<div dir="ltr"><div dir="ltr">Hi Deniz,<div><br></div><div>Sorry, It might be tough to further help you with the thyroid dose, as I don't have experience with the dose. </div><div><br></div><div>Many experts are on the Gate list and hopefully will help you. <br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div><br></div><div><br></div></div></div></div></div></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Nov 7, 2021 at 5:37 PM Deniz Erkal <<a href="mailto:dnzrklfzk@gmail.com">dnzrklfzk@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hello, you have made the changes you requested, but cannot receive data for thyroid and nasofarengeal.What do you think might be the reason for this?<br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Khalid Hussain <<a href="mailto:khalidhussain1134@gmail.com" target="_blank">khalidhussain1134@gmail.com</a>>, 7 Kas 2021 Paz, 12:19 tarihinde şunu yazdı:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div>Dear Erkal,</div><div><br></div><div>Sorry for the late reply, as I was sick and today came back to my workplace.</div><div>There was a little problem, probably in the </div><div><br></div><div><font color="#ff0000">/gate/application/start</font></div><div>which I replaced with </div><div>/<font color="#ff0000">gate/application/startDAQ</font><br></div><div>Please see the attached zip file. Now it working</div><div><br></div><div>Please change the material with the one that you defined in material db file.</div><div><br></div><div>I have changed the material to Breast just for checking.</div><div>Now it running.</div><div><br></div><div>Now its running.</div></div></div></div></div><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Nov 4, 2021 at 10:35 PM Deniz Erkal <<a href="mailto:dnzrklfzk@gmail.com" target="_blank">dnzrklfzk@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">#-------------------oooooOOOOO00000OOOOOooooo---------------------#<br><br># Example of Carbon beam in water tank. Output is a 3D dose<br># distribution map (with associated uncertainty) and map of producted<br># C11.<br><br>#-------------------oooooOOOOO00000OOOOOooooo---------------------#<br><br><br>#=====================================================<br># VERBOSE and VISUALISATION<br>#=====================================================<br><br>/control/execute mac/verbose.mac<br><br># to use the visualisation :<br># - uncomment the following line<br># - use Gate --qt<br># - in the interface, type /control/execute mac/main.mac<br>#/control/execute mac/visu.mac<br><br><br>#=====================================================<br># GEOMETRY<br>#=====================================================<br><br>/gate/geometry/setMaterialDatabase data/GateMaterials.db<br><br># WORLD<br>/gate/world/setMaterial Air<br>/gate/world/geometry/setXLength 2.0 m<br>/gate/world/geometry/setYLength 2.0 m<br>/gate/world/geometry/setZLength 2.0 m<br><br># BrainSphere<br>/gate/world/daughters/name BrainSphere<br>/gate/world/daughters/insert ellipsoid<br>/gate/BrainSphere/setMaterial Brain<br>/gate/BrainSphere/geometry/setXLength 6.58 cm<br>/gate/BrainSphere/geometry/setYLength 8.57 cm<br>/gate/BrainSphere/geometry/setZLength 5.73 cm<br>/gate/BrainSphere/placement/setTranslation 0 0 0 cm<br>/gate/BrainSphere/placement/setRotationAxis 0 1 0<br>/gate/BrainSphere/placement/setRotationAngle 90 deg <br>/gate/BrainSphere/vis/setVisible 1<br>/gate/BrainSphere/vis/setColor white<br><br><br># UpperSpine<br>/gate/world/daughters/name UpperSpine<br>/gate/world/daughters/insert eltub<br>/gate/UpperSpine/setMaterial SpineBone<br>/gate/UpperSpine/geometry/setLong 2.45 cm<br>/gate/UpperSpine/geometry/setShort 1.73 cm<br>/gate/UpperSpine/geometry/setHeight 5 cm<br>/gate/UpperSpine/placement/setRotationAxis 0 1 0<br>/gate/UpperSpine/placement/setRotationAngle 90 deg<br>/gate/UpperSpine/vis/setVisible 1<br>/gate/UpperSpine/vis/setColor yellow<br><br># Thyroid<br>/gate/world/daughters/name Thyroid<br>/gate/world/daughters/insert cylinder<br>/gate/Thyroid/setMaterial Thyroid<br>/gate/Thyroid/geometry/setRmin 0.83 cm<br>/gate/Thyroid/geometry/setRmax 1.85 cm<br>/gate/Thyroid/geometry/setHeight 4.50 cm<br>/gate/Thyroid/geometry/setPhiStart 0 deg<br>/gate/Thyroid/geometry/setDeltaPhi 360 deg<br>/gate/Thyroid/placement/setTranslation 0 -3 13 cm<br>/gate/Thyroid/placement/setRotationAxis 0 1 0<br>/gate/Thyroid/placement/setRotationAngle 90 deg<br>/gate/Thyroid/vis/setVisible 1<br>/gate/Thyroid/vis/setColor blue<br><br># Nazofarengeal<br>/gate/world/daughters/name Nazofarengeal<br>/gate/world/daughters/insert cylinder<br>/gate/Nazofarengeal/setMaterial Nazofarengeal<br>#/gate/Nazofarengeal/setMaterial G4_WATER<br>/gate/Nazofarengeal/geometry/setRmin 4.00 cm<br>/gate/Nazofarengeal/geometry/setRmax 4.50 cm<br>/gate/Nazofarengeal/geometry/setHeight 3.00 cm<br>/gate/Nazofarengeal/geometry/setPhiStart 0 deg<br>/gate/Nazofarengeal/geometry/setDeltaPhi 180 deg<br>/gate/Nazofarengeal/placement/setTranslation 0 0 4.50 cm<br>/gate/Nazofarengeal/placement/setRotationAxis 0 1 0<br>/gate/Nazofarengeal/placement/setRotationAngle 90 deg<br>/gate/Nazofarengeal/vis/setVisible 1<br>/gate/Nazofarengeal/vis/setColor green<br><br><br>#=====================================================<br># PHYSICS<br>#=====================================================<br><br>/gate/physics/addPhysicsList QGSP_BERT_HP_EMY<br><br>/gate/physics/displayCuts<br>/gate/physics/print output/physics.txt<br><br>#=====================================================<br># CUTS<br>#=====================================================<br><br>/gate/physics/Gamma/SetCutInRegion world 1 mm<br>/gate/physics/Electron/SetCutInRegion world 1 mm<br>/gate/physics/Positron/SetCutInRegion world 1 mm<br><br>#/gate/physics/Gamma/SetCutInRegion target 0.1 mm<br>#/gate/physics/Electron/SetCutInRegion target 0.1 mm<br>#/gate/physics/Positron/SetCutInRegion target 0.1 mm<br><br>/gate/physics/SetMaxStepSizeInRegion world 1 mm<br>/gate/physics/ActivateStepLimiter proton<br>/gate/physics/ActivateStepLimiter deuteron<br>/gate/physics/ActivateStepLimiter triton<br>/gate/physics/ActivateStepLimiter alpha<br>/gate/physics/ActivateStepLimiter GenericIon<br><br>/gate/physics/ActivateStepLimiter proton<br>/gate/physics/ActivateStepLimiter e-<br><br># Verbose physic list (uncomment to display)<br>/gate/physics/displayCuts<br>/gate/physics/processList Enabled<br># /gate/physics/processList Initialized<br><br>#=====================================================<br># OUTPUT - DETECTOR<br>#=====================================================<br><br>/gate/actor/addActor SimulationStatisticActor stat<br>/gate/actor/stat/save output/stat.txt<br>/gate/actor/stat/saveEveryNSeconds 20<br><br># ----------------------------------------------------<br># the following actor stores 3D distributions of<br># dose/edep/uncertainty/nbHit into files (mhd image file format)<br><br>/gate/actor/addActor ProductionAndStoppingActor carbonMap<br>/gate/actor/carbonMap/save output1/C11.root<br>/gate/actor/carbonMap/attachTo BrainSphere<br>/gate/actor/carbonMap/stepHitType random<br>/gate/actor/carbonMap/setVoxelSize 4 4 4 mm<br>/gate/actor/carbonMap/addFilter particleFilter<br>/gate/actor/carbonMap/particleFilter/addParticle C11<br>/gate/actor/carbonMap/saveEveryNSeconds 20<br><br>### A simple linac with backup X,Y and MLC<br>#/gate/geometry/setMaterialDatabase data/PreciseMaterials.db<br>#/control/execute mac/precise_Linac.mac<br><br>/gate/actor/addActor DoseActor doseDistribution<br>/gate/actor/doseDistribution/save output1/IDD-C11.root<br>/gate/actor/doseDistribution/attachTo BrainSphere<br>/gate/actor/doseDistribution/stepHitType random<br>/gate/actor/doseDistribution/setVoxelSize 1.00 1.00 1.00 cm<br>/gate/actor/doseDistribution/setPosition 0 0 0 cm<br>/gate/actor/doseDistribution/saveEveryNSeconds 20<br>#/gate/actor/doseDistribution/addFilter particleFilter<br>#/gate/actor/doseDistribution/particleFilter/addParticle C11<br>/gate/actor/doseDistribution/enableEdep true<br>/gate/actor/doseDistribution/enableUncertaintyEdep false<br>/gate/actor/doseDistribution/enableDose true<br>/gate/actor/doseDistribution/enableUncertaintyDose false<br>/gate/actor/doseDistribution/enableNumberOfHits false<br><br>/gate/actor/addActor DoseActor doseDistribution3<br>/gate/actor/doseDistribution3/save output1/IDD-Thyroid.root<br>/gate/actor/doseDistribution3/attachTo Thyroid<br>/gate/actor/doseDistribution3/stepHitType random<br>/gate/actor/doseDistribution/setVoxelSize 1.00 1.00 1.00 cm<br>/gate/actor/doseDistribution3/setPosition 0 0 0 cm<br>/gate/actor/doseDistribution3/saveEveryNSeconds 20<br>#/gate/actor/doseDistribution3/addFilter particleFilter<br>#/gate/actor/doseDistribution3/particleFilter/addParticle C11<br>/gate/actor/doseDistribution3/enableEdep true<br>/gate/actor/doseDistribution3/enableUncertaintyEdep false<br>/gate/actor/doseDistribution3/enableDose true<br>/gate/actor/doseDistribution3/enableUncertaintyDose true<br>/gate/actor/doseDistribution3/enableNumberOfHits false<br><br>/gate/actor/addActor DoseActor doseNazo<br>/gate/actor/doseNazo/save output1/IDD-Nazofarengeal.root<br>/gate/actor/doseNazo/attachTo Nazofarengeal<br>/gate/actor/doseNazo/stepHitType random<br>/gate/actor/doseNazo/setVoxelSize 1.00 1.00 1.00 cm<br>/gate/actor/doseNazo/setPosition 0 0 0 cm<br>/gate/actor/doseNazo/saveEveryNSeconds 20<br>#/gate/actor/doseNazo/addFilter particleFilter<br>#/gate/actor/doseNazo/particleFilter/addParticle C11<br>/gate/actor/doseNazo/enableEdep true<br>/gate/actor/doseNazo/enableUncertaintyEdep false<br>/gate/actor/doseNazo/enableDose true<br>/gate/actor/doseNazo/enableUncertaintyDose false<br>/gate/actor/doseNazo/enableNumberOfHits false<br><br>/gate/actor/addActor SecondaryProductionActor Secondaries<br>/gate/actor/Secondaries/save secondary-list.root<br>/gate/actor/Secondaries/attachTo BrainSphere<br><br>#=====================================================<br># INITIALISATION<br>#=====================================================<br><br>/gate/run/initialize<br><br>#=====================================================<br># BEAMS<br>#=====================================================<br><br># Carbon 12 beam<br>/gate/source/addSource C12 gps<br>/gate/source/C12/gps/particle ion<br>/gate/source/C12/gps/ion 6 12<br>/gate/source/C12/gps/ene/type Mono<br>/gate/source/C12/gps/ene/mono 2314.24 MeV<br>/gate/source/C12/gps/pos/type Beam<br>/gate/source/C12/gps/pos/shape Circle<br>/gate/source/C12/gps/pos/sigma_x 2.0 mm<br>/gate/source/C12/gps/pos/sigma_y 2.0 mm<br>/gate/source/C12/gps/ang/type beam2d<br>/gate/source/C12/gps/ang/sigma_x 0 deg<br>/gate/source/C12/gps/ang/sigma_y 0 deg<br>/gate/source/C12/gps/pos/centre 0.0 0.0 4.5 cm<br><br># Proton beam<br>#/gate/source/addSource prot gps<br>#/gate/source/prot/gps/particle proton<br>#/gate/source/prot/gps/ene/type Gauss<br>#/gate/source/prot/gps/ene/mono 150 MeV<br>#/gate/source/prot/gps/ene/sigma 10. MeV<br>#/gate/source/prot/gps/ang/type cos<br>#/gate/source/prot/gps/ang/type beam1d<br>#/gate/source/prot/gps/ang/sigma_r 0. deg<br>#/gate/source/prot/gps/pos/type Beam<br>#/gate/source/prot/gps/pos/shape Circle<br>#/gate/source/prot/gps/pos/centre 0. 0. 30. cm<br>#/gate/source/prot/gps/pos/radius 3. mm<br>#/gate/source/prot/gps/pos/sigma_r 0.2 mm<br><br>#/gate/source/addSource mybeam LinacBeam<br>#/gate/source/mybeam/setSourceFromPhaseSpaceFilename data/linac-beam.root<br>#/gate/source/mybeam/attachTo linacPhSPlane <br>#/gate/source/mybeam/setMaxLeafDistanceAccordingToTime data/precise_BeamSource.rmax<br><br>#=====================================================<br># START BEAMS<br>#=====================================================<br><br>/gate/random/setEngineName MersenneTwister<br>/gate/random/setEngineSeed auto<br>/gate/application/setTotalNumberOfPrimaries 100<br>/gate/application/start<br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Khalid Hussain <<a href="mailto:khalidhussain1134@gmail.com" target="_blank">khalidhussain1134@gmail.com</a>>, 4 Kas 2021 Per, 20:31 tarihinde şunu yazdı:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="auto">Yes please I will check your email and guide you as per the best of my knowledge.</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Nov 4, 2021, 10:28 PM Deniz Erkal <<a href="mailto:dnzrklfzk@gmail.com" target="_blank">dnzrklfzk@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hello, there is an error in the codes I wrote. Can't receive data, can you help me with this?<br></div><div class="gmail_quote"><div dir="ltr" class="gmail_attr"><br></div></div>
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