Import Geant4 11.0.0 source tree
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Gabriele Cosmo
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---------------Geant4 doiPET example---------------------
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Author list to be updated, with names of co-authors and contributors from National Institute of Radiological Sciences (NIRS)
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Abdella M. Ahmed (1, 2), Andrew Chacon (1, 2), Harley Rutherford (1, 2),
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Hideaki Tashima (3), Go Akamatsu (3), Akram Mohammadi (3), Eiji Yoshida (3), Taiga Yamaya (3)
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Susanna Guatelli (2), and Mitra Safavi-Naeini (1, 2)
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*Corresponding authors
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e-mail: abdella.ahmed@health.nsw.gov.au
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mitras@ansto.gov.au
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susanna@uow.edu.au
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(1) Australian Nuclear Science and Technology Organisation, Australia
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(2) University of Wollongong, Australia
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(3) National Institute of Radiological Sciences, Japan
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================================================================================================
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Introduction:
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This example simulates depth-of-interaction (doi) enabled positron emission tomography (PET) scanner
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and NEMA NU phantoms.The example can be executed in a multithreading mode. Some realistic approches
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of identifying crystal ID are presented.
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- The center of mass of the position of interaction is identified based on energy weighting
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* Note: the following steps are performed if the option for AngerLogic is enabled (ApplyAngerLogic: true) in
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the inputParameter.txt
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- Four ideal photomultiplier tubes (PMTs) are placed at each corner of the crystal block
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- Perform Anger type calculation method to identify the position of interaction in 2D based
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- Shift the position response based on the reflector pattern
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- DOI is identified by using a look-up-table and
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- Crystal ID in 3D is determined
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The above steps are illustrated figuratively in the supplementary document.
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================================================================================================
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1-Geometry and Phantoms
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The detector construction has two main parts: constructing the PET system and placing the phantoms.
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The PET system is constructed from depth-of-interaction (DOI)detectors blocks. Each detector consisted
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of 16 x 16 x 4 crystal array constructed from GSO scintillation material. Materials are defined in the
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DefineMaterials() using Geant4 NIST database. The geometrical specifications are given (and can be changed)
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in the GlobalParameters.hh file.
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The scanner has 4 ring detectors. The detectors are covered with Aluminum material. Gaps between crystal
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elements, as well as adjacent rings are introduced.
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Various types of NEMA NU phantoms has been provided and are defined in the ConstructPhantom() method.
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To precisely create the image quality phantom, the G4UnionSolid from the Constructive Solid Geometry (CSG)
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has been used. The type, position and size of the phantoms can be changed using the macro file when necessary.
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A macro file is provided for each type of phantom imaging. For example, to run the simulation with image quality
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phantom, the run_imageQualityPhantom_wholeBody.mac should be used.
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2- PHYSICS LIST
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The physics list contains standard electromagnetic processes and the radioactiveDecay module for GenericIon. It is
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defined in the PhysicsList class as a Geant4 modular physics list with registered physics builders provided in Geant4:
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- G4DecayPhysics - defines all particles and their decay processes
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- G4RadioactiveDecayPhysics - defines radioactiveDecay for GenericIon
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- G4EmStandardPhysics_option3 - defines EM standard processes
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3- ACTION INITALIZATION
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The ActionInitialization class instantiates and registers to Geant4 kernel all user action classes by invoking the
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ActionInitialization::Build().
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4- PRIMARY GENERATOR
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The default particle beam is F-18 ion at rest defined in the GPS (General Particle Source). The GPS is used for all types
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of activity distribution. Various macro files are provided with the name appended on it for specific simulation. The following
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macro files are provided:
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run_imageQualityPhantom_wholeBody.mac
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run_imageQualityPhantom_smallAnimal.mac
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run_NECR.mac
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run_sensitivity.mac
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run_spatialResolution.mac
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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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5-EVENT ACTION
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At the end of each event, the information is extracted by calling FindInteractingCrystal() function and associative container
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(multimap and set methods) and the containers are cleared by calling the Clear() function.
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6- STEPPING ACTION
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The SteppingAction class is the one which is used to track the steps. In the stepping action, interaction information of the
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photon with the crystal and the phantoms are extracted. The interaction information (such as energy deposition, blockID, crystalID, etc)
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is passed into the Analysis.cc class, which outputs the result into an ASCII file.
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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
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the physical volume.
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7-ANALYSIS
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In the doiPETAnalysis class, several realistic parameters are provided. Deadtime of the detector and/or module, efficiency of the detector,
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crystal dependent energy resoltion, etc are provided. The parameters can be changed in the inputparameters.txt file.
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***** Geant4 ROOT ANALYSIS
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/Path/doiPET/build/ and type:
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cmake -DWITH_ANALYSIS_USE=ON -DGeant4_DIR=/path/to/geant4_install_dir ../
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***** How to run a simulation:
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Be in the build director
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/Path/doiPET/build/ cmake ../
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/Path/doiPET/build/ make
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/Path/doiPET/build/ ./doiPET run.mac
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Simulation output:
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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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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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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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#Choose the type of output: singlesOutput or coincidenceOutput
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TypeOfOutput: coincidenceOutput
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- Use the code analysis.cpp to analyse the raw simulation output data stored in the "resultCoincidence.data" or "resultCoincidence.root" file.
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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
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as follows:
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Compile: g++ analysis.cpp -o analysis `root-config --cflags --libs`
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Run: ./analysis
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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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The reference data for this example are in: https://bitbucket.org/AbdellaAhmed/doipet_advancedexample_referencedata
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The user can compare his/her simulation results with this data, after elaborating them with the provided analysis scripts.
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=================== end ====================
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