[Gate-users] Ecat7 help - empty sinogram output
Siti Salasiah MusNMey
ctsalasiah1950 at gmail.com
Mon Feb 25 03:19:23 CET 2013
Hi,
I am curious about an empty sinogram after simulationg voxelized phantom
NCAT using ecat7 scanner. I have been waiting for 1 week but the result is
a total disappointment.
I am using NCAT voxelized phantom defined as this. I even set the source
activity using this: (In Mbq), try with bigger numbers so that total counts
would be significant but unfortunately the SINOGRAM is EMPTY (min value=0,
max value=0). First I started with 5s simulation, its empty then 1800s ALSO
empty.
Is there any advice on this?
Thank you.
Siti
*Activity_Range_NCAT.dat*
5
0 0 0
2 2 20000000
4 4 40000000
60 60 100000000
75 75 250000000
*ncat_header_act.h33*
!INTERFILE :=
!imaging modality := nucmed
!originating system := greetings
!version of keys := 3.3
date of keys := 1996:09:24
conversion program := (X)MedCon
program author := Erik Nolf
program version := 0.7.4
program date := 2002:02:18
;
!GENERAL DATA :=
!data offset in bytes := 0
!name of data file := Section1_act.i33
patient name := hf
!patient ID := 271097
patient dob := 0000:00:00
patient sex := Unknown
!study ID := brain
exam type := pet study
data compression := none
data encode := none
;
!GENERAL IMAGE DATA :=
!type of data := Tomographic
!total number of images := 16
study date := 1997:11:28
study time := 00:00:00
imagedata byte order := LITTLEENDIAN
;
number of energy windows := 1
;
energy window [1] :=
energy window lower level [1] :=
energy window upper level [1] :=
flood corrected := N
decay corrected := N
;
!SPECT STUDY (general) :=
number of detector heads := 1
;
!number of images/energy window := 16
!process status := Reconstructed
!matrix size [1] := 64
!matrix size [2] := 64
!number format := unsigned integer
!number of bytes per pixel := 2
scaling factor (mm/pixel) [1] := +6.250000e+00
scaling factor (mm/pixel) [2] := +6.250000e+00
!number of projections := 16
!extent of rotation :=
!time per projection (sec) := 0
study duration (sec) := 0
!maximum pixel count := +2.000000e+02
patient orientation := head_in
patient rotation := supine
;
!SPECT STUDY (reconstructed data) :=
method of reconstruction := Unknown
!number of slices := 16
number of reference frame := 0
slice orientation := Transverse
slice thickness (pixels) := +6.250000e+00
centre-centre slice separation (pixels) := +6.250000e+00
filter name := Unknown
filter parameters := Cutoff
method of attenuation correction := measured
scatter corrected := N
oblique reconstruction := N
!END OF INTERFILE :=
*Range_atten_NCAT.dat*
5
0.0 0.0 Air false 0.0 0.0 0.0 0.2
0.1 650.0 Lung true 0.0 1.0 1.0 0.2
651.0 934.0 Body true 1.0 0.0 1.0 0.2
935.0 1132.0 SpineBone true 0.0 0.0 1.0 0.2
1133.0 1372.0 RibBone true 1.0 0.0 0.0 0.2
*ncat_header_atn.h33*
!INTERFILE :=
!imaging modality := nucmed
!originating system := greetings
!version of keys := 3.3
date of keys := 1996:09:24
conversion program := (X)MedCon
program author := Erik Nolf
program version := 0.7.4
program date := 2002:02:18
;
!GENERAL DATA :=
!data offset in bytes := 0
!name of data file := Section1_atn.i33
patient name := hf
!patient ID := 271097
patient dob := 0000:00:00
patient sex := Unknown
!study ID := brain
exam type := pet study
data compression := none
data encode := none
;
!GENERAL IMAGE DATA :=
!type of data := Tomographic
!total number of images := 16
study date := 1997:11:28
study time := 00:00:00
imagedata byte order := LITTLEENDIAN
;
number of energy windows := 1
;
energy window [1] :=
energy window lower level [1] :=
energy window upper level [1] :=
flood corrected := N
decay corrected := N
;
!SPECT STUDY (general) :=
number of detector heads := 1
;
!number of images/energy window := 16
!process status := Reconstructed
!matrix size [1] := 64
!matrix size [2] := 64
!number format := unsigned integer
!number of bytes per pixel := 2
scaling factor (mm/pixel) [1] := +6.250000e+00
scaling factor (mm/pixel) [2] := +6.250000e+00
!number of projections := 16
!extent of rotation :=
!time per projection (sec) := 0
study duration (sec) := 0
!maximum pixel count := +2.000000e+02
patient orientation := head_in
patient rotation := supine
;
!SPECT STUDY (reconstructed data) :=
method of reconstruction := Unknown
!number of slices := 16
number of reference frame := 0
slice orientation := Transverse
slice thickness (pixels) := +6.250000e+00
centre-centre slice separation (pixels) := +6.250000e+00
filter name := Unknown
filter parameters := Cutoff
method of attenuation correction := measured
scatter corrected := N
oblique reconstruction := N
!END OF INTERFILE :=
*NCATsource.mac*
#
#
# V O X E L S O U R C E B A S E D O N T H E H O F F M A N B R A
I N P H A N T O M
#Declaration of the fact that a voxelized source will be used
/gate/source/addSource voxel_NCAT voxel
#Declaration that voxelized source will be entered using interfile format
/gate/source/voxel_NCAT/reader/insert interfile
#Interfile file
/gate/source/voxel_NCAT/interfileReader/translator/insert range
/gate/source/voxel_NCAT/interfileReader/rangeTranslator/readTable
activity_range_NCAT.dat
/gate/source/voxel_NCAT/interfileReader/rangeTranslator/describe 1
/gate/source/voxel_NCAT/interfileReader/readFile ncat_header_act.h33
/gate/source/voxel_NCAT/setPosition -200.0 -200.0 -50.0 mm
/gate/source/voxel_NCAT/setType backtoback
/gate/source/voxel_NCAT/gps/particle gamma
/gate/source/voxel_NCAT/setForcedUnstableFlag true
/gate/source/voxel_NCAT/setForcedHalfLife 6586.2 s
/gate/source/voxel_NCAT/gps/energytype Mono
/gate/source/voxel_NCAT/gps/monoenergy 0.511 MeV
/gate/source/voxel_NCAT/gps/confine NULL
/gate/source/voxel_NCAT/gps/angtype iso
/gate/source/voxel_NCAT/dump 1
/gate/source/list
*NCATphantom.mac*
#Create a phantom
/gate/world/daughters/name hof_brain
/gate/world/daughters/insert regularMatrix
#Read the file
/gate/hof_brain/geometry/insertReader interfile
/gate/hof_brain/interfileReader/insertTranslator range
/gate/hof_brain/interfileReader/rangeTranslator/readTable
range_atten_NCAT.dat
/gate/hof_brain/interfileReader/rangeTranslator/describe 1
/gate/hof_brain/interfileReader/readFile ncat_header_atn.h33
/gate/hof_brain/placement/setTranslation 0. 0. 0. mm
#/gate/hof_brain/placement/setRotationAxis 1 0 0
#/gate/hof_brain/placement/setRotationAngle 0 deg
/gate/hof_brain/attachVoxelPhantomSD
*Ecat_mac file*
# #
# Y O U R C O M P L E T E G A T E S I M U L A T I O N #
# #
# #
###############################################################
#-------------------oooooOOOOO00000OOOOOooooo---------------------#
# #
# R U N T H E V I S U A L I S A T I O N A N D #
# C O N S T R U C T Y O U R E X P E R I M E N T A L A R E A #
# #
#-------------------oooooOOOOO00000OOOOOooooo---------------------#
#=====================================================
# 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 55.0 cm #44.2
/gate/ecat/geometry/setRmin 50.0 cm #41.2
/gate/ecat/geometry/setHeight 15.52 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
/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---------------------#
/control/execute NCATphantom.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
/geometry/test/recursive_test
#-------------------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
###################################################
# 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 false
/gate/output/sinogram/setFileName NCATSinogram
/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 NCATSinogramEcat
/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 #
# #
#-------------------oooooOOOOO00000OOOOOooooo---------------------#
/control/execute NCATsource.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 1800. s
/gate/application/setTimeStart 0. s
/gate/application/setTimeStop 1800. s
#
# LET'S RUN THE SIMULATION!
#
/gate/application/startDAQ
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