[Gate-users] use of doseactor, voxelized phantom and source to generate dose and edep map
Eng. M Pharaon
pharaon_m at hotmail.com
Sun May 31 14:04:36 CEST 2020
Dear Park
It seems that something is weird in the final results or there is something that I didn’t fully understand in Gate code . me too am not having a good results all the time
I'm facing a problem with dose by region actor and my whole project is depending on solving this problem so I could have accurate results .
When I use this actor on low energies, such as 0.01 Mev , the deposited energy results are good and I could confirm from mhd output file that all the energy has been located in the source origin.
But when I use energies for example from 0.3 to 2 Mev, I get results lower than they should be compared to the same voxel phantom results that has been simulated using mcnp code,
Could that be the same problem you faced?
Below you can check the macrofiles I am using
#/control/execute verbose.mac
#/control/execute ../mac/visu.mac
#==============================
# GEOMETRY
#==============================
/gate/geometry/setMaterialDatabase ../data/GateMaterials.db
#----------------------
# World
#----------------------
/gate/world/geometry/setXLength 300 cm
/gate/world/geometry/setYLength 300 cm
/gate/world/geometry/setZLength 300 cm
/gate/world/setMaterial Air
/gate/world/vis/setVisible 0
# Body
/gate/world/daughters/name phantom
/gate/world/daughters/insert ImageNestedParametrisedVolume
/gate/phantom/geometry/setImage ../data/Segm.mhd
/gate/phantom/geometry/setRangeToMaterialFile ../data/range_geo.dat
#==============================
# PHYSICS
#==============================
#----------------------
# Physics List
#----------------------
/gate/physics/addPhysicsList emlivermore
#----------------------
# Cuts and Step limiters
#----------------------
/gate/physics/Electron/SetCutInRegion world 0.01 mm
/gate/physics/Gamma/SetCutInRegion world 0.01 mm
/gate/physics/Electron/SetCutInRegion phantom 0.001 mm
/gate/physics/Gamma/SetCutInRegion phantom 0.001 mm
/gate/physics/SetMaxStepSizeInRegion phantom 0.001 mm
/gate/physics/ActivateStepLimiter e-
/gate/physics/displayCuts
#########/gate/physics/addPhysicsList emlivermore
#########/gate/physics/Gamma/SetCutInRegion world 10.0 mm
##########/gate/physics/Electron/SetCutInRegion world 10.0 mm
##########/gate/physics/Positron/SetCutInRegion world 10.0 mm
##########/gate/physics/Gamma/SetCutInRegion phantom 0.1 mm
##########/gate/physics/Electron/SetCutInRegion phantom 0.1 mm
##########/gate/physics/Positron/SetCutInRegion phantom 0.1 mm
#==============================
# DETECTORS
#==============================
# It is possible to save a DoseActor as a 3D matrix.
/gate/actor/addActor DoseActor dose3D
/gate/actor/dose3D/attachTo phantom
/gate/actor/dose3D/stepHitType random
/gate/actor/dose3D/setResolution 1346 693 147
/gate/actor/dose3D/enableDose true
/gate/actor/dose3D/save ../output/output.mhd
/gate/actor/dose3D/inputDoseByRegions ../data/Segm.mhd
/gate/actor/dose3D/outputDoseByRegions ../output/DoseByRegions.txt
#==============================
# INITIALISATION
#==============================
/gate/run/initialize
#==============================
# BEAM
#==============================
# Source
/gate/source/addSource phantom voxel
# DECLARATION THAT THE VOXELIZED SOURCE WILL BE ENTERED USING IMAGE DATA
/gate/source/phantom/reader/insert image
/gate/source/phantom/imageReader/translator/insert range
/gate/source/phantom/imageReader/rangeTranslator/readTable ../data/ActivityRange.dat
/gate/source/phantom/imageReader/rangeTranslator/describe 1
# THE FOLLOWING LINE ALLOWS YOU TO INSERT THE IMAGE DATA USING THE APPROPRIATE EXTENSION FILE
/gate/source/phantom/imageReader/readFile ../data/Segm.mhd
# THE DEFAULT POSITION OF THE VOXELIZED SOURCE IS IN THE 1ST QUARTER
# SO THE VOXELIZED SOURCE HAS TO BE SHIFTED OVER HALF ITS DIMENSION IN THE NEGATIVE DIRECTION ON EACH AXIS
/gate/source/phantom/setPosition -673 -346.5 -73.5 mm
# THE FOLLOWING LINES CHARACTERIZE THE SIZE (NO DIFFERENCE WITH AN ANALYTICAL SOURCE)
/gate/source/phantom/gps/particle gamma
/gate/source/phantom/gps/energytype Mono
/gate/source/phantom/gps/monoenergy 0.1 MeV
/gate/source/phantom/gps/angtype iso
#==============================
#==============================
# START SIMULATION
#==============================
/gate/random/setEngineName MersenneTwister
/gate/random/setEngineSeed auto
/gate/application/setTotalNumberOfPrimaries 1000
/gate/application/start
==============================================================
#activity range file
1
135 135 1
Best Regards
Eng. Pharaon
From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org> On Behalf Of Hyun Soo Park
Sent: Saturday, May 30, 2020 5:43 AM
To: gate-users at lists.opengatecollaboration.org
Subject: [Gate-users] use of doseactor, voxelized phantom and source to generate dose and edep map
Hello, Gate users,
We just have a relatively simple task of estimating internal radiation dosimetry of 18F-labeled PET tracer using doseactor, voxelized phantom and source. However, me and my colleagues are struggling with this beautiful research tool because of lack of experiences and not enough understandings about it.
We acquired PET/CT images using the radiotracer at varying time points to describe the biodistribution of the tracer. CT images were the voxelized phantom and PET images were the matched voxelized source.
By following to many contributors’ exercices and examples, we’ve finally generated following macro that returns common outputs of internal dosimetry by GATE (i.e., Dose and Edep, etc).
Our questions are obvious:
1) is the following macro defined well to generate Dose and Edep map for given voxelized phantom and source?
2) definition of the fluorine-18 was appropriate?
3) how could we measure dose of a specific organ, such as kidney, using dose map? Could it be done by common VOI analysis measuring voxel mean value?
4) the latest simulation gave us non-sense results of showing continuously increasing dose in a organ, while the radioactivity is apparently decreasing as time. how could it be explained?
Best wishes, and have a great weekend!
Park
#=====================================================
# VEROBOSITY
#=====================================================
/control/execute mac/verbose.mac
#=====================================================
# VISUALISATION
#=====================================================
/control/execute mac/visu.mac
#=====================================================
# GEOMETRY
#=====================================================
/gate/geometry/setMaterialDatabase data/GateMaterials.db
# World
/gate/world/geometry/setXLength 10 cm
/gate/world/geometry/setYLength 10 cm
/gate/world/geometry/setZLength 10 cm
/gate/world/setMaterial Air
/gate/world/vis/setVisible 1
/gate/world/vis/forceWireframe
# Voxel phantom
/gate/world/daughters/name ct
/gate/world/daughters/insert ImageRegularParametrisedVolume
/gate/ct/geometry/setRangeToMaterialFile data/range_geo.dat
/gate/ct/geometry/setImage data/ct-gate.mhd
/gate/ct/setSkipEqualMaterials 1
/gate/ct/vis/setVisible 1
# /gate/ct/vis/setColor blue
/gate/ct/vis/forceWireframe
# /gate/geometry/rebuild
#=====================================================
# PHYSICS
#=====================================================
/gate/physics/addPhysicsList emstandard_opt3
/gate/physics/addProcess RadioactiveDecay #to generate decay process of F-18
#=====================================================
# DETECTORS
#=====================================================
/gate/actor/addActor DoseActor doseDistribution
/gate/actor/doseDistribution/attachTo ct
/gate/actor/doseDistribution/stepHitType random
/gate/actor/doseDistribution/setSize 30 28.8 99 mm #Size in mm
/gate/actor/doseDistribution/setPosition 0 0 0 cm # Origin
/gate/actor/doseDistribution/setResolution 58 48 165 #Size (pixel)
/gate/actor/doseDistribution/enableEdep true
/gate/actor/doseDistribution/enableUncertaintyEdep true
/gate/actor/doseDistribution/enableSquaredEdep false
/gate/actor/doseDistribution/enableDose true #from true
/gate/actor/doseDistribution/setDoseAlgorithm VolumeWeighting
# /gate/actor/doseDistribution/enableDoseToWater true #new set
/gate/actor/doseDistribution/enableUncertaintyDose true #from true
/gate/actor/doseDistribution/enableSquaredDose false
/gate/actor/doseDistribution/enableNumberOfHits true
/gate/actor/doseDistribution/save output/output.mhd
/gate/actor/addActor SimulationStatisticActor stat
/gate/actor/stat/save output/stat.txt
/gate/actor/stat/saveEveryNSeconds 60
#=====================================================
# INITIALISATION
#=====================================================
/gate/run/initialize
#=====================================================
# SOURCE :
#=====================================================
#Description
#Ion
/gate/source/addSource ion voxel
/gate/source/ion/reader/insert image
/gate/source/ion/imageReader/translator/insert linear
/gate/source/ion/imageReader/linearTranslator/setScale 1. Bq
/gate/source/ion/imageReader/readFile data/pt-gate.mhd
/gate/source/ion/imageReader/verbose 1
/gate/source/ion/setPosition -15.0 -14.4 -49.5 mm
/gate/source/ion/gps/particle ion
/gate/source/ion/gps/ion 9 18 0 0 #F-18
/gate/source/ion/gps/energytype Mono
/gate/source/ion/gps/monoenergy 0. keV
/gate/source/ion/gps/angtype iso
/gate/source/ion/setForcedUnstableFlag true
/gate/source/ion/useDefaultHalfLife 6586 s
/gate/source/ion/dump 1
# /gate/source/list
#=====================================================
# RANDOM
#=====================================================
/gate/random/setEngineName MersenneTwister
/gate/random/setEngineSeed auto
#=====================================================
# START
#=====================================================
/gate/application/noGlobalOutput
/vis/enable
/gate/application/setTotalNumberOfPrimaries 500000 #acceptable uncertainty is at 500000
/gate/application/start
--
연구중점교수, 분당서울대학교병원
전화번호:
(사무실) +82-31-787-2936
(휴대전화) +82-10-8833-2806
팩스: +82-31-787-4018
이메일: hyuns at snu.ac.kr
<mailto:hyuns at snu.ac.kr>
Hyun Soo Park, PhD
--
Research professor
Department of Nuclear Medicine
Seoul National University Bundang Hospital, Seongnam, Korea
Telephone:
(Office) +82-31-787-2936
(Mobile) +82-10-8833-2806
Fax: +82-31-787-4018
email: hyuns at snu.ac.kr<mailto:hyuns at snu.ac.kr>
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