[Gate-users] internal dosimetry
Eng. M Pharaon
pharaon_m at hotmail.com
Thu Mar 5 16:46:45 CET 2020
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EP
Forward
Eng. M Pharaon
Wed 3/4/2020 6:19 PM
* Gate Email
ATT00001.txt
483 bytes
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
Mohamad Pharaon
Nuclear Engineer
Teacher Assistant at Faculty Of
Mechanical And Electrical Engineering
________________________________
From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org> on behalf of Eng. M Pharaon <pharaon_m at hotmail.com>
Sent: Wednesday, March 4, 2020 6:19 PM
To: Gate Email <gate-users at lists.opengatecollaboration.org>
Subject: [Gate-users] internal dosimetry
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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