[Gate-users] Reconstructed Hoffman brain phantom-noisy and less counts
Siti Salasiah MusNMey
ctsalasiah1950 at gmail.com
Tue Feb 5 07:55:17 CET 2013
Hi,
I experimented with voxelised Hoffman brain phantom as shown in the Gate
examples and plug in the voxelized source and phantom in
PET_Ecat_System.mac. I implemented the simulation for 3600 s as in order to
produce many counts in the image. My macro file as as below and the
reconstructed image using STIR (3D sinogram) is shown in AMIDE as below:
However it seems that the image is noisy and has insufficient counts. How
can I improve this?
To be truth, I am not very sure about the setting of
/gate/application/setTimeSlice 3600 s
/gate/application/setTimeStart 0 s
/gate/application/setTimeStop 3600 s
does it mean with longer simulation the more counts we have in GATE?
Thank you in advance for any advices.
Siti
Malaysia
#=====================================================
# VISUALISATION
#=====================================================
#/vis/disable
#/vis/open OGLSX
#/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 400. cm
/gate/world/geometry/setYLength 400. cm
/gate/world/geometry/setZLength 400. 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---------------------#
# E C A T
/gate/world/daughters/name ecat
/gate/world/daughters/insert cylinder
/gate/ecat/setMaterial Air
/gate/ecat/geometry/setRmax 44.2 cm
/gate/ecat/geometry/setRmin 41.2 cm
/gate/ecat/geometry/setHeight 15.52 cm
#ate/ecat/setTranslation 0.0 0.0 0.0 0.0 cm
/gate/ecat/vis/forceWireframe
# B L O C K
/gate/ecat/daughters/name block
/gate/ecat/daughters/insert box
/gate/block/placement/setTranslation 427.0 0.0 0.0 mm
/gate/block/geometry/setXLength 30.0 mm
/gate/block/geometry/setYLength 35.8594 mm
/gate/block/geometry/setZLength 38.7 mm
/gate/block/setMaterial Air
/gate/block/vis/forceWireframe
# C R Y S T A L
/gate/block/daughters/name crystal
/gate/block/daughters/insert box
#ate/ecat/setTranslation 0.0 0.0 0.0 0.0 cm
/gate/crystal/geometry/setXLength 30.0 mm
/gate/crystal/geometry/setYLength 4.4 mm
/gate/crystal/geometry/setZLength 4.75 mm
/gate/crystal/setMaterial BGO
/gate/crystal/vis/setColor yellow
# R E P E A T C R Y S T A L
/gate/crystal/repeaters/insert cubicArray
/gate/crystal/cubicArray/setRepeatNumberX 1
/gate/crystal/cubicArray/setRepeatNumberY 8
/gate/crystal/cubicArray/setRepeatNumberZ 8
/gate/crystal/cubicArray/setRepeatVector 0. 4.4942 4.85 mm
# R E P E A T BLOCK
/gate/block/repeaters/insert linear
/gate/block/linear/setRepeatNumber 4
/gate/block/linear/setRepeatVector 0. 0. 38.8 mm
/gate/block/repeaters/insert ring
/gate/block/ring/setRepeatNumber 72
# T U N G S T E N S H I E L D
/gate/world/daughters/name carter
/gate/world/daughters/insert cylinder
/gate/carter/setMaterial Air
/gate/carter/geometry/setRmax 44. cm
/gate/carter/geometry/setRmin 28. cm
/gate/carter/geometry/setHeight 9. cm
/gate/carter/placement/setTranslation 0.0 0.0 12.5 cm
/gate/carter/vis/forceWireframe
/gate/carter/daughters/name carter1
/gate/carter/daughters/insert cylinder
/gate/carter1/setMaterial Tungsten
/gate/carter1/geometry/setRmax 30.0 cm
/gate/carter1/geometry/setRmin 29.0 cm
/gate/carter1/geometry/setHeight 3.0 cm
/gate/carter1/vis/setColor grey
/gate/carter1/placement/setTranslation 0.0 0.0 -3 cm
/gate/carter/daughters/name carter2
/gate/carter/daughters/insert cylinder
/gate/carter2/setMaterial Tungsten
/gate/carter2/geometry/setRmax 40.7 cm
/gate/carter2/geometry/setRmin 30.0 cm
/gate/carter2/geometry/setHeight 1.0 cm
/gate/carter2/vis/setColor grey
/gate/carter2/placement/setTranslation 0.0 0.0 -2 cm
/gate/carter/daughters/name carter3
/gate/carter/daughters/insert cylinder
/gate/carter3/setMaterial Tungsten
/gate/carter3/geometry/setRmax 40.7 cm
/gate/carter3/geometry/setRmin 39.7 cm
/gate/carter3/geometry/setHeight 3.0 cm
/gate/carter3/vis/setColor grey
/gate/carter3/placement/setTranslation 0.0 0.0 0 cm
/gate/carter/daughters/name carter4
/gate/carter/daughters/insert cylinder
/gate/carter4/setMaterial Tungsten
/gate/carter4/geometry/setRmax 43.7 cm
/gate/carter4/geometry/setRmin 40.7 cm
/gate/carter4/geometry/setHeight 1.0 cm
/gate/carter4/vis/setColor grey
/gate/carter4/placement/setTranslation 0.0 0.0 1 cm
# A T T A C H S Y S T E M
/gate/systems/ecat/block/attach block
/gate/systems/ecat/crystal/attach crystal
# A T T A C H C R Y S T A L SD
/gate/crystal/attachCrystalSD
#-------------------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 H A N T O M #
# #
#-------------------oooooOOOOO00000OOOOOooooo---------------------#
#=====================================================
# VOXEL PHANTOM
#=====================================================
/control/execute VoxelizedPhantom.mac
#=====================================================
# PHYSICS
#=====================================================
/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 PenelopeModel
/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 MultipleScattering e+
/gate/physics/addProcess MultipleScattering e-
/gate/physics/processList Enabled
/gate/physics/processList Initialized
#=====================================================
# CUTS
#=====================================================
/gate/physics/Gamma/SetCutInRegion crystal 1.0 cm
/gate/physics/Electron/SetCutInRegion crystal 1.0 cm
/gate/physics/Positron/SetCutInRegion crystal 1.0 cm
/gate/physics/Gamma/SetCutInRegion hof_brain 0.1 mm
/gate/physics/Electron/SetCutInRegion hof_brain 0.1 mm
/gate/physics/Positron/SetCutInRegion hof_brain 0.1 mm
/gate/physics/SetMaxStepSizeInRegion hof_brain 0.01 mm
#=====================================================
# INITIALISATION
#=====================================================
/gate/run/initialize
#-------------------oooooOOOOO00000OOOOOooooo---------------------#
# #
# D E F I N I T I O N O F Y O U R A C Q U I S I T I O N #
# D I G I T I Z E R & C O I N C I D E N C E S H O R T E R #
# #
#-------------------oooooOOOOO00000OOOOOooooo---------------------#
# A D D E R
/gate/digitizer/Singles/insert adder
# R E A D O U T
/gate/digitizer/Singles/insert readout
/gate/digitizer/Singles/readout/setDepth 1
# E N E R G Y B L U R R I N G
/gate/digitizer/Singles/insert blurring
/gate/digitizer/Singles/blurring/setResolution 0.26
/gate/digitizer/Singles/blurring/setEnergyOfReference 511. keV
# E N E R G Y C U T
/gate/digitizer/Singles/insert thresholder
/gate/digitizer/Singles/thresholder/setThreshold 250. keV
/gate/digitizer/Singles/insert upholder
/gate/digitizer/Singles/upholder/setUphold 750. keV
# D E A D T I M E
/gate/digitizer/Singles/insert deadtime
/gate/digitizer/Singles/deadtime/setDeadTime 3000000. ps
/gate/digitizer/Singles/deadtime/setMode paralysable
/gate/digitizer/Singles/deadtime/chooseDTVolume block
# C O I N C I S O R T E R
/gate/digitizer/Coincidences/setWindow 10. ns
/gate/digitizer/Coincidences/setOffset 0. ns
/gate/digitizer/Coincidences/describe
/gate/digitizer/name delay
/gate/digitizer/insert coincidenceSorter
/gate/digitizer/delay/setWindow 10. ns
/gate/digitizer/delay/setOffset 500. ns
/gate/digitizer/delay/describe
/gate/digitizer/name finalCoinc
/gate/digitizer/insert coincidenceChain
/gate/digitizer/finalCoinc/addInputName delay
/gate/digitizer/finalCoinc/addInputName Coincidences
/gate/digitizer/finalCoinc/usePriority true
/gate/digitizer/finalCoinc/describe
#-------------------oooooOOOOO00000OOOOOooooo---------------------#
# #
# D E F I N I T I O N O F #
# Y O U R O U T P U T F I L E #
# #
#-------------------oooooOOOOO00000OOOOOooooo---------------------#
# R A N D O M
# 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
# S E T U P - R O O T F I L E
/gate/output/root/disable
#/gate/output/root/setFileName YourPETSimu
#/gate/output/root/setRootSinglesAdderFlag 1
#/gate/output/root/setRootSinglesReadoutFlag 1
#/gate/output/root/setRootHitFlag 1
#/gate/output/root/setRootSinglesFlag 1
#/gate/output/root/setRootCoincidencesFlag 1
###################################################
# E C A T 7 O U T P U T
#
# W I T H N E W F U N C T I O N A L I T I E S
# *-*-* according to the coincidence sorter *-*-*
#
# 01 J U N E 2 0 0 6
###################################################
/gate/output/sinogram/enable
/gate/output/sinogram/setTangCrystalBlurring 1.8 mm
/gate/output/sinogram/setAxialCrystalBlurring 1.8 mm
/gate/output/sinogram/verbose 2
/gate/output/sinogram/RawOutputEnable
/gate/output/sinogram/setFileName PhantomSinogram
/gate/output/sinogram/StoreDelayeds
/gate/output/sinogram/StoreScatters
/gate/output/sinogram/setInputDataName finalCoinc
/gate/output/sinogram/describe
/gate/output/ecat7/enable
/gate/output/ecat7/verbose 2
/gate/output/ecat7/setFileName PhantomSinogramEcat
/gate/output/ecat7/describe
/gate/output/ecat7/mashing 2
/gate/output/ecat7/span 9
/gate/output/ecat7/maxringdiff 22
/gate/output/ecat7/system 962
/gate/output/ecat7/IsotopeCode F-18
/gate/output/ecat7/IsotopeHalflife 6586.2 second
/gate/output/ecat7/IsotopeBranchingFraction 1.0
#-------------------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---------------------#
/control/execute Verbose.mac
#-------------------oooooOOOOO00000OOOOOooooo---------------------#
# #
# D E F I N I T I O N O F #
# Y O U R S O U R C E S
# VOXELIZED SOURCE #
# #
#-------------------oooooOOOOO00000OOOOOooooo---------------------#
/control/execute VoxelizedSource.mac
#/gate/source/list
#-------------------oooooOOOOO00000OOOOOooooo---------------------#
# #
# S T A R T A C Q U I S I T I O N #
# T I M E P A R A M E T E R S #
# #
#-------------------oooooOOOOO00000OOOOOooooo---------------------#
#
# EXPERIMENT
#
/gate/application/setTimeSlice 3600 s
/gate/application/setTimeStart 0 s
/gate/application/setTimeStop 3600 s
#
# LET'S RUN THE SIMULATION!
#
/gate/application/startDAQ
[image: Inline image 1]
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