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<TITLE>simulating a voxelized phantom using GATE 4.0 with the speed up options</TITLE>
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<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">Hi Gate users,</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">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)</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri"> 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?</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri"> </FONT></SPAN><SPAN LANG="en-us"> </SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B></B></SPAN><SPAN LANG="en-us"><B><FONT FACE="Calibri">Old Physics</FONT></B></SPAN><SPAN LANG="en-us"><B></B></SPAN><SPAN LANG="en-us"><B><FONT FACE="Calibri"> macro</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B><FONT COLOR="#FF0000" FACE="Calibri"># EM P R O C E S S</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B><FONT COLOR="#FF0000" FACE="Calibri">/gate/physics/gamma/selectRayleigh lowenergy</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B><FONT COLOR="#FF0000" FACE="Calibri">/gate/physics/gamma/selectPhotoelectric lowenergy</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B><FONT COLOR="#FF0000" FACE="Calibri">/gate/physics/gamma/selectCompton lowenergy</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri"># 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 </FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">/gate/physics/setElectronCut 2. mm</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri"># I N A C T I V E X - R A Y S</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">/gate/physics/setXRayCut 10. keV</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">/gate/physics/setDeltaRayCut 10. keV</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B></B></SPAN><SPAN LANG="en-us"><B><FONT FACE="Calibri">New Physics macro</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B><FONT COLOR="#FF0000" FACE="Calibri"># EM P R O C E S S</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B><FONT COLOR="#FF0000" FACE="Calibri">/gate/physics/gamma/selectFictitious volumeTrace</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B><FONT COLOR="#FF0000" FACE="Calibri">/gate/physics/gamma/selectGammaConversion inactive</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B><FONT COLOR="#FF0000" FACE="Calibri">/gate/physics/gamma/selectRayleigh inactive</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B><FONT COLOR="#FF0000" FACE="Calibri">/gate/physics/gamma/selectPhotoelectric standard</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B><FONT COLOR="#FF0000" FACE="Calibri">/gate/physics/gamma/selectCompton standard</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri"># 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 </FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">/gate/physics/setElectronCut 2. mm</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri"># I N A C T I V E X - R A Y S</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">/gate/physics/setXRayCut 10. keV</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">/gate/physics/setDeltaRayCut 10. keV</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B></B></SPAN><SPAN LANG="en-us"><B><FONT FACE="Calibri">T</FONT></B></SPAN><SPAN LANG="en-us"><B></B></SPAN><SPAN LANG="en-us"><B><FONT FACE="Calibri">he new macro for a voxelized phantom is</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">/gate/world/daughters/name lung_phantom</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">#</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B><FONT COLOR="#FF0000" FACE="Calibri"># this is the new line for</FONT></B></SPAN><SPAN LANG="en-us"><B> <FONT COLOR="#0000FF" FACE="Calibri">regular parameterization</FONT></B></SPAN><SPAN LANG="en-us"><B><FONT COLOR="#FF0000" FACE="Calibri"> and</FONT></B></SPAN><SPAN LANG="en-us"><B> <FONT COLOR="#0000FF" FACE="Calibri">fictitious interaction</FONT></B></SPAN><SPAN LANG="en-us"><B></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B><FONT COLOR="#FF0000" FACE="Calibri">#</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B><FONT COLOR="#FF0000" FACE="Calibri">/gate/world/daughters/insert fictitiousVoxelMap</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B><FONT COLOR="#FF0000" FACE="Calibri">/gate/lung_phantom/setFictitiousEnergy 10 keV</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B><FONT COLOR="#FF0000" FACE="Calibri">/gate/lung_phantom/setElectronCut 50 cm</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B><FONT COLOR="#0000FF" FACE="Calibri">/gate/world/daughters/insert regularMatrix : regular navigation</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B><FONT COLOR="#FF0000" FACE="Calibri">#####------------------------------------------------------------------------</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B><FONT COLOR="#FF0000" FACE="Calibri">## The simulation time can be further reduced by discarding </FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B><FONT COLOR="#FF0000" FACE="Calibri">## lower energy photons within the phantom. Photons with an energy below the</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B><FONT COLOR="#FF0000" FACE="Calibri">## discard energy limit are not simulated</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><B><FONT COLOR="#FF0000" FACE="Calibri">#/gate/lung_phantom/setGammaDiscardEnergy 50 keV</FONT></B></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">#</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">/gate/lung_phantom/geometry/insertReader interfile</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">/gate/lung_phantom/interfileReader/insertTranslator range</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">/gate/lung_phantom/interfileReader/rangeTranslator/readTable range_CT.dat</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">/gate/lung_phantom/interfileReader/rangeTranslator/describe 1</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">#</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri"># list the organs which should not compressed</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">#</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">/gate/lung_phantom/interfileReader/readFile newptmodpixelCT.h33</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">/gate/lung_phantom/placement/setTranslation 0. 0. 0. mm</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">/gate/lung_phantom/placement/setRotationAxis 1 0 0</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">/gate/lung_phantom/placement/setRotationAngle 0 deg</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">/gate/lung_phantom/attachVoxelPhantomSD</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">/gate/lung_phantom/addOutput doseOutput</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">/gate/output/doseOutput/saveUncertainty true</FONT></SPAN></P>
<P DIR=LTR><SPAN LANG="en-us"><FONT FACE="Calibri">/gate/output/doseOutput/setFileName lung_phantom_paraDose.bin</FONT></SPAN></P>
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