[Gate-users] internal dosimetry

[Eng. M Pharaon]

dear gate users;
i am trying to simulate internal dosimetry in human organs using DICOM CT images and i am facing difficulties with using the correct sources and how i could located them in specific organ.
please have a look on the input file and advise .
please note that the input file i used a TPSPencilBeam because as i mention before i didn't know the correct way to locate the source in organ


#ALIAS

#Voxelized geometry
/control/alias type "complex"

## DENSITY TOLERANCE
/control/alias dt "0.01"


#================================================================

  # VISUALISATION
#/control/execute ../mac/visu.mac
#/vis/disable

#================================================================

  # MATERIALS
/gate/geometry/setMaterialDatabase    ../data/HFMaterials.db

#================================================================

# WORLD
/gate/world/setMaterial                 Air
/gate/world/geometry/setXLength         3 m
/gate/world/geometry/setYLength         3 m
/gate/world/geometry/setZLength         3 m
/gate/world/vis/setVisible              0

/control/execute ../data/MAN_phantom.mac

#================================================================

  # PHYSICS

/gate/physics/addPhysicsList QBBC_EMZ

#================================================================

  # PARAMETERS
/control/alias cut "0.1"
/control/alias step "0.1"

  #Cut
/gate/physics/Gamma/SetCutInRegion      patient 0.1 mm
/gate/physics/Electron/SetCutInRegion   patient 0.1 mm
/gate/physics/Positron/SetCutInRegion   patient 0.1 mm


  #Tracking cut
/gate/physics/SetMinRemainingRangeInRegion patient 0.1 mm
/gate/physics/ActivateSpecialCuts e-
/gate/physics/ActivateSpecialCuts proton

  #stepLimiter
/gate/physics/SetMaxStepSizeInRegion world 100 mm
/gate/physics/SetMaxStepSizeInRegion patient 0.1 mm
/gate/physics/ActivateStepLimiter proton
/gate/physics/ActivateStepLimiter deuteron
/gate/physics/ActivateStepLimiter triton
/gate/physics/ActivateStepLimiter alpha
/gate/physics/ActivateStepLimiter GenericIon

#================================================================

  # OUTPUTS

/control/execute ../data/actor.mac
/gate/actor/addActor                                              DoseActor  dose3D
/gate/actor/dose3D/attachTo                                       patient
/gate/actor/dose3D/stepHitType                                    random
/gate/actor/dose3D/setResolution                                  512 512 8
/gate/actor/dose3D/enableDose                                     true
/gate/actor/dose3D/save                                           ../output/output.mhd
/gate/actor/dose3D/inputDoseByRegions                             ../data/SYRPhantom.mhd
/gate/actor/dose3D/outputDoseByRegions                            ../output/DoseByRegions.txt
#/gate/actor/dose3D/addRegion                                      1000: 89, 90, 91
#/gate/actor/dose3D/addRegion                                      1001: 92, 93, 94

#================================================================

  # INITIALISATION

/gate/run/initialize

#================================================================

  # SOURCE

# TPSPencilBeam SOURCE

#/gate/source/addSource                          TPS     TPSPencilBeam
#/gate/source/TPS/setTestFlag                    false
#/gate/source/TPS/setFlatGenerationFlag          false
##/gate/source/TPS/setPlan                        ../data/PlanDescriptionffcenter.txt
#/gate/source/TPS/setPlan                       ../data/PlanDescriptionFilspots.txt
#/gate/source/TPS/setParticleType                proton
#/gate/source/TPS/setSpotIntensityAsNbIons       true
#/gate/source/TPS/setSourceDescriptionFile       ../data/SourceDescriptionFile.txt
#/gate/source/TPS/setBeamConvergence             true
/gate/source/addSource mybeam gps
/gate/source/mybeam/gps/particle proton
/gate/source/mybeam/gps/energy 8 MeV
/gate/source/mybeam/gps/energytype Mono
/gate/source/mybeam/gps/type Point
/gate/source/mybeam/gps/direction 0 0 1
/gate/source/mybeam/gps/pos/centre 0. 0. -0.01 cm

#================================================================

  # SEED
/gate/random/setEngineSeed 1234567890
#/gate/random/setEngineName MersenneTwister
#/gate/random/setEngineSeed auto

#================================================================

  # START BEAMS
/gate/application/setTotalNumberOfPrimaries 10000
/gate/application/start
#/geometry/test/run
------------------------------
#HU conversion & Schneider tables

/gate/HounsfieldMaterialGenerator/SetMaterialTable ../data/Schneider2000MaterialsTable.txt
/gate/HounsfieldMaterialGenerator/SetDensityTable ../data/Schneider2000DensitiesTable.txt
/gate/HounsfieldMaterialGenerator/SetDensityTolerance 0.1 g/cm3
/gate/HounsfieldMaterialGenerator/SetOutputMaterialDatabaseFilename ../data/HUmaterials-0.1.db
/gate/HounsfieldMaterialGenerator/SetOutputHUMaterialFilename ../data/HU2mat-0.1.txt
/gate/HounsfieldMaterialGenerator/Generate

#patient virtual container
/gate/world/daughters/name patient_box
/gate/world/daughters/insert box
/gate/patient_box/setMaterial G4_AIR
/gate/patient_box/geometry/setXLength 50 cm
/gate/patient_box/geometry/setYLength 50 cm
/gate/patient_box/geometry/setZLength 50 cm


/gate/patient_box/vis/setColor        yellow

# Patient geometry description
/gate/patient_box/daughters/name patient
/gate/patient_box/daughters/insert ImageNestedParametrisedVolume

/gate/patient/geometry/TranslateTheImageAtThisIsoCenter 0.0 0.0 0.0 mm

/control/alias dg "0"

/gate/patient/placement/setTranslation 0.0 0.0 0.0 cm
/gate/patient_box/placement/setRotationAxis           0 1 0
/gate/patient_box/placement/setRotationAngle          0 deg

/gate/geometry/setMaterialDatabase                  ../data/HUmaterials-0.1.db
/gate/patient/geometry/setHUToMaterialFile          ../data/HU2mat-0.1.txt
#/gate/patient/geometry/setImage                     ../data/phantom.mhd
/gate/patient/geometry/setImage                     ../data/SYRPhantom.mhd
/gate/patient/vis/setColor            red

                     Mohamad Pharaon
                           Nuclear Engineer
             Teacher Assistant at Faculty Of
        Mechanical And Electrical Engineering
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