[Gate-users] problem of voxellized source

Yanfei Mao yanfei_mao017 at yahoo.com
Thu Aug 11 00:25:59 CEST 2011


Hi all,

I use GATE v5 for SPECT simulation. I use voxellized  phantom and source. The projection I get always has a black area in the centre. However, when I didn't put phantom, source and detector in the centre of the coordinate, the black area disappears. It doesn't have black area when I use analytical phantom and source. Is it a bug?

Thank you!
Yanfei Mao

------------------------------------------------------

my code:

/vis/open OGLSX
/vis/viewer/reset
/vis/drawView 45 45
/vis/viewer/zoom 2
/vis/viewer/set/style surface
/vis/drawVolume
/tracking/storeTrajectory 1
/vis/scene/endOfEventAction accumulate
/vis/viewer/update
/gate/geometry/enableAutoUpdate

#     W O R L D
/gate/world/geometry/setXLength 100 cm
/gate/world/geometry/setYLength 100 cm
/gate/world/geometry/setZLength 100 cm

# Scanner Head
/gate/world/daughters/insert 3axes
/gate/world/daughters/name SPECThead
/gate/world/daughters/insert box
/gate/SPECThead/geometry/setXLength  7. cm
/gate/SPECThead/geometry/setYLength 21. cm
/gate/SPECThead/geometry/setZLength 21. cm
/gate/SPECThead/placement/setTranslation  20.0 10. 0. cm
/gate/SPECThead/setMaterial Air
/gate/SPECThead/vis/forceWireframe
/gate/SPECThead/repeaters/insert ring
/gate/SPECThead/ring/setRepeatNumber 1 

# Shielding
/gate/SPECThead/daughters/name shielding
/gate/SPECThead/daughters/insert box
/gate/shielding/geometry/setXLength  7. cm
/gate/shielding/geometry/setYLength 21. cm
/gate/shielding/geometry/setZLength 21. cm
/gate/shielding/placement/setTranslation  0. 0. 0. cm
/gate/shielding/setMaterial Lead
/gate/shielding/vis/setColor red
/gate/shielding/vis/forceWireframe

# Collimator
/gate/SPECThead/daughters/name collimator
/gate/SPECThead/daughters/insert box
/gate/collimator/geometry/setXLength 3. cm
/gate/collimator/geometry/setYLength 19. cm
/gate/collimator/geometry/setZLength 19. cm
/gate/collimator/placement/setTranslation  -2. 0. 0. cm
/gate/collimator/setMaterial Lead
/gate/collimator/vis/setColor red
/gate/collimator/vis/forceWireframe

# Insert the first hole of air in the collimator
/gate/collimator/daughters/name hole
/gate/collimator/daughters/insert hexagone
/gate/hole/geometry/setHeight 3. cm
/gate/hole/geometry/setRadius .75 mm
/gate/hole/placement/setRotationAxis 0 1 0
/gate/hole/placement/setRotationAngle 90 deg
/gate/hole/setMaterial Air
# Repeat the hole in an array
/gate/hole/repeaters/insert cubicArray
/gate/hole/cubicArray/setRepeatNumberX 1
/gate/hole/cubicArray/setRepeatNumberY 104 
/gate/hole/cubicArray/setRepeatNumberZ 60 
/gate/hole/cubicArray/setRepeatVector 0. 1.80  3.12 mm
# Repeat these holes in a linear
/gate/hole/repeaters/insert linear
/gate/hole/linear/setRepeatNumber 2
/gate/hole/linear/setRepeatVector 0. 0.90 1.56 mm

# Crystal
/gate/SPECThead/daughters/name crystal
/gate/SPECThead/daughters/insert box
/gate/crystal/geometry/setXLength 1. cm
/gate/crystal/geometry/setYLength  19. cm
/gate/crystal/geometry/setZLength  19. cm
/gate/crystal/placement/setTranslation  0. 0. 0. cm
/gate/crystal/setMaterial NaI
/gate/crystal/vis/setColor yellow

# Back-compartment
/gate/SPECThead/daughters/name compartment
/gate/SPECThead/daughters/insert box
/gate/compartment/geometry/setXLength 2.5 cm
/gate/compartment/geometry/setYLength 19. cm
/gate/compartment/geometry/setZLength 19. cm
/gate/compartment/placement/setTranslation   1.75 0. 0. cm
/gate/compartment/setMaterial Glass
/gate/compartment/vis/setColor grey

# PHANTOM
/gate/world/daughters/name hof_brain 
/gate/world/daughters/insert regularMatrix
/gate/hof_brain/geometry/insertReader interfile
/gate/hof_brain/interfileReader/insertTranslator range
/gate/hof_brain/interfileReader/rangeTranslator/readTable rang_atn.dat
/gate/hof_brain/interfileReader/rangeTranslator/describe 1
/gate/hof_brain/interfileReader/readFile test_pha.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
/gate/hof_brain/addOutput doseOutput
/gate/output/doseOutput/saveUncertainty true
/gate/output/doseOutput/setFileName hof_brain_paraDose.bin

#    M O V E M E N T S   O F   T H E   H E A D
/gate/SPECThead/moves/insert orbiting
/gate/SPECThead/orbiting/setSpeed 0.15 deg/s
/gate/SPECThead/orbiting/setPoint1 0 0 0 cm
/gate/SPECThead/orbiting/setPoint2 0 0 1 cm

# S H O W   H O W   T H E   G E O M E T R Y   M O V E   W I T H   T I M E
/gate/timing/setTime 0. s 

# Crystal SD
/gate/crystal/attachCrystalSD

# Phantom SD
/gate/SPECThead/attachPhantomSD
/gate/shielding/attachPhantomSD
/gate/collimator/attachPhantomSD
/gate/hole/attachPhantomSD
/gate/compartment/attachPhantomSD
/gate/hof_brain/attachPhantomSD

#       EM  P R O C E S S
/gate/physics/gamma/selectRayleigh lowenergy
/gate/physics/gamma/selectPhotoelectric standard
/gate/physics/gamma/selectCompton standard

#    I N A C T I V E    S E C O N D A R Y   E L E C T R O N S 
/gate/physics/setElectronCut 1. m

#    I N A C T I V E    X - R A Y S
/gate/physics/setXRayCut 1. GeV
/gate/physics/setDeltaRayCut 1. GeV

/gate/geometry/enableAutoUpdate
/run/initialize

#    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 0.15
/gate/digitizer/Singles/blurring/setEnergyOfReference 140. keV

#       E N E R G Y   C U T
/gate/digitizer/Singles/insert thresholder
/gate/digitizer/Singles/thresholder/setThreshold 126. keV
/gate/digitizer/Singles/insert upholder
/gate/digitizer/Singles/upholder/setUphold 154. keV

#  R A N D O M
/gate/random/setEngineName JamesRandom
/gate/random/setEngineSeed default
/gate/random/verbose 1

#       S E T U P  - R O O T  F I L E
/gate/output/root/setRootSinglesAdderFlag 0 
/gate/output/root/setRootSinglesBlurringFlag 0 
/gate/output/root/setRootSinglesThresholderFlag 0
/gate/output/root/setRootSinglesUpholderFlag 0

#       S E T U P  - A S C I I  F I L E
/gate/output/ascii/setOutFileSinglesAdderFlag 0
/gate/output/ascii/setOutFileSinglesBlurringFlag 0
/gate/output/ascii/setOutFileSinglesThresholderFlag 0
/gate/output/ascii/setOutFileSinglesUpholderFlag 0
/gate/output/ascii/setOutFileSinglesFlag 0
/gate/output/ascii/setOutFileHitsFlag 0

#       I N T E R F I L E   P R O J E C T I O N
/gate/output/projection/pixelSizeX 1. cm
/gate/output/projection/pixelSizeY 1. cm
/gate/output/projection/pixelNumberX 19 
/gate/output/projection/pixelNumberY 19
/gate/output/projection/projectionPlane YZ

/control/verbose 0
/grdm/verbose 0
/run/verbose 0
/event/verbose 0
/tracking/verbose 0
/gate/application/verbose 0
/gate/generator/verbose 0
/gate/stacking/verbose 0
/gate/event/verbose 0
/gate/source/verbose 0

#          G A M M A
/gate/source/addSource voxel_brain voxel
/gate/source/voxel_brain/reader/insert interfile
/gate/source/voxel_brain/interfileReader/translator/insert range
/gate/source/voxel_brain/interfileReader/rangeTranslator/readTable rang.dat
/gate/source/voxel_brain/interfileReader/rangeTranslator/describe 1
/gate/source/voxel_brain/interfileReader/readFile test_pha.h33 
/gate/source/voxel_brain/gps/particle gamma
/gate/source/voxel_brain/setForcedUnstableFlag true
/gate/source/voxel_brain/setForcedHalfLife 21600. s
/gate/source/voxel_brain/gps/energytype Mono
/gate/source/voxel_brain/gps/monoenergy 0.140 MeV
/gate/source/voxel_brain/setPosition   -95. -95. -95. mm
/gate/source/voxel_brain/gps/confine NULL
/gate/source/voxel_brain/gps/angtype iso
/gate/source/voxel_brain/gps/mintheta 90. deg
/gate/source/voxel_brain/gps/maxtheta 90. deg
/gate/source/voxel_brain/gps/minphi    180. deg
/gate/source/voxel_brain/gps/maxphi  180. deg
/gate/source/voxel_brain/dump 1
/gate/source/list

#       E X P E R I M E N T
/gate/application/setTimeSlice      37.5  s
/gate/application/setTimeStart      0.    s
/gate/application/setTimeStop       37.5  s
/gate/application/startDAQ

----------------------------------------------------------------------------
test_pha.i33:

!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 := test_p.i33
patient name := hf
!patient ID := 271097
patient dob := 0000:00:00
patient sex := Unknown
!study ID := brain
exam type := Spect study
data compression := none
data encode := none
;
!GENERAL IMAGE DATA :=
!type of data := Tomographic
!total number of images := 19
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 := 19
!process status := Reconstructed
!matrix size [1] := 19
!matrix size [2] := 19
!number format := unsigned integer
!number of bytes per pixel := 2
scaling factor (mm/pixel) [1] := +1.000000e+01
scaling factor (mm/pixel) [2] := +1.000000e+01
!number of projections := 19
!extent of rotation := 
!time per projection (sec) := 0
study duration (sec) := 0
!maximum pixel count := +2.000000e+07
patient orientation := head_in
patient rotation := supine
;
!SPECT STUDY (reconstructed data) :=
method of reconstruction := Unknown
!number of slices := 19
number of reference frame := 0
slice orientation := Transverse
slice thickness (pixels) := +1.000000e+01
centre-centre slice separation (pixels) := +1.000000e+01
filter name := Unknown
filter parameters := Cutoff
method of attenuation correction := measured
scatter corrected := N
oblique reconstruction := N
!END OF INTERFILE :=
--------------------------------------------------------

rang.dat:

2
0        0      0
50       50     30

---------------------------------------------------------
rang_atn.dat
 2
 0          0          Air             false  0.0 0.0 0.0 1.0  
 50         50         Heart           true   0.0 1.0 0.0 1.0     
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