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

[John Apostolakis]

I consulted with my colleagues in Geant4 geometry, and we have a suggestion:

To eliminate the possibility that the use of the advanced feature of 
RegularNavigation is the cause for the differences which you observe, 
you can try to run setting its option SkipEqualMaterials to 0.  This 
will check whether the skipping of volume boundaries is relevant to the 
differences.

Best regards,
John Apostolakis

> -------- Original Message --------
> Subject:        [Gate-users] simulating a voxelized phantom using GATE 4.0
> with the speed up options
> Date:   Wed, 10 Dec 2008 18:20:29 -0500
> From:   <kangh at mskcc.org>
> To:     <gate-users at lists.healthgrid.org>
>
>
>
> 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
>
> *T**he new macro for a voxelized phantom is*
>
> /gate/world/daughters/name lung_phantom
>
> #
>
> *#  this is the new line for** regular parameterization** and**
> fictitious interaction*
>
> *#*
>
> */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/readTable range_CT.dat
>
> /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/attachVoxelPhantomSD
>
> /gate/lung_phantom/addOutput doseOutput
>
> /gate/output/doseOutput/saveUncertainty true
>
> /gate/output/doseOutput/setFileName lung_phantom_paraDose.bin
>
>
> Microsoft Office PowerPoint Slide
>
>
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