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 		      Geant4 - Brachytherapy example
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                             README
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The brachytherapy example is currently maintained and upgraded by Susanna Guatelli (1), Albert Le (1) and Dean Cutajar (1), with the support of
Luciano Pandola (2)  

1. Centre For Medical Radiation Physics (CMRP), University of Wollongong, NSW, Australia.
2. LNS, INFN, Catania, Italy.

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Contact: susanna@uow.edu.au
         deanc@uow.edu.au
         geant4-advanced-examples@cern.ch
        
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List of past co-authors: 
S. George, S. Agostinelli, F. Foppiano, S. Garelli, M. G. Pia, M. Tropeano

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----> Introduction.                                                     
                                                                       
Brachytherapy example simulates  the energy deposit in a water phantom, produced by: 
1) Iridium sources (Flexisource and TG186).                     
2) Iodine sources (Bebig Isoseed and Oncura 6711 I-125).           
3) Leipzig Applicator with an iridium source (model from the Istituto Tumori, Genova, Italy).   

The Flexisource, an Ir-192 source manufactured by Nucletron, an Elekta company, is a source commonly used for high dose rate brachytherapy treatments. 
The geometry of the Flexisource was adapted from D. Granero, J. Pérez-Calatayud, E. Casal, et al, 
"A dosimetric study on the Ir-192 high dose rate Flexisource", Med. Phys. 33 (12), 2006, 4578-82.

The TG186 source is a generic Ir-192 source created to provide developers of model based dose engines with a method of validating new dose calculation techniques.
Details of the TG186 source may be obtained from Facundo Ballester, Åsa Carlsson Tedgren, Domingo Granero, et al,
"A generic high-dose rate 192Ir brachytherapy source for evaluation of model-based dose calculations beyond the TG-43 formalism", Med. Phys. 42, 2015, 3048-62

In particular in this example it is shown how to:
- model a radioactive source  in terms of radiation field and geometry
- model the radiation field with the General Particle Source  with two alternative methods:
   1) Define the energy spectrum of photons exiting the radioactive core
   2) Modelling the Radioactive decay
- calculate the energy deposition in a phantom by means of the G4 scoring mesh
- define the physics by means of a Geant4 Modular Physics List
- save results in an analysis ROOT file              
- calculate the dose rate distribution along the main axis of the source
- compare the calculated dose rate distribution to reference data. 

In the case of the example, the dose rate distribution of a Flexisource is compared to D. Granero, 
J. Pérez-Calatayud, E. Casal, et al,"A dosimetric study on the Ir-192 high dose rate Flexisource", Med. Phys. 33 (12), 2006, 4578-82. 
The dose rate distribution of the Oncura 6711 I-125 source is compared to J. Dolan, Z. Lia, J. F. Williamson, "Monte Carlo and experimental
dosimetry of an I-125 brachytherapy seed", Med. Phys. 33(12), 2006.

The example can be executed in multithreading mode.

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----> 1.Experimental set-up.                                            

The default source is a Ir-192 Flexisource set in the center of a water phantom with size 30 cm. 
The phantom is set in the World volume filled with air.

The primary radiation field is defined by means of the GeneralParticleSource                           
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----> 2.SET-UP 
                                          
A standard Geant4 example CMakeLists.txt is provided.                   

Setup for analysis:
By default, the example has no analysis component. 

To compile and use the application with the analysis on, build the example with the following command:
cmake -DWITH_ANALYSIS_USE=ON -DGeant4_DIR=/path/to/Geant4_installation /path/to/brachytherapy_example                                                     
          
The installation of ROOT is required (http://root.cern.ch/drupal/).

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----> 3.How to run the example.                                         

- Batch mode:
  $G4WORKDIR/bin/Linux-g++/Brachy FlexiSourceMacro.mac  
  $G4WORKDIR/bin/Linux-g++/Brachy LeipzigSourceMacro.mac      
  $G4WORKDIR/bin/Linux-g++/Brachy IridiumSourceMacro.mac                
  $G4WORKDIR/bin/Linux-g++/Brachy IodiumSourceMacro.mac (model of the Bebig Isoseed I-125)  
  $G4WORKDIR/bin/Linux-g++/Brachy OncuraIodineSourceMacro.mac (model of the Oncura 6711 I-125)         
  $G4WORKDIR/bin/Linux-g++/Brachy LeipzigSourceMacro.mac 
                                                                        
- Interative mode:                                                      
  3) $G4WORKDIR/bin/Linux-g++/Brachy
     VisualisationMacro.mac is loaded automatically.         
                                                                         
* How to change the absorber material of the phantom:                                                                 
idle>/phantom/selectMaterial  materialName

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----> 4. Primary radiation Field

The radiation field is defined with the General Particle Source.

Two alternative options are offered:
1) Define gamma as primary radiation field. The gamma are originated from the radioactive core.
This radiation field is defined in:
iodine_source_primary.mac and iridium_source_primary.mac

2) Model the radioactive Decay. The primary particle is the radionuclide.
This option is modelled in iodine_decay.mac and TG186_iridium_decay.mac

The GPS macros are executed in VisualisationMacro.mac by default, FlexiSourceMacro.mac, IodineSourceMacro.mac, LeipzigSourceMacro.mac

- The Flexisource is the default source of the example.
- In VisualisationMacro.mac the source is the default one. iridium_source_primary.mac is executed to define the radiation field emerging from the iridium core.
- In FlexiSourceMacro.mac the Flexi Ir source geometry is selected via interactive command. The radiation field is defined in the iridium_source_primary.mac.
- In IodineSourceMacro.mac, the Bebig Isoseed I-125  brachytherapy source  is modelled. The radiation field is modelled in terms of emitted photons in iodine_source_primary.mac. 
  Alternatively the radioactive decay of I can be modelled using teh macro iodine_decay.mac.
- In LeipzigSourceMacro.mac, A Leipzig applicator (design provided by Istituto Tumori, Genova) is modelled. The iridium_source_leipzig_primary.mac defines the radiation field of the Ir core.
- The TG186SourceMacro.mac models the reference bIr brachytherapy source. The radiation field can be either defined with the iridium_source_primary.mac (spectrum of the emitted photons) or with TG186_iridium_decay.mac (model of the Ir decay).
- OncuraIodineSourceMacro.mac models both the geometry and the radioactive decay of the Oncura 6711 I-125 source.
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----> 5. Physics List

The electromagnetic Livermore Low Energy physics is active as well as the radioactive decay.
The cut is 0.05 mm.

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----> 6. Scoring mesh

The scoring mesh is used to calculate the energy deposition in the plane containing the source (z=0 plane)
integrated over the whole run. The scoring mesh is defined in the input macro files.
T
he default output format of the scoring is changed in the class BrachyUserScoreWriter.
The scoring mesh is fixed  with a size of 20.025 cm along x and y. The bin size is 0.25 mm along x, y and z. 

When running in interactive mode there is no scoring mesh.The user has to add it with appropriate UI                                                            

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----> 7. Simulation output                                               

The output is:

- ASCII file EnergyDeposition.out, with xx (mm), yy(mm), zz(mm), and energy deposition (keV), in the phantom.
  To limit the use of memory, the energy deposition is scored only in the plane containing the source, however this can be changed by the user.
 
  By default:
  EnergyDeposition_Flexi.out contains the Edep when the Flexi source is selected.
  EnergyDeposition_iodine.out contains the Edep when Iodine Bebig Isoseed source is selected.
  EnergyDeposition_TG186.out contains the Edep when the TG186 source is selected.
  EnergyDeposition_Leipzig.out contains the Edep when the Iridium source with Leipzig applicator is selected.
  EnergyDeposition_Oncura.out contains the Edep when the Iodine Oncura 6711 source is selected. 

- brachytherapy.root, containing 
  - a 2D histogram with the energy deposition in the phantom. The macro macro.C is provided as example 
    to open brachytherapy.root in ROOT interactive session and to plot the results of the simulation. 
    The ROOT file will be created if the example is built with the WITH_ANALYSIS_USE=ON option (see section 2).                   
  - 1D histogram withe the plot of energy spectrum of gamma emitted by the radioactive decay when gamma are generated directly as 
    primary particles or whenthey derive from Radioactive Decay(see section 4). 
    plot_primary.C is provided as example to open brachytherapy.root and to plot the energy spectra                                                                

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----> 8.Visualisation                                                     

A macro is provided ad example of visualisation:  VisualisationMacro.mac. 

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-----> 9. Comparison to reference data

The ROOT macros macro.C and plot_primary.C are provided to plot the results of the simulation, contained
in the brachytherapy.root file. 

The ROOT macro TG43_relative_dose.C has brachytherapy.root as input file. It calculates the dose rate distribution along the main axis of 
the brachytherapy source. The dose rate is normalised to 1 at 1 cm distance from the centre. 
The output file is geant4_dose.txt with two columns: 
distance from the centre (cm) dose rate distribution

The user can then compare the dose rate distribution calculated with the example to reference data.

Directory "comparison":
As an example, the dose rate distribution calculated with the Flexisource is compared to reference data from D. Granero, J. Pérez-Calatayud, E. Casal, et al,  "A dosimetric study on the Ir-192 high dose rate Flexisource", Med. Phys. 33 (12), 2006, 4578-82.

The compare.C is a ROOT macro which reads the dose rate distribution calculated with the Flexisource (geant4.txt generated with the advanced example and 280 M histories ) against the reference. 

The directory "comparison" contains:
- the reference data, granero.txt
- the data obtained in Geant4.10.3: geant4.txt, 280 M events. geant4.txt is obtained when executing the macro TG43_relative_dose.C
- comparison.C - macro to read geant4.txt and granero.txt and compare them in the same plot

-----> 10. Regression testing of Geant4
- the macros to run are in test_macro
- the results should be processed with analysis.C