<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> <html> <head> <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type"> </head> <body bgcolor="#ffffff" text="#000000"> 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 <blockquote cite="mid:50C74E87FB16FB4F9356E175CA15423E03204573@STR.ciemat.es" type="cite"> -------- 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:   <a class="moz-txt-link-rfc2396E" href="mailto:kangh@mskcc.org"><kangh@mskcc.org></a> To:     <a class="moz-txt-link-rfc2396E" href="mailto:gate-users@lists.healthgrid.org"><gate-users@lists.healthgrid.org></a> 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      =====================================================================           Please note that this e-mail and any files transmitted with it may be      privileged, confidential, and protected from disclosure under      applicable law. If the reader of this message is not the intended      recipient, or an employee or agent responsible for delivering this      message to the intended recipient, you are hereby notified that any      reading, dissemination, distribution, copying, or other use of this      communication or any of its attachments is strictly prohibited.  If      you have received this communication in error, please notify the      sender immediately by replying to this message and deleting this      message, any attachments, and all copies and backups from your      computer. <hr size="4" width="90%"> <center><img src="cid:part1.08010302.06040409@cern.ch"></center> </blockquote> </body> </html>