT4, for modelling indium-111 SPECT data, the quantification of which is of foremost importance for dosimetric studies. To that end, acquisitions of (111)In line sources in air and in water and of a cylindrical phantom were performed, together with the corresponding simulations. The simulation model included Monte Carlo modelling of the camera collimator and of a back-compartment accounting for photomultiplier tubes and associated electronics. Energy spectra, spatial resolution, sensitivity values, images and count profiles obtained for experimental and simulated data were compared. An excellent agreement was found between experimental and simulated energy spectra. For source-to-collimator distances varying from 0 to 20 cm, simulated and experimental spatial resolution differed by less than 2% in air, while the simulated sensitivity values were within 4% of the experimental values. The simulation of the cylindrical phantom closely reproduced the experimental data. These results suggest that GATE enables accurate simulation of (111)In SPECT acquisitions.
Department of Medical Physics, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA. scmidtr@mskcc.org
The recently developed GATE (GEANT4 application for tomographic emission) Monte Carlo package, designed to simulate positron emission tomography (PET) and single photon emission computed tomography (SPECT) scanners, provides the ability to model and account for the effects of photon noncollinearity, off-axis detector penetration, detector size and response, positron range, photon scatter, and patient motion on the resolution and quality of PET images. The objective of this study is to validate a model within GATE of the General Electric (GE) Advance/Discovery Light Speed (LS) PET scanner. Our three-dimensional PET simulation model of the scanner consists of 12 096 detectors grouped into blocks, which are grouped into modules as per the vendor's specifications. The GATE results are compared to experimental data obtained in accordance with the National Electrical Manufactures Association/Society of Nuclear Medicine (NEMA/SNM), NEMA NU 2-1994, and NEMA NU 2-2001 protocols. The respective phantoms are also accurately modeled thus allowing us to simulate the sensitivity, scatter fraction, count rate performance, and spatial resolution. In-house software was developed to produce and analyze sinograms from the simulated data. With our model of the GE Advance/Discovery LS PET scanner, the ratio of the sensitivities with sources radially offset 0 and 10 cm from the scanner's main axis are reproduced to within 1% of measurements. Similarly, the simulated scatter fraction for the NEMA NU 2-2001 phantom agrees to within less than 3% of measured values (the measured scatter fractions are 44.8% and 40.9 +/- 1.4% and the simulated scatter fraction is 43.5 +/- 0.3%). The simulated count rate curves were made to match the experimental curves by using deadtimes as fit parameters. This resulted in deadtime values of 625 and 332 ns at the Block and Coincidence levels, respectively. The experimental peak true count rate of 139.0 kcps and the peak activity concentration of 21.5 kBq/cc were matched by the simulated results to within 0.5% and 0.1% respectively. The simulated count rate curves also resulted in a peak NECR of 35.2 kcps at 10.8 kBq/cc compared to 37.6 kcps at 10.0 kBq/cc from averaged experimental values. The spatial resolution of the simulated scanner matched the experimental results to within 0.2 mm.
U650 INSERM, Laboratoire du Traitement de l'information medicale (LaTIM), CHU Morvan, Université de Bretagne Occidentale, Brest, 29609, France. Frederic.Lamare@univ-brest.fr
A newly developed simulation toolkit, GATE (Geant4 Application for Tomographic Emission), was used to develop a Monte Carlo simulation of a fully three-dimensional (3D) clinical PET scanner. The Philips Allegro/GEMINI PET systems were simulated in order to (a) allow a detailed study of the parameters affecting the system's performance under various imaging conditions, (b) study the optimization and quantitative accuracy of emission acquisition protocols for dynamic and static imaging, and (c) further validate the potential of GATE for the simulation of clinical PET systems. A model of the detection system and its geometry was developed. The accuracy of the developed detection model was tested through the comparison of simulated and measured results obtained with the Allegro/GEMINI systems for a number of NEMA NU2-2001 performance protocols including spatial resolution, sensitivity and scatter fraction. In addition, an approximate model of the system's dead time at the level of detected single events and coincidences was developed in an attempt to simulate the count rate related performance characteristics of the scanner. The developed dead-time model was assessed under different imaging conditions using the count rate loss and noise equivalent count rates performance protocols of standard and modified NEMA NU2-2001 (whole body imaging conditions) and NEMA NU2-1994 (brain imaging conditions) comparing simulated with experimental measurements obtained with the Allegro/GEMINI PET systems. Finally, a reconstructed image quality protocol was used to assess the overall performance of the developed model. An agreement of <3% was obtained in scatter fraction, with a difference between 4% and 10% in the true and random coincidence count rates respectively, throughout a range of activity concentrations and under various imaging conditions, resulting in <8% differences between simulated and measured noise equivalent count rates performance. Finally, the image quality validation study revealed a good agreement in signal-to-noise ratio and contrast recovery coefficients for a number of different volume spheres and two different (clinical level based) tumour-to-background ratios. In conclusion, these results support the accurate modelling of the Philips Allegro/GEMINI PET systems using GATE in combination with a dead-time model for the signal flow description, which leads to an agreement of <10% in coincidence count rates under different imaging conditions and clinically relevant activity concentration levels.
ELIS Department, Ghent University, Sint-Pietersnieuwstraat, 41 B-9000 Ghent, Belgium. Steven.Staelens@ugent.be
Geant4 application for tomographic emission (GATE) is a recently developed simulation platform based on Geant4, specifically designed for PET and SPECT studies. In this paper we present validation results of GATE based on the comparison of simulations against experimental data, acquired with a standard SPECT camera. The most important components of the scintillation camera were modelled. The photoelectric effect. Compton and Rayleigh scatter are included in the gamma transport process. Special attention was paid to the processes involved in the collimator: scatter, penetration and lead fluorescence. A LEHR and a MEGP collimator were modelled as closely as possible to their shape and dimensions. In the validation study, we compared the simulated and measured energy spectra of different isotopes: 99mTc, 22Na, 57Co and 67Ga. The sensitivity was evaluated by using sources at varying distances from the detector surface. Scatter component analysis was performed in different energy windows at different distances from the detector and for different attenuation geometries. Spatial resolution was evaluated using a 99mTc source at various distances. Overall results showed very good agreement between the acquisitions and the simulations. The clinical usefulness of GATE depends on its ability to use voxelized datasets. Therefore, a clinical extension was written so that digital patient data can be read in by the simulator as a source distribution or as an attenuating geometry. Following this validation we modelled two additional camera designs: the Beacon transmission device for attenuation correction and the Solstice scanner prototype with a rotating collimator. For the first setup a scatter analysis was performed and for the latter design. the simulated sensitivity results were compared against theoretical predictions. Both case studies demonstrated the flexibility and accuracy of GATE and exemplified its potential benefits in protocol optimization and in system design.
Geometry and tracking (GEANT4) is a Monte Carlo package designed for high energy physics experiments. It is used as the basis layer for Monte Carlo simulations of nuclear medicine acquisition systems in GEANT4 Application for Tomographic Emission (GATE). GATE allows the user to realistically model experiments using accurate physics models and time synchronization for detector movement through a script language contained in a macro file. The downside of this high accuracy is long computation time. This paper describes a platform independent computing approach for running GATE simulations on a cluster of computers in order to reduce the overall simulation time. Our software automatically creates fully resolved, nonparametrized macros accompanied with an on-the-fly generated cluster specific submit file used to launch the simulations. The scalability of GATE simulations on a cluster is investigated for two imaging modalities, positron emission tomography (PET) and single photon emission computed tomography (SPECT). Due to a higher sensitivity, PET simulations are characterized by relatively high data output rates that create rather large output files. SPECT simulations, on the other hand, have lower data output rates but require a long collimator setup time. Both of these characteristics hamper scalability as a function of the number of CPUs. The scalability of PET simulations is improved here by the development of a fast output merger. The scalability of SPECT simulations is improved by greatly reducing the collimator setup time. Accordingly, these two new developments result in higher scalability for both PET and SPECT simulations and reduce the computation time to more practical values.
本地下载：
使用phantom进行simulate之前，应该弄懂几个问题：
W.P. Segars, B.M.W. Tsui, E.C. Frey, G.A. Johnson, and S.S. Berr, "Development of a 4D digital mouse
phantom for molecular imaging research", Molecular Imaging & Biology, Vol. 6, Issue 3, p. 149-159, 2004.
尽管 voxelized phantom 现在可以读入了，但是当phantom的size比较大时（比如128x128x128, 0.5mm3/voxel），显示就会出错：
Shawn, 中国人，目前在美国一所大学从事医疗器械方面的研究工作。这里是他根据自己的学习兴趣创建的学习小组，欢迎有共同兴趣的朋友加入。一起学习，一起进步。Sharing is good!
