[Gate-users] Gate-users Digest, Vol 128, Issue 18

Pietrzyk, Uwe u.pietrzyk at fz-juelich.de
Tue Jan 24 16:06:40 CET 2017 

Hello Amir Chabrial,

you are experiencing a typical problem when using Monte Carlo
simulation and comparing the results with those from experimental
measurements. Very often a deviation from exact matching of simulation
and measurement are observed, as can also happen, between separate
measurements of different devices of the same type  and between separate
simulations of the same system but based on different programs or
even between different versions of the same program.
The publication you are comparing with is from 2006 and there definitely
is a difference in the two versions of GATE used for the study and the
most recant one which is version 7.2. 
Also, an agreement between measurement and simulation will remain limited
to between 5 to 10 % as long as there are details, which have not been exactly
incorporated in the simulation, like coupling of a crystal and the photosensor,
which might easily result in misclassification of an event belonging to
the “scattered” or” unscattered” events. In addition, the detection efficiency
is often not taken into account, i.e. is assumed to be 100%, but which
in a real experiment will be varying around 90 %, depending on what level
your are determining such factors. In fact such details are also described
in detail in the publication of Lamare et al. Differences between simulated
and measured are expected and are acceptable as long as they can be
explained based on “physical”  effects.

I hope this helps to answer your question and do not hesitate to contact the
gate-users mailing list!

Kind regards and best wishes,

Uwe Pietrzyk

/----------------------------------------------------------------------
Prof. Dr. Uwe Pietrzyk
Diplom-Physiker
Institut für Neurowissenschaften und Medizin / INM-4
Forschungszentrum Jülich GmbH
52425 Jülich
Tel: +49-2461-61 4763
Fax: +49-2461-61 2820
Mobil: +49-162-103-4871
eMail: U.Pietrzyk at fz-juelich.de
http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html
&
Bergische Universität Wuppertal
Fakultät für Mathematik und Naturwissenschaften
Büro:  D.08.01
Gaußstr. 20
42097 Wuppertal
Tel: +49-(0)202-439-3523
Fax: +49-(0)202-439-2811
eMail: Uwe.Pietrzyk at uni-wuppertal.de
http://www.medizinphysik.uni-wuppertal.de
----------------------------------------------------------------------/

On 21 Jan 2017, at 14:13, Amir Ghabrial <eng_amir_shawky at hotmail.com> wrote:

> 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
> 
> From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org> on behalf of gate-users-request at lists.opengatecollaboration.org <gate-users-request at lists.opengatecollaboration.org>
> Sent: Saturday, 21 January 2017 3:13 AM
> To: gate-users at lists.opengatecollaboration.org
> Subject: Gate-users Digest, Vol 128, Issue 18
>  
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>    1. Re: Gate (Pietrzyk, Uwe)
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> 
> ----------------------------------------------------------------------
> 
> 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
> 52425 Jülich
> Tel: +49-2461-61 4763
> Fax: +49-2461-61 2820
> Mobil: +49-162-103-4871
> eMail: U.Pietrzyk at fz-juelich.de
> http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html
> Forschungszentrum Jülich - Physik der Medizinischen ...
> www.fz-juelich.de
> Die Forschungs- und Entwicklungsarbeiten des Institutsbereichs Physik der Medizinischen Bildgebung (INM-4) des Instituts für Neurowissenschaften konzentrieren sich ...
> 
> 
> &
> Bergische Universität Wuppertal
> Fakultät für Mathematik und Naturwissenschaften
> Büro:  D.08.01
> Gaußstr. 20
> 42097 Wuppertal
> Tel: +49-(0)202-439-3523
> Fax: +49-(0)202-439-2811
> eMail: Uwe.Pietrzyk at uni-wuppertal.de
> http://www.medizinphysik.uni-wuppertal.de
> Startseite Medizinphysik - Medizinphysik - BERGISCHE ...
> www.medizinphysik.uni-wuppertal.de
> Medizinische Physik. Die Arbeitsgruppe beschäftigt sich mit der Analyse medizinischer und biomedizinischer Bilder verschiedener Modalität wie Positronen-Emissions ...
> 
> 
> ----------------------------------------------------------------------/
> 
> 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 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > #=====================================================
> > # 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
> > _______________________________________________
> > Gate-users mailing list
> > Gate-users at lists.opengatecollaboration.org
> > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> Gate-users Info Page
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> To see the collection of prior postings to the list, visit the Gate-users Archives. (The current archive is only available to the list ...
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