<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"> <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> <meta name="Generator" content="Microsoft Word 14 (filtered medium)"> <style></style> </head> <body lang="EN-US" link="blue" vlink="purple"> <div class="WordSection1"> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hello,<o:p></o:p></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Please always use the mailing-list so that everybody can benefit of the comments or provide new inputs.<o:p></o:p></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I am not familiar with PET simulations, I am more on the radiation therapy side, but if I understand correctly, you have 8 simulations with 8 dose maps, so yes you have to some them up to get the total dose to each organ.<o:p></o:p></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">At least I would do it like this…<o:p></o:p></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Does anyone has a better suggestion?<o:p></o:p></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p> <p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Best,<o:p></o:p></span></p> <p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Loïc</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p> <p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Arun Gupta [mailto:arunaiims1984@gmail.com] <br> <b>Sent:</b> Friday, July 01, 2016 11:14 AM<br> <b>To:</b> Grevillot Loic<br> <b>Subject:</b> Re: [Gate-users] Regarding Voxelized Dosimetry<o:p></o:p></span></p> <p class="MsoNormal"><o:p> </o:p></p> <div> <p class="MsoNormal">Dear Loic,<o:p></o:p></p> <div> <p class="MsoNormal"><o:p> </o:p></p> </div> <div> <p class="MsoNormal">Thank you very much for the reply.<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-bottom:12.0pt">Actually I have used the Dose Actor for dose output file which is as follow.<o:p></o:p></p> </div> <div> <p class="MsoNormal">#=============================================================================<br> # DOSE ACTOR<br> #=============================================================================<br> <br> /gate/actor/addActor DoseActor doseDistribution <br> /gate/actor/doseDistribution/attachTo mouse <br> /gate/actor/doseDistribution/saveEveryNEvents 1000000 <br> <br> /gate/actor/doseDistribution/stepHitType random <br> /gate/actor/doseDistribution/setSize 43.86 43.86 95.03 mm <br> /gate/actor/doseDistribution/setPosition 0 0 0 cm <br> /gate/actor/doseDistribution/setResolution 96 96 208 <br> /gate/actor/doseDistribution/enableEdep false <br> /gate/actor/doseDistribution/enableUncertaintyEdep false <br> /gate/actor/doseDistribution/enableSquaredEdep false <br> /gate/actor/doseDistribution/enableDose true <br> /gate/actor/doseDistribution/enableUncertaintyDose true <br> /gate/actor/doseDistribution/enableSquaredDose false <br> /gate/actor/doseDistribution/enableNumberOfHits false <br> /gate/actor/doseDistribution/save output/mouse.hdr<br> <br> /gate/actor/addActor SimulationStatisticActor stat <br> /gate/actor/stat/save output/stat-mouse1.txt <br> /gate/actor/stat/saveEveryNSeconds 3600 <br> <br> /gate/actor/resetAfterSaving 1<o:p></o:p></p> </div> <div> <p class="MsoNormal"><o:p> </o:p></p> </div> <div> <p class="MsoNormal">The output as analyze file(.hdr/.img) for dose, Edep and uncertainty are obtained. <o:p></o:p></p> </div> <div> <p class="MsoNormal">I am using MRIcro tool for Absorbed dose calculation. For this, I drew 3D ROs for organs on CT image and then I imported the same saved 3D ROIs on Dose map image. <o:p></o:p></p> </div> <div> <p class="MsoNormal">Then the total no. of ROs and the mean value per voxel were multiplied to get the absorbed dose of that organ in Gy. <o:p></o:p></p> </div> <div> <p class="MsoNormal">there are 8 PET scans done as I explained in last email. I performed the simulations by using simulation time based on PET scan time. For example total scan time of single PET is 900 sec and I used 1/10th of the scan time that is 90 sec as simulation time. The absorbed dose obtained by above method was then multiplied by 10 at the end to compensate for total scan time. This method gives very high absorbed dose in individual organs. And again there are 8 PET scans for which I did separate simulations. <o:p></o:p></p> </div> <div> <p class="MsoNormal">Now I want to ask if I want to estimate total absorbed to any organ then the absorbed dose obtained from each PET scan by above method should be added?<o:p></o:p></p> </div> <div> <p class="MsoNormal">Is there ant other method for estimating the absorbed dose?<o:p></o:p></p> </div> <div> <p class="MsoNormal"><o:p> </o:p></p> </div> <div> <p class="MsoNormal">Kindly give some suggestions. <o:p></o:p></p> </div> </div> <div> <p class="MsoNormal"><o:p> </o:p></p> <div> <p class="MsoNormal">On Thu, Jun 30, 2016 at 8:22 PM, Grevillot Loic <<a href="mailto:loic.grevillot@medaustron.at" target="_blank">loic.grevillot@medaustron.at</a>> wrote:<o:p></o:p></p> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi,</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I do not see how you score the dose in the below macro, but it should be MeV and Gy for energy and dose, respectively.</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">If you score doses in none squared area, there might be some artifacts (not for energy).</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I never extracted doses to organs directly from Gate, but cannot you do that using some clinical software?</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Good luck,</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Loïc</span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Gate-users [mailto:<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>] <b>On Behalf Of </b>Arun Gupta<br> <b>Sent:</b> Thursday, June 30, 2016 12:45 PM<br> <b>To:</b> <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank"> gate-users@lists.opengatecollaboration.org</a>; <a href="mailto:sebastien.jan@cea.fr" target="_blank"> sebastien.jan@cea.fr</a><br> <b>Subject:</b> [Gate-users] Regarding Voxelized Dosimetry</span><o:p></o:p></p> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Dear all,<o:p></o:p></p> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I have been working on voxelized dosimetry using GATE version 7.0. I am using preclinical PET imaging data (mouse PET) for voxelized source and Mouse CT atlas images for voxelized phantom. .<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">The PET imaging was done for 8 different time points (8 PET scans altogether) post injection of nearly 1.50 MBq of 64Cu labelled compound.<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I performed the simulation by preparing voxlizedphantom and voxelizedsource macros based on CT atlas image and PET images respectively.I have matched the resolution of both CT and PET images and I used Interfile image format for both phantom and source images.<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I used Attenuation_range.dat based on CT atlas but used linear translator for source based on the activity injected which was calculated as the product of scaling factor of PET image and Conversion factor. <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I used emstandard physics macro by defining the CUTS parameters but used manually. <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I used the simulation time as 1/10th of the scan duration of each PET scans and performed the simulations for all 8 PET scans separately.<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt">I got the ouput dose map and uncertianity in dose for 8 simulations for 8 PET scans.<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Now I would like to know whether the voxel value on dosemap image is in Gray and energy deposition is in MeV? I am using MRIcro for image processing.<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I drew the 3D ROIs of organ of interest on CT images and imported the save 3D ROIs on Dose map image for Absorbed Dose calculation. <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt">I would like to know how should I get the total absorbed dose of any organ in this case? <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">The following are the macros I used.<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">#===========================================================<br> # VOXELIZED GEOMETRY<br> #===========================================================<br> # World<br> /gate/world/geometry/setXLength 50 cm<br> /gate/world/geometry/setYLength 50 cm<br> /gate/world/geometry/setZLength 50 cm<br> /gate/world/setMaterial Air<br> #/gate/world/vis/setVisible 1<br> #/gate/world/vis/forceWireframe<br> <br> ### Image Regular Parameterized volume<br> <br> /gate/world/daughters/name mouse<br> /gate/world/daughters/insert ImageRegularParametrisedVolume<br> /gate/mouse/geometry/setImage data/m000-CT_reorient.h33<br> /gate/mouse/geometry/setRangeToMaterialFile data/Atten_Range.dat<br> <br> /gate/mouse/placement/setTranslation 0. 0. 0. mm<br> <br> /gate/mouse/attachPhantomSD<br> <br> #===========================================================<br> # VOXELIZED SOURCE<br> #===========================================================<br> <br> /gate/source/addSource PET_UCNP voxel<br> <br> /gate/source/PET_UCNP/reader/insert interfile<br> /gate/source/PET_UCNP/interfileReader/translator/insert linear<br> /gate/source/PET_UCNP/interfileReader/linearTranslator/setScale 0.0012725287 Bq <br> /gate/source/PET_UCNP/interfileReader/readFile data/m003-UCNP_PET_1.h33<br> /gate/source/PET_UCNP/setPosition -21.93 -21.93 -47.515 mm<br> <br> /gate/source/PET_UCNP/gps/particle ion<br> /gate/source/PET_UCNP/gps/ion 29 64 0 0<br> /gate/source/PET_UCNP/gps/energytype Mono<br> /gate/source/PET_UCNP/gps/monoenergy 0. MeV<br> /gate/source/PET_UCNP/setForcedUnstableFlag true<br> /gate/source/PET_UCNP/setForcedHalfLife 45723.6 s<br> /gate/source/PET_UCNP/dump 1<br clear="all"> <o:p></o:p></p> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><br> ############################################################<br> # PHYSICS<br> ############################################################<br> <br> /gate/physics/addProcess PhotoElectric<br> /gate/physics/processes/PhotoElectric/setModel StandardModel<br> <br> /gate/physics/addProcess Compton<br> /gate/physics/processes/Compton/setModel StandardModel<br> <br> /gate/physics/addProcess RayleighScattering<br> /gate/physics/processes/RayleighScattering/setModel PenelopeModel<br> <br> /gate/physics/addProcess GammaConversion<br> /gate/physics/processes/GammaConversion/setModel StandardModel<br> <br> /gate/physics/addProcess ElectronIonisation<br> /gate/physics/processes/ElectronIonisation/setModel StandardModel e-<br> /gate/physics/processes/ElectronIonisation/setModel StandardModel e+<br> <br> /gate/physics/addProcess Bremsstrahlung<br> /gate/physics/processes/Bremsstrahlung/setModel StandardModel e-<br> /gate/physics/processes/Bremsstrahlung/setModel StandardModel e+<br> <br> /gate/physics/addProcess PositronAnnihilation<br> <br> /gate/physics/addProcess MultipleScattering e+<br> /gate/physics/addProcess MultipleScattering e-<br> <br> ## In case of Ion source ##<br> <br> /gate/physics/addProcess IonIonisation<br> /gate/physics/addProcess RadioactiveDecay<br> <br> /gate/physics/setEMin 0.1 keV<br> /gate/physics/setEMax 10 GeV<br> <br> /gate/physics/processList Enabled<br> /gate/physics/processList Initialized<br> <br> ############################################################<br> # CUTS<br> ############################################################<br> <br> /gate/physics/Gamma/SetCutInRegion world 0.1 mm<br> /gate/physics/Electron/SetCutInRegion world 0.1 mm<br> /gate/physics/Positron/SetCutInRegion world 0.1 mm<br> <br> /gate/physics/Gamma/SetCutInRegion mouse 0.01 mm<br> /gate/physics/Electron/SetCutInRegion mouse 0.01 mm<br> /gate/physics/Positron/SetCutInRegion mouse 0.01 mm<br> <br> /gate/physics/SetMaxStepSizeInRegion mouse 0.001 mm<br> <br> #===========================================================<br> # RANDOM<br> #===========================================================<br> <br> /gate/random/setEngineName MersenneTwister<br> <br> /gate/random/setEngineSeed default <br> /gate/random/verbose 0<br> <br> #============================================================<br> # START<br> #===========================================================<br> <br> /gate/application/noGlobalOutput<br> <br> /gate/application/setTimeSlice 10 s <br> /gate/application/setTimeStart 0 s <br> /gate/application/setTimeStop 90 s<br> <br> /gate/application/startDAQ<o:p></o:p></p> </div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <p><span style="font-size:9.5pt">It will be highly appreciated if you help me in this case.</span><o:p></o:p></p> <p><span style="font-size:9.5pt">Thank you.</span><o:p></o:p></p> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <div> <p style="margin:0in;margin-bottom:.0001pt;background:white;vertical-align:middle"> <span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;background:white">Arun Gupta</span><o:p></o:p></p> <p style="margin:0in;margin-bottom:.0001pt;background:white;vertical-align:middle"> <span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;background:white">Ph.D. Student </span><o:p></o:p></p> <p style="margin:0in;margin-bottom:.0001pt;background:white;vertical-align:middle"> <span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;background:white">Functional and Molecular Imaging System Lab</span><o:p></o:p></p> <p style="margin:0in;margin-bottom:.0001pt;background:white;vertical-align:middle"> <span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;background:white">Nuclear Medicine department</span><o:p></o:p></p> <p style="margin:0in;margin-bottom:.0001pt;background:white;vertical-align:middle"> <span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;background:white">College of Medicine </span><o:p></o:p></p> <p style="margin:0in;margin-bottom:.0001pt;background:white;vertical-align:middle"> <span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;background:white">Seoul National Univ. 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