| Geant4 Cross Reference |
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2 ---------------Geant4 doiPET example---------- 2 ---------------Geant4 doiPET example---------------------
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4 Author list to be updated, with names of co-a 4 Author list to be updated, with names of co-authors and contributors from National Institute of Radiological Sciences (NIRS)
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6 Abdella M. Ahmed (1, 2), Andrew Chacon (1, 2) 6 Abdella M. Ahmed (1, 2), Andrew Chacon (1, 2), Harley Rutherford (1, 2),
7 Hideaki Tashima (3), Go Akamatsu (3), Akram M 7 Hideaki Tashima (3), Go Akamatsu (3), Akram Mohammadi (3), Eiji Yoshida (3), Taiga Yamaya (3)
8 Susanna Guatelli (2), and Mitra Safavi-Naeini 8 Susanna Guatelli (2), and Mitra Safavi-Naeini (1, 2)
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10 *Corresponding authors
10 *Corresponding authors
11 e-mail: abdella.ahmed@health.nsw.gov.au
11 e-mail: abdella.ahmed@health.nsw.gov.au
12 mitras@ansto.gov.au
12 mitras@ansto.gov.au
13 susanna@uow.edu.au
13 susanna@uow.edu.au
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15 (1) Australian Nuclear Science and Technology 15 (1) Australian Nuclear Science and Technology Organisation, Australia
16 (2) University of Wollongong, Australia
16 (2) University of Wollongong, Australia
17 (3) National Institute of Radiological Science 17 (3) National Institute of Radiological Sciences, Japan
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21 Introduction:
21 Introduction:
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23 This example simulates depth-of-interaction (d 23 This example simulates depth-of-interaction (doi) enabled positron emission tomography (PET) scanner
24 and NEMA NU phantoms.The example can be execut 24 and NEMA NU phantoms.The example can be executed in a multithreading mode. Some realistic approches
25 of identifying crystal ID are presented.
25 of identifying crystal ID are presented.
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27 - The center of mass of the position of int 27 - The center of mass of the position of interaction is identified based on energy weighting
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29 * Note: the following steps are performed if 29 * Note: the following steps are performed if the option for AngerLogic is enabled (ApplyAngerLogic: true) in
30 the inputParameter.txt
30 the inputParameter.txt
31 - Four ideal photomultiplier tubes (PMTs) ar 31 - Four ideal photomultiplier tubes (PMTs) are placed at each corner of the crystal block
32 - Perform Anger type calculation method to i 32 - Perform Anger type calculation method to identify the position of interaction in 2D based
33 - Shift the position response based on the r 33 - Shift the position response based on the reflector pattern
34 - DOI is identified by using a look-up-table 34 - DOI is identified by using a look-up-table and
35 - Crystal ID in 3D is determined
35 - Crystal ID in 3D is determined
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37 The above steps are illustrated figuratively i 37 The above steps are illustrated figuratively in the supplementary document.
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40 1-Geometry and Phantoms
40 1-Geometry and Phantoms
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42 The detector construction has two main parts: 42 The detector construction has two main parts: constructing the PET system and placing the phantoms.
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44 The PET system is constructed from depth-of-in 44 The PET system is constructed from depth-of-interaction (DOI)detectors blocks. Each detector consisted
45 of 16 x 16 x 4 crystal array constructed from 45 of 16 x 16 x 4 crystal array constructed from GSO scintillation material. Materials are defined in the
46 DefineMaterials() using Geant4 NIST database. 46 DefineMaterials() using Geant4 NIST database. The geometrical specifications are given (and can be changed)
47 in the GlobalParameters.hh file.
47 in the GlobalParameters.hh file.
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49 The scanner has 4 ring detectors. The detector 49 The scanner has 4 ring detectors. The detectors are covered with Aluminum material. Gaps between crystal
50 elements, as well as adjacent rings are introd 50 elements, as well as adjacent rings are introduced.
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52 Various types of NEMA NU phantoms has been pro 52 Various types of NEMA NU phantoms has been provided and are defined in the ConstructPhantom() method.
53 To precisely create the image quality phantom, 53 To precisely create the image quality phantom, the G4UnionSolid from the Constructive Solid Geometry (CSG)
54 has been used. The type, position and size of 54 has been used. The type, position and size of the phantoms can be changed using the macro file when necessary.
55 A macro file is provided for each type of phan 55 A macro file is provided for each type of phantom imaging. For example, to run the simulation with image quality
56 phantom, the run_imageQualityPhantom_wholeBody 56 phantom, the run_imageQualityPhantom_wholeBody.mac should be used.
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58 2- PHYSICS LIST
58 2- PHYSICS LIST
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60 The physics list contains standard electromagn 60 The physics list contains standard electromagnetic processes and the radioactiveDecay module for GenericIon. It is
61 defined in the PhysicsList class as a Geant4 m 61 defined in the PhysicsList class as a Geant4 modular physics list with registered physics builders provided in Geant4:
62 - G4DecayPhysics - defines all particles an 62 - G4DecayPhysics - defines all particles and their decay processes
63 - G4RadioactiveDecayPhysics - defines radio 63 - G4RadioactiveDecayPhysics - defines radioactiveDecay for GenericIon
64 - G4EmStandardPhysics_option3 - defines EM 64 - G4EmStandardPhysics_option3 - defines EM standard processes
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66 3- ACTION INITALIZATION
66 3- ACTION INITALIZATION
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68 The ActionInitialization class instantiates 68 The ActionInitialization class instantiates and registers to Geant4 kernel all user action classes by invoking the
69 ActionInitialization::Build().
69 ActionInitialization::Build().
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71 4- PRIMARY GENERATOR
71 4- PRIMARY GENERATOR
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73 The default particle beam is F-18 ion at rest 73 The default particle beam is F-18 ion at rest defined in the GPS (General Particle Source). The GPS is used for all types
74 of activity distribution. Various macro files 74 of activity distribution. Various macro files are provided with the name appended on it for specific simulation. The following
75 macro files are provided:
75 macro files are provided:
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77 run_imageQualityPhantom_wholeBody.mac
77 run_imageQualityPhantom_wholeBody.mac
78 run_imageQualityPhantom_smallAnimal.mac
78 run_imageQualityPhantom_smallAnimal.mac
79 run_NECR.mac
79 run_NECR.mac
80 run_sensitivity.mac
80 run_sensitivity.mac
81 run_spatialResolution.mac
81 run_spatialResolution.mac
82 run_normalization.mac (This one is not given i 82 run_normalization.mac (This one is not given in the NEMA NU manual but it is an important part of image reconstruction)
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84 5-EVENT ACTION
84 5-EVENT ACTION
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86 At the end of each event, the information is e 86 At the end of each event, the information is extracted by calling FindInteractingCrystal() function and associative container
87 (multimap and set methods) and the containers 87 (multimap and set methods) and the containers are cleared by calling the Clear() function.
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90 6- STEPPING ACTION
90 6- STEPPING ACTION
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92 The SteppingAction class is the one which is u 92 The SteppingAction class is the one which is used to track the steps. In the stepping action, interaction information of the
93 photon with the crystal and the phantoms are e 93 photon with the crystal and the phantoms are extracted. The interaction information (such as energy deposition, blockID, crystalID, etc)
94 is passed into the Analysis.cc class, which ou 94 is passed into the Analysis.cc class, which outputs the result into an ASCII file.
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96 Generation of the source (F-18 ion) is confine 96 Generation of the source (F-18 ion) is confined in the physical volume by killing the event in the SteppingAction class when it is out of
97 the physical volume.
97 the physical volume.
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99 7-ANALYSIS
99 7-ANALYSIS
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101 In the doiPETAnalysis class, several realistic 101 In the doiPETAnalysis class, several realistic parameters are provided. Deadtime of the detector and/or module, efficiency of the detector,
102 crystal dependent energy resoltion, etc are p 102 crystal dependent energy resoltion, etc are provided. The parameters can be changed in the inputparameters.txt file.
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104 ***** Geant4 ROOT ANALYSIS
104 ***** Geant4 ROOT ANALYSIS
105 /Path/doiPET/build/ and type:
105 /Path/doiPET/build/ and type:
106 cmake -DWITH_ANALYSIS_USE=ON -DGeant4_DIR=/pat 106 cmake -DWITH_ANALYSIS_USE=ON -DGeant4_DIR=/path/to/geant4_install_dir ../
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109 ***** How to run a simulation:
109 ***** How to run a simulation:
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111 Be in the build director
111 Be in the build director
112 /Path/doiPET/build/ cmake ../
112 /Path/doiPET/build/ cmake ../
113 /Path/doiPET/build/ make
113 /Path/doiPET/build/ make
114 /Path/doiPET/build/ ./doiPET run.mac
114 /Path/doiPET/build/ ./doiPET run.mac
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116 Simulation output:
116 Simulation output:
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118 ASCII and ROOT files are created depending on 118 ASCII and ROOT files are created depending on the type of the output format. The following information of the event is written in the output file:
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120 EventID, BlockID, tangentialCrystalID, AxialCr 120 EventID, BlockID, tangentialCrystalID, AxialCrystalID, DOI_ID, time, and Energy deposition in the crystal is written to the file as a list-mode format.
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122 The user can choose to make the output either 122 The user can choose to make the output either in singles or coincidence mode in the inputParameter.txt file as follows:
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124 #Choose the type of output: singlesOutput or c 124 #Choose the type of output: singlesOutput or coincidenceOutput
125 TypeOfOutput: coincidenceOutput
125 TypeOfOutput: coincidenceOutput
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127 - Use the code analysis.cpp to analyse the raw 127 - Use the code analysis.cpp to analyse the raw simulation output data stored in the "resultCoincidence.data" or "resultCoincidence.root" file.
128 Before compiling, change the option in the hea 128 Before compiling, change the option in the header whether to analyse ASCII or root file (e.g. to use root file #define UseROOT). Then complie the code
129 as follows:
129 as follows:
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132 Compile: g++ analysis.cpp -o analysis `roo 132 Compile: g++ analysis.cpp -o analysis `root-config --cflags --libs`
133 Run: ./analysis
133 Run: ./analysis
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135 Then, the axial sensitivity will be saved in a 135 Then, the axial sensitivity will be saved in a CSV file, and the total sensitivty will be displayed in the screen.
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137 The reference data for this example are in: ht 137 The reference data for this example are in: https://bitbucket.org/AbdellaAhmed/doipet_advancedexample_referencedata
138 The user can compare his/her simulation result 138 The user can compare his/her simulation results with this data, after elaborating them with the provided analysis scripts.
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