[Gate-users] simulating a voxelized phantom using GATE 4.0 with the speed up options

kangh at mskcc.org kangh at mskcc.org
Thu Dec 11 00:20:29 CET 2008

Hi Gate users,

I have run simulations with both GATE 3.2 and 4.0.  To expedite
simulation,  I  used the newly implemented "regular navigator" and
"fictitious interaction tracking algorithm" for voxelized phantoms (Gate
manual  p104 ~ 106).  I had to modify both phantom and physics macros
for GATE 4.0 to work with these two options.  Since "fictitious
interaction tracking algorithm" can be used only together with standard
processes (Compton, photoelectric) as well as lowenergy Compton and
Rayleigh and the other gamma processes (i.e. GammaConversion) should be
set inactive, I had to change physics processes.   I also modify the
voxelized phantom macro to activate the options for speed up (I copied
the macro in this email)
 The differences are in # EM process in the old and new physics macros.
I noticed that the simulation time with GATE4.0 with the two options is
much faster.  However, when I compared some parameters of output root
files, I found that there are big differences.  I have added the plots
of sinogramS and sinogramTheta which show the most distinct differences
between the two versions.  I am wondering whether anyone already saw or
expected the differences from changing physics process or putting energy
cut on discarding low energy photons within the phantom (50KeV for our
case).   Did anyone have the same problem?
Old Physics  macro
#       EM  P R O C E S S
/gate/physics/gamma/selectRayleigh lowenergy
/gate/physics/gamma/selectPhotoelectric lowenergy
/gate/physics/gamma/selectCompton lowenergy
#       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 2. mm
#       I N A C T I V E    X - R A Y S
/gate/physics/setXRayCut 10. keV
/gate/physics/setDeltaRayCut 10. keV

New Physics macro
#       EM  P R O C E S S
/gate/physics/gamma/selectFictitious volumeTrace
/gate/physics/gamma/selectGammaConversion inactive
/gate/physics/gamma/selectRayleigh inactive
/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 2. mm
#       I N A C T I V E    X - R A Y S
/gate/physics/setXRayCut 10. keV
/gate/physics/setDeltaRayCut 10. keV

The new macro for a voxelized phantom is
/gate/world/daughters/name lung_phantom
#  this is the new line for regular parameterization and fictitious
/gate/world/daughters/insert fictitiousVoxelMap
/gate/lung_phantom/setFictitiousEnergy 10 keV
/gate/lung_phantom/setElectronCut 50 cm
/gate/world/daughters/insert regularMatrix     : regular navigation
##   The simulation time can be further reduced by discarding 
##   lower energy photons within the phantom. Photons with an energy
below the
##   discard energy limit are not simulated
#/gate/lung_phantom/setGammaDiscardEnergy 50 keV
/gate/lung_phantom/geometry/insertReader interfile
/gate/lung_phantom/interfileReader/insertTranslator range
/gate/lung_phantom/interfileReader/rangeTranslator/describe 1
# list the organs which should not compressed
/gate/lung_phantom/interfileReader/readFile newptmodpixelCT.h33
/gate/lung_phantom/placement/setTranslation  0. 0. 0. mm
/gate/lung_phantom/placement/setRotationAxis 1 0 0
/gate/lung_phantom/placement/setRotationAngle 0 deg
/gate/lung_phantom/addOutput doseOutput
/gate/output/doseOutput/saveUncertainty true
/gate/output/doseOutput/setFileName lung_phantom_paraDose.bin

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