<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">Hi,<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">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.<o:p></o:p></span></p> <p class="MsoNormal"><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).<o:p></o:p></span></p> <p class="MsoNormal"><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?<o:p></o:p></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Good luck,<o:p></o:p></span></p> <p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Loïc<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""> Gate-users [mailto:gate-users-bounces@lists.opengatecollaboration.org] <b>On Behalf Of </b>Arun Gupta<br> <b>Sent:</b> Thursday, June 30, 2016 12:45 PM<br> <b>To:</b> gate-users@lists.opengatecollaboration.org; sebastien.jan@cea.fr<br> <b>Subject:</b> [Gate-users] Regarding Voxelized Dosimetry<o:p></o:p></span></p> <p class="MsoNormal"><o:p> </o:p></p> <div> <p class="MsoNormal">Dear all,<o:p></o:p></p> <div> <p class="MsoNormal"><o:p> </o:p></p> </div> <div> <p class="MsoNormal">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">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">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">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">I used emstandard physics macro by defining the CUTS parameters but used manually. <o:p></o:p></p> </div> <div> <p class="MsoNormal">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="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">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">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="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">The following are the macros I used.<o:p></o:p></p> </div> <div> <p class="MsoNormal">#===========================================================<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"><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.<o:p></o:p></span></p> <p><span style="font-size:9.5pt">Thank you.<o:p></o:p></span></p> <div> <p class="MsoNormal"><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. Hospital</span><o:p></o:p></p> <p style="margin:0in;margin-bottom:.0001pt"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;background:white">103 Daehakro, Jongno-gu, Seoul, 110-799, Korea</span><o:p></o:p></p> <p><o:p> </o:p></p> </div> <div> <p class="MsoNormal"><span style="font-size:10.0pt;color:black;background:white"><o:p> </o:p></span></p> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class="WordSection1"> <p class="MsoNormal"><small><span style=""><o:p></o:p></span><b><span style="font-family: "Verdana","sans-serif"; color: rgb(17, 35, 89);" lang="EN-GB">Disclaimer:</span></b><br> <span style="font-family: "Verdana","sans-serif"; color: rgb(17, 35, 89);" lang="EN-GB">Please notice our E-Mail Disclaimer <a href="http://www.medaustron.at/email-disclaimer/"><span style="color: rgb(17, 35, 89);">http://www.medaustron.at/email-disclaimer/</span></a></span></small><span style=""><o:p></o:p></span><o:p> </o:p></p> </div> <br> </body> </html>