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 ---------------Geant4 doiPET example---------------------
 ===========================================================
  Author list to be updated, with names of co-authors and contributors from National Institute of Radiological Sciences (NIRS)
 
  Abdella M. Ahmed (1, 2), Andrew Chacon (1, 2), Harley Rutherford (1, 2),
  Hideaki Tashima (3), Go Akamatsu (3), Akram Mohammadi (3), Eiji Yoshida (3), Taiga Yamaya (3)
  Susanna Guatelli (2), and Mitra Safavi-Naeini (1, 2)
 
 *Corresponding authors
 e-mail: abdella.ahmed@health.nsw.gov.au
         mitras@ansto.gov.au 
         susanna@uow.edu.au
 
 (1) Australian Nuclear Science and Technology Organisation, Australia
 (2) University of Wollongong, Australia
 (3) National Institute of Radiological Sciences, Japan
 
 ================================================================================================
 
 Introduction:
 
 This example simulates depth-of-interaction (doi) enabled positron emission tomography (PET) scanner 
 and NEMA NU phantoms.The example can be executed in a multithreading mode. Some realistic approches 
 of identifying crystal ID are presented.
   
    - The center of mass of the position of interaction is identified based on energy weighting 
    
   * Note: the following steps are performed if the option for AngerLogic is enabled (ApplyAngerLogic: true) in 
     the inputParameter.txt
   - Four ideal photomultiplier tubes (PMTs) are placed at each corner of the crystal block
   - Perform Anger type calculation method to identify the position of interaction in 2D based
   - Shift the position response based on the reflector pattern
   - DOI is identified by using a look-up-table and
   - Crystal ID in 3D is determined 
 
 The above steps are illustrated figuratively in the supplementary document.
 
 ================================================================================================
 1-Geometry and Phantoms
 
 The detector construction has two main parts: constructing the PET system and placing the phantoms.
 
 The PET system is constructed from depth-of-interaction (DOI)detectors blocks. Each detector consisted 
 of 16 x 16 x 4 crystal array constructed from GSO scintillation material. Materials are defined in the 
 DefineMaterials() using Geant4 NIST database. The geometrical specifications are given (and can be changed) 
 in the GlobalParameters.hh file. 
 
 The scanner has 4 ring detectors. The detectors are covered with Aluminum material. Gaps between crystal 
 elements, as well as adjacent rings are introduced.
 
 Various types of NEMA NU phantoms has been provided and are defined in the ConstructPhantom() method. 
 To precisely create the image quality phantom, the G4UnionSolid from the Constructive Solid Geometry (CSG) 
 has been used. The type, position and size of the phantoms can be changed using the macro file when necessary. 
 A macro file is provided for each type of phantom imaging. For example, to run the simulation with image quality 
 phantom, the run_imageQualityPhantom_wholeBody.mac should be used.
         
  2- PHYSICS LIST
 
 The physics list contains standard electromagnetic processes and the radioactiveDecay module for GenericIon. It is 
 defined in the PhysicsList class as a Geant4 modular physics list with registered physics builders provided in Geant4:
    - G4DecayPhysics - defines all particles and their decay processes
    - G4RadioactiveDecayPhysics - defines radioactiveDecay for GenericIon
    - G4EmStandardPhysics_option3 - defines EM standard processes
     
  3- ACTION INITALIZATION
 
    The ActionInitialization class instantiates and registers to Geant4 kernel all user action classes by invoking the 
 ActionInitialization::Build().
 
  4- PRIMARY GENERATOR
 
 The default particle beam is F-18 ion at rest defined in the GPS (General Particle Source). The GPS is used for all types 
 of activity distribution. Various macro files are provided with the name appended on it for specific simulation. The following 
 macro files are provided:
  
 run_imageQualityPhantom_wholeBody.mac
 run_imageQualityPhantom_smallAnimal.mac
 run_NECR.mac
 run_sensitivity.mac
 run_spatialResolution.mac
 run_normalization.mac (This one is not given in the NEMA NU manual but it is an important part of image reconstruction) 
    
 5-EVENT ACTION
 
 At the end of each event, the information is extracted by calling FindInteractingCrystal() function and associative container
 (multimap and set methods) and the containers are cleared by calling the Clear() function.
 
                 
  6- STEPPING ACTION
 
 The SteppingAction class is the one which is used to track the steps. In the stepping action, interaction information of the 
 photon with the crystal and the phantoms are extracted. The interaction information (such as energy deposition, blockID, crystalID, etc)
 is passed into the Analysis.cc class, which outputs the result into an ASCII file. 
 
 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 
 the physical volume.
 
 7-ANALYSIS
 
 In the doiPETAnalysis class, several realistic parameters are provided. Deadtime of the detector and/or module, efficiency of the detector, 
 crystal dependent energy resoltion,  etc are provided. The parameters can be changed in the inputparameters.txt file. 
  
 ***** Geant4 ROOT ANALYSIS
 /Path/doiPET/build/ and type:
 cmake -DWITH_ANALYSIS_USE=ON -DGeant4_DIR=/path/to/geant4_install_dir ../
 
 
 ***** How to run a  simulation:
 
 Be in the build director
 /Path/doiPET/build/ cmake ../
 /Path/doiPET/build/ make
 /Path/doiPET/build/ ./doiPET run.mac
 
 Simulation output:
 
 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:
 
 EventID, BlockID, tangentialCrystalID, AxialCrystalID, DOI_ID, time, and Energy deposition in the crystal is written to the file as a list-mode format. 
 
 The user can choose to make the output either in singles or coincidence mode in the inputParameter.txt file as follows:
 
 #Choose the type of output: singlesOutput or coincidenceOutput
 TypeOfOutput: coincidenceOutput
 
 - Use the code analysis.cpp to analyse the raw simulation output data stored in the "resultCoincidence.data" or "resultCoincidence.root" file.
 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
 as follows:
 
 
     Compile: g++ analysis.cpp -o analysis `root-config --cflags --libs`
     Run: ./analysis
 
 Then, the axial sensitivity will be saved in a CSV file, and the total sensitivty will be displayed in the screen.
 
 The reference data for this example are in: https://bitbucket.org/AbdellaAhmed/doipet_advancedexample_referencedata
 The user can compare his/her simulation results with this data, after elaborating them with the provided analysis scripts.
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