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1 =========================================================== 2 ---------------Geant4 doiPET example--------------------- 3 =========================================================== 4 Author list to be updated, with names of co-authors and contributors from National Institute of Radiological Sciences (NIRS) 5 6 Abdella M. Ahmed (1, 2), Andrew Chacon (1, 2), Harley Rutherford (1, 2), 7 Hideaki Tashima (3), Go Akamatsu (3), Akram Mohammadi (3), Eiji Yoshida (3), Taiga Yamaya (3) 8 Susanna Guatelli (2), and Mitra Safavi-Naeini (1, 2) 9 10 *Corresponding authors 11 e-mail: abdella.ahmed@health.nsw.gov.au 12 mitras@ansto.gov.au 13 susanna@uow.edu.au 14 15 (1) Australian Nuclear Science and Technology Organisation, Australia 16 (2) University of Wollongong, Australia 17 (3) National Institute of Radiological Sciences, Japan 18 19 ================================================================================================ 20 21 Introduction: 22 23 This example simulates depth-of-interaction (doi) enabled positron emission tomography (PET) scanner 24 and NEMA NU phantoms.The example can be executed in a multithreading mode. Some realistic approches 25 of identifying crystal ID are presented. 26 27 - The center of mass of the position of interaction is identified based on energy weighting 28 29 * Note: the following steps are performed if the option for AngerLogic is enabled (ApplyAngerLogic: true) in 30 the inputParameter.txt 31 - Four ideal photomultiplier tubes (PMTs) are placed at each corner of the crystal block 32 - Perform Anger type calculation method to identify the position of interaction in 2D based 33 - Shift the position response based on the reflector pattern 34 - DOI is identified by using a look-up-table and 35 - Crystal ID in 3D is determined 36 37 The above steps are illustrated figuratively in the supplementary document. 38 39 ================================================================================================ 40 1-Geometry and Phantoms 41 42 The detector construction has two main parts: constructing the PET system and placing the phantoms. 43 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 GSO scintillation material. Materials are defined in the 46 DefineMaterials() using Geant4 NIST database. The geometrical specifications are given (and can be changed) 47 in the GlobalParameters.hh file. 48 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 introduced. 51 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, the G4UnionSolid from the Constructive Solid Geometry (CSG) 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 phantom imaging. For example, to run the simulation with image quality 56 phantom, the run_imageQualityPhantom_wholeBody.mac should be used. 57 58 2- PHYSICS LIST 59 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 modular physics list with registered physics builders provided in Geant4: 62 - G4DecayPhysics - defines all particles and their decay processes 63 - G4RadioactiveDecayPhysics - defines radioactiveDecay for GenericIon 64 - G4EmStandardPhysics_option3 - defines EM standard processes 65 66 3- ACTION INITALIZATION 67 68 The ActionInitialization class instantiates and registers to Geant4 kernel all user action classes by invoking the 69 ActionInitialization::Build(). 70 71 4- PRIMARY GENERATOR 72 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 are provided with the name appended on it for specific simulation. The following 75 macro files are provided: 76 77 run_imageQualityPhantom_wholeBody.mac 78 run_imageQualityPhantom_smallAnimal.mac 79 run_NECR.mac 80 run_sensitivity.mac 81 run_spatialResolution.mac 82 run_normalization.mac (This one is not given in the NEMA NU manual but it is an important part of image reconstruction) 83 84 5-EVENT ACTION 85 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 are cleared by calling the Clear() function. 88 89 90 6- STEPPING ACTION 91 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 extracted. The interaction information (such as energy deposition, blockID, crystalID, etc) 94 is passed into the Analysis.cc class, which outputs the result into an ASCII file. 95 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. 98 99 7-ANALYSIS 100 101 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 provided. The parameters can be changed in the inputparameters.txt file. 103 104 ***** Geant4 ROOT ANALYSIS 105 /Path/doiPET/build/ and type: 106 cmake -DWITH_ANALYSIS_USE=ON -DGeant4_DIR=/path/to/geant4_install_dir ../ 107 108 109 ***** How to run a simulation: 110 111 Be in the build director 112 /Path/doiPET/build/ cmake ../ 113 /Path/doiPET/build/ make 114 /Path/doiPET/build/ ./doiPET run.mac 115 116 Simulation output: 117 118 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: 119 120 EventID, BlockID, tangentialCrystalID, AxialCrystalID, DOI_ID, time, and Energy deposition in the crystal is written to the file as a list-mode format. 121 122 The user can choose to make the output either in singles or coincidence mode in the inputParameter.txt file as follows: 123 124 #Choose the type of output: singlesOutput or coincidenceOutput 125 TypeOfOutput: coincidenceOutput 126 127 - 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 header whether to analyse ASCII or root file (e.g. to use root file #define UseROOT). Then complie the code 129 as follows: 130 131 132 Compile: g++ analysis.cpp -o analysis `root-config --cflags --libs` 133 Run: ./analysis 134 135 Then, the axial sensitivity will be saved in a CSV file, and the total sensitivty will be displayed in the screen. 136 137 The reference data for this example are in: https://bitbucket.org/AbdellaAhmed/doipet_advancedexample_referencedata 138 The user can compare his/her simulation results with this data, after elaborating them with the provided analysis scripts. 139 =================== end ====================