[Gate-users] Gate-users Digest, Vol 128, Issue 18
Amir Ghabrial
eng_amir_shawky at hotmail.com
Sat Jan 21 14:13:16 CET 2017
Dear Prof. Dr. Uwe Pietrzyk
I am using GATE V7.2, and I am comparing my results with
"Validation of a Monte Carlo simulation of the Philips Allegro/GEMINI PET systems using GATE" by F Lamare et al.
which compare the Gate results and the experimental one obtained by "Surti."
and I tried other systems such as Siemens MCT and Biograph 6, and I get a scatter fraction higher than the experimental and the simulated ones.
And for the sensitivity using NEMA phantom, I get higher values as well.
So I'm not sure where the problem is. Thank you for your time and considerations
many thanks
Amir
________________________________
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Today's Topics:
1. Re: Gate (Pietrzyk, Uwe)
----------------------------------------------------------------------
Message: 1
Date: Fri, 20 Jan 2017 16:13:32 +0000
From: "Pietrzyk, Uwe" <u.pietrzyk at fz-juelich.de>
To: Amir Ghabrial <eng_amir_shawky at hotmail.com>
Cc: "gate-users at lists.opengatecollaboration.org"
<gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] Gate
Message-ID: <13042378-349E-4EA1-A414-E946EFF990C1 at fz-juelich.de>
Content-Type: text/plain; charset="windows-1252"
Hello Amir Ghabrial,
maybe you could add some more information:
- which version of GATE-7 exactly you are using? 7.0, 7.1, 7.2??
- what / who is “others”?? What (Publication??) exactly are you
comparing your simulation to.
Kind regards,
Uwe Pietrzyk
/----------------------------------------------------------------------
Prof. Dr. Uwe Pietrzyk
Diplom-Physiker
Institut für Neurowissenschaften und Medizin / INM-4
Forschungszentrum Jülich GmbH
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----------------------------------------------------------------------/
On 20 Jan 2017, at 15:04, Amir Ghabrial <eng_amir_shawky at hotmail.com> wrote:
> Dear Gate Users,
>
>
> I'm simulating the allegro system with NEMA 2007 scatter fraction phantom, the results aren't matching as the others simulated the same code and got the same results as the experimental which around 40 % , I'm getting a scatter fraction of over 44% , I was wondering where is the problem as i'm using GATE V7 ??
>
>
> many thanks in advance
> Amir
>
> P.S attached here the GATE code
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> #=====================================================
> # VISUALISATION
> #=====================================================
>
> /vis/disable
>
> #/vis/open VRML2FILE
> #/vis/viewer/set/viewpointThetaPhi 60 60
> #/vis/viewer/zoom 6.0
> #/vis/drawVolume
> #/tracking/storeTrajectory 1
> #/vis/scene/add/trajectories
> #/vis/scene/endOfEventAction accumulate
>
> /control/execute Verbose.mac
>
>
> #=====================================================
> # GEOMETRY
> #=====================================================
>
>
> /gate/geometry/setMaterialDatabase GateMaterials.db
>
>
> #
> # W O R L D
> #
> /gate/world/geometry/setXLength 200. cm
> /gate/world/geometry/setYLength 200. cm
> /gate/world/geometry/setZLength 300. cm
>
>
> #-------------------oooooOOOOO00000OOOOOooooo---------------------#
> # #
> # D E F I N I T I O N A N D D E S C R I T I O N #
> # O F Y O U R P E T D E V I C E #
> # #
> #-------------------oooooOOOOO00000OOOOOooooo---------------------#
>
> # CYLINDRICAL
> # D E T E C T O R
> /gate/world/daughters/name cylindricalPET
> /gate/world/daughters/insert cylinder
> /gate/cylindricalPET/setMaterial Air
> /gate/cylindricalPET/geometry/setRmax 52. cm
> /gate/cylindricalPET/geometry/setRmin 28. cm
> /gate/cylindricalPET/geometry/setHeight 24.02 cm
> /gate/cylindricalPET/vis/forceWireframe
> /gate/cylindricalPET/vis/setColor white
>
>
>
> # S H I E L D I N G
> /gate/cylindricalPET/daughters/name Shielding
> /gate/cylindricalPET/daughters/insert cylinder
> /gate/Shielding/setMaterial Lead
> /gate/Shielding/geometry/setRmax 46.132 cm
> /gate/Shielding/geometry/setRmin 28.0 cm
> /gate/Shielding/geometry/setHeight 2.86 cm
> /gate/Shielding/vis/forceSolid
> #/gate/Shielding/vis/forceWireframe
> /gate/Shielding/vis/setColor white
>
> # R E P E A T S H I E L D I N G
> /gate/Shielding/repeaters/insert linear
> /gate/Shielding/linear/setRepeatNumber 2
> /gate/Shielding/linear/setRepeatVector 0.0 0.0 21.16 cm
>
>
> # D E T E C T O R = R S E C T O R
> /gate/cylindricalPET/daughters/name rsector
> /gate/cylindricalPET/daughters/insert box
> /gate/rsector/geometry/setXLength 40.0 mm
> /gate/rsector/geometry/setYLength 94.5 mm
> /gate/rsector/geometry/setZLength 18.3 cm
> /gate/rsector/setMaterial Glass
> /gate/rsector/placement/setTranslation 45.2 0.0 0.0 cm
> /gate/rsector/vis/forceWireframe
>
>
>
> # M O D U L E
> /gate/rsector/daughters/name module
> /gate/rsector/daughters/insert box
> /gate/module/geometry/setXLength 20. mm
> /gate/module/geometry/setYLength 94.5 mm
> /gate/module/geometry/setZLength 18.3 cm
> /gate/module/setMaterial PTFE
> /gate/module/placement/setTranslation -10.0 0.0 0.0 mm
> /gate/module/vis/forceWireframe
>
> # C R Y S T A L
> /gate/module/daughters/name crystal
> /gate/module/daughters/insert box
> /gate/crystal/geometry/setXLength 20.0 mm
> /gate/crystal/geometry/setYLength 4.0 mm
> /gate/crystal/geometry/setZLength 6.0 mm
> /gate/crystal/setMaterial GSO
> /gate/crystal/placement/setTranslation 0.0 0.0 0.0 mm
>
> # L A Y E R G S O
> /gate/crystal/daughters/name GSO
> /gate/crystal/daughters/insert box
> /gate/GSO/geometry/setXLength 20.0 mm
> /gate/GSO/geometry/setYLength 4.0 mm
> /gate/GSO/geometry/setZLength 6.0 mm
> /gate/GSO/placement/setTranslation 0.0 0.0 0.0 mm
> /gate/GSO/setMaterial GSO
>
> # R E P E T I T I O N C R Y S T A L
> /gate/crystal/repeaters/insert cubicArray
> /gate/crystal/cubicArray/setRepeatNumberX 1
> /gate/crystal/cubicArray/setRepeatNumberY 22
> /gate/crystal/cubicArray/setRepeatNumberZ 29
> /gate/crystal/cubicArray/setRepeatVector 0.0 4.3 6.3 mm
>
>
> # R E P E T I T I O N R S E C T O R
>
> /gate/rsector/repeaters/insert ring
> /gate/rsector/ring/setRepeatNumber 28
>
>
> # A T T A C H S Y S T E M
> /gate/systems/cylindricalPET/rsector/attach rsector
> /gate/systems/cylindricalPET/module/attach module
> /gate/systems/cylindricalPET/crystal/attach crystal
> /gate/systems/cylindricalPET/layer0/attach GSO
>
>
>
>
> # C U R V E D P A T I E N T B E D
> /gate/world/daughters/name bed
> /gate/world/daughters/insert cylinder
> /gate/bed/placement/setTranslation 0.0 9.0 0.0 cm
> /gate/bed/geometry/setRmax 22.0 cm
> /gate/bed/geometry/setRmin 20.0 cm
> /gate/bed/geometry/setPhiStart 225 deg
> /gate/bed/geometry/setDeltaPhi 90 deg
> #/gate/bed/geometry/setYLength 2.0 cm
> /gate/bed/geometry/setHeight 179.0 cm
> /gate/bed/setMaterial Plastic #Carbon material is also recommended with defined density of 1.4g/cc
> /gate/bed/vis/setColor gray
>
>
>
>
> # A T T A C H C R Y S T A L SD
>
> /gate/GSO/attachCrystalSD
>
>
> /gate/systems/cylindricalPET/describe
>
>
> #-------------------oooooOOOOO00000OOOOOooooo---------------------#
> # #
> # A T T A C H P H A N T O M S D & #
> # A T T A C H C R Y S T A L S D #
> # #
> #-------------------oooooOOOOO00000OOOOOooooo---------------------#
>
>
>
> /gate/world/daughters/name NEMAphantom
> /gate/world/daughters/insert cylinder
> /gate/NEMAphantom/placement/setTranslation 0.0 0.0 0.0 cm
> /gate/NEMAphantom/placement/alignToZ
> # Full cylinder so Rmin=0.0cm
> /gate/NEMAphantom/geometry/setRmax 10.15 cm
> /gate/NEMAphantom/geometry/setHeight 70.0 cm
> /gate/NEMAphantom/setMaterial Polyethylene
> /gate/NEMAphantom/vis/forceWireframe
> /gate/NEMAphantom/vis/setColor cyan
>
>
> /gate/world/daughters/name srcSurround
> /gate/world/daughters/insert cylinder
> /gate/srcSurround/placement/setTranslation 0.0 -4.5 0.0 cm
> # Full cylinder so Rmin=0.0cm
> /gate/srcSurround/geometry/setRmax 3.2 mm
> /gate/srcSurround/geometry/setHeight 70.0 cm
> /gate/srcSurround/setMaterial Air
> /gate/srcSurround/vis/forceWireframe
> /gate/srcSurround/vis/setColor magenta
>
>
> /gate/srcSurround/daughters/name srcVol
> /gate/srcSurround/daughters/insert cylinder
> /gate/srcVol/placement/setTranslation 0.0 0.0 0.0 cm
> /gate/srcVol/geometry/setRmax 2.4 mm
> /gate/srcVol/geometry/setRmin 1.6 mm
> /gate/srcVol/geometry/setHeight 70.0 cm
> /gate/srcVol/setMaterial Glass
> /gate/srcVol/vis/forceWireframe
> /gate/srcVol/vis/setColor white
>
>
> /gate/srcSurround/daughters/name srcWater
> /gate/srcSurround/daughters/insert cylinder
> /gate/srcWater/placement/setTranslation 0.0 0.0 0.0 cm
> # Full cylinder so Rmin=0.0cm
> /gate/srcWater/geometry/setRmax 1.6 mm
> /gate/srcWater/geometry/setHeight 70 cm
> /gate/srcWater/setMaterial Water
> /gate/srcWater/vis/forceWireframe
> /gate/srcWater/vis/setColor red
>
>
> #-------------------oooooOOOOO00000OOOOOooooo---------------------#
> # #
> # A T T A C H P H A N T O M S D & #
> # A T T A C H C R Y S T A L S D #
> # #
> #-------------------oooooOOOOO00000OOOOOooooo---------------------#
>
> /gate/NEMAphantom/attachPhantomSD
> /gate/srcSurround/attachPhantomSD
> /gate/srcVol/attachPhantomSD
> /gate/srcWater/attachPhantomSD
> /gate/bed/attachPhantomSD
>
> /gate/Shielding/attachPhantomSD
>
> #=====================================================
> # PHYSICS
> #=====================================================
> #
> # P H Y S I C S
> #
> /gate/physics/addProcess PhotoElectric
> /gate/physics/processes/PhotoElectric/setModel StandardModel
>
> /gate/physics/addProcess Compton
> /gate/physics/processes/Compton/setModel StandardModel
>
> /gate/physics/addProcess RayleighScattering
> /gate/physics/processes/RayleighScattering/setModel LivermoreModel
>
> /gate/physics/addProcess ElectronIonisation
> /gate/physics/processes/ElectronIonisation/setModel StandardModel e-
> /gate/physics/processes/ElectronIonisation/setModel StandardModel e+
>
> /gate/physics/addProcess Bremsstrahlung
> /gate/physics/processes/Bremsstrahlung/setModel StandardModel e-
> /gate/physics/processes/Bremsstrahlung/setModel StandardModel e+
>
> /gate/physics/addProcess PositronAnnihilation
>
> /gate/physics/addProcess eMultipleScattering
> /gate/physics/processes/eMultipleScattering/setGeometricalStepLimiterType e- distanceToBoundary
> /gate/physics/processes/eMultipleScattering/setGeometricalStepLimiterType e+ distanceToBoundary
>
> /gate/physics/addProcess RadioactiveDecay
>
> /gate/physics/processList Enabled
> /gate/physics/processList Initialized
>
> #
> # C U T S
> #
>
>
> /gate/physics/Gamma/SetCutInRegion NEMAphantom 1.0 cm
> /gate/physics/Electron/SetCutInRegion NEMAphantom 1.0 cm
> /gate/physics/Positron/SetCutInRegion NEMAphantom 1.0 cm
>
> #=====================================================
> # CUTS
> #=====================================================
> # Cuts for particle in NEMACylinder
>
> /gate/physics/Gamma/SetCutInRegion GSO 1.0 cm
> /gate/physics/Electron/SetCutInRegion GSO 1.0 cm
> /gate/physics/Positron/SetCutInRegion GSO 1.0 cm
>
>
>
>
> /gate/physics/processList Enabled
> /gate/physics/processList Initialized
>
>
>
>
> #=====================================================
> # INITIALISATION
> #=====================================================
>
> /gate/run/initialize
>
>
> #=====================================================
> # Show how the geometry moves with time
> #=====================================================
>
> #/control/execute MoveVisu.mac
>
> #=====================================================
> # D I G I T I Z E R: DETECTOR ELECTRONIC RESPONSE
> #=====================================================
>
> /gate/digitizer/Singles/insert adder
> /gate/digitizer/Singles/insert readout
> /gate/digitizer/Singles/readout/setDepth 1
>
> /gate/digitizer/Singles/insert blurring
> /gate/digitizer/Singles/blurring/setResolution 0.13
> /gate/digitizer/Singles/blurring/setEnergyOfReference 511.0 keV
>
> /gate/digitizer/Singles/insert thresholder
> /gate/digitizer/Singles/thresholder/setThreshold 410.0 keV
> /gate/digitizer/Singles/insert upholder
> /gate/digitizer/Singles/upholder/setUphold 665.0 keV
>
> /gate/digitizer/Singles/insert timeResolution
> /gate/digitizer/Singles/timeResolution/setTimeResolution 5.53 ns
>
>
>
> #=====================================================
> # C O I N C I D E N C E S O R T E R
> #=====================================================
>
> /gate/digitizer/Coincidences/setWindow 5.53 ns
>
> /gate/digitizer/name delay
> /gate/digitizer/insert coincidenceSorter
> /gate/digitizer/delay/setWindow 5.53 ns
> /gate/digitizer/delay/setOffset 500.0 ns
>
> #=====================================================
> # P A R T I C L E S O U R C E
> #=====================================================
> #-------------------oooooOOOOO00000OOOOOooooo---------------------#
> # #
> # D E F I N I T I O N O F #
> # Y O U R V E R B O S I T Y L E V E L #
> # #
> #-------------------oooooOOOOO00000OOOOOooooo---------------------#
>
>
>
> # F A S T P R O D U C T I O N M O D U L E F O R F - 1 8 I S O T O P E S
>
>
> # F A S T P R O D U C T I O N M O D U L E F O R F - 1 8 I S O T O P E S
> /gate/source/addSource F18CylinderSource
> /gate/source/F18CylinderSource/setActivity 2200000.0 becquerel
> /gate/source/F18CylinderSource/gps/particle e+
> /gate/source/F18CylinderSource/setForcedUnstableFlag true
> /gate/source/F18CylinderSource/setForcedHalfLife 6586.2 s
> /gate/source/F18CylinderSource/gps/energytype Fluor18
> /gate/source/F18CylinderSource/gps/type Volume
> /gate/source/F18CylinderSource/gps/shape Cylinder
> /gate/source/F18CylinderSource/gps/radius 1.6 mm
> /gate/source/F18CylinderSource/gps/halfz 70.0 cm
> /gate/source/F18CylinderSource/gps/angtype iso
> /gate/source/F18CylinderSource/gps/centre 0.0 -4.5 0.0 cm
>
>
> /gate/source/list
>
> #=====================================================
> # D A T A O U T P U T
> #=====================================================
> #/gate/output/ascii/enable
> #/gate/output/ascii/setFileName allegro
> #/gate/output/ascii/setOutFileHitsFlag 0
> #/gate/output/ascii/setOutFileSinglesFlag 1
> #/gate/output/ascii/setOutFileCoincidencesFlag 1
>
>
> /gate/output/root/enable
> /gate/output/root/setFileName allegro
> /gate/output/root/setRootHitFlag 1
> /gate/output/root/setRootSinglesFlag 1
> /gate/output/root/setRootCoincidencesFlag 1
> /gate/output/root/setRootdelayFlag 1
>
> #====================================================
> # R A N D O M E N G I N E A N D S E E D
> #====================================================
> # JamesRandom Ranlux64 MersenneTwister
> /gate/random/setEngineName JamesRandom
> #/gate/random/setEngineSeed default
> #/gate/random/setEngineSeed auto
> #/gate/random/setEngineSeed 123456789
> /gate/random/setEngineSeed default
> #/gate/random/resetEngineFrom fileName
> /gate/random/verbose 1
>
> #=====================================================
> # M E A S U R E M E N T S E T T I N G S
> #=====================================================
>
> /gate/application/setTimeSlice 5 s
> /gate/application/setTimeStart 0 s
> /gate/application/setTimeStop 5 s
>
> /gate/application/startDAQ
> _______________________________________________
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