<div dir="ltr">Hi, <div>Thank you for your tips!</div><div><br></div><div>The simulation gave me better results by changing the source to a volume source and by reviewing the b- spectrum.</div><div>Nevertheless, further from the source, the s-values decrease faster than the ones in the reference. </div><div>I think the authors did not make any energy cut so I do not understand what else could be wrong. </div><div><br></div><div>Attached, I send you an example of the comparison between my values and the reference ones, as well as my code. <br></div><div><br></div><div>Thank you in advance<br></div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">陈戈飞 <<a href="mailto:xiaofeizaina@126.com" target="_blank">xiaofeizaina@126.com</a>> escreveu no dia quarta, 10/02/2021 à(s) 17:18:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi<br>This problem also bothered me very long time. You should set the shape of source as a cube with size 2.21mm 2.21mm 2.21mm. Because it's not a point source.<br>As for matlab, maybe it's too small to show. Try to plot it with logarithm scale.<br><br>Regards<br><br><p>At 2021-02-11 00:30:37, "Maria Inês Ribeiro" <<a href="mailto:mid.ribeiro@campus.fct.unl.pt" target="_blank">mid.ribeiro@campus.fct.unl.pt</a>> wrote:</p><blockquote id="gmail-m_6121459375416126408gmail-m_-6831884351991350653isReplyContent" style="padding-left:1ex;margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204)"><div dir="ltr"><div>Hello <span name="陈戈飞">陈戈飞 and Ashok, <br></span></div><div><span name="陈戈飞"><br></span></div><div><span name="陈戈飞">I tried my best to implement your suggestions (thank you sooo much). I found reasonable s-values comparing to the one indicates at <a href="http://medphys.it" target="_blank">medphys.it</a></span></div><div><span name="陈戈飞">For example, my center voxel s-value is of 4.5 mGy/(MBq s) and theirs is 3 mGy/(MBq s). <br></span></div><div><span name="陈戈飞">However, 2 things seem a bit strange:<br></span></div><div><span name="陈戈飞">1) when I load the dose map at MATLAB, I get a lot of zeros in the border voxels of my kernel. I am using a 11x11x11 kernel, each with 2,21 mm. This is not supposed to be happening.<br></span></div><div><span name="陈戈飞">2) The values are a bit different from the reference values. Do you know if the source should have any additional spectrums that I should worry about? anyway if I add more spectrums, the dose will only increase, which is not good.... <br></span></div><div><span name="陈戈飞">A simulates my source as follows: <br></span></div><div><span name="陈戈飞"><br></span></div><div><span name="陈戈飞">/gate/source/addSource Y90Source<br>/gate/source/Y90Source/setActivity 1 MBq<br>/gate/source/Y90Source/gps/particle e-<br>/gate/source/Y90Source/gps/energytype Arb<br>/gate/source/Y90Source/gps/hist/type arb<br>/gate/source/Y90Source/gps/hist/point 0.0571 0.0426<br>/gate/source/Y90Source/gps/hist/point 0.1713 0.0518<br>/gate/source/Y90Source/gps/hist/point 0.2855 0.0594<br>/gate/source/Y90Source/gps/hist/point 0.3997 0.0649<br>/gate/source/Y90Source/gps/hist/point 0.5139 0.0686<br>/gate/source/Y90Source/gps/hist/point 0.6281 0.0708<br>/gate/source/Y90Source/gps/hist/point 0.7423 0.0717<br>/gate/source/Y90Source/gps/hist/point 0.8565 0.0715<br>/gate/source/Y90Source/gps/hist/point 0.9707 0.0704<br>/gate/source/Y90Source/gps/hist/point 1.0849 0.0685<br>/gate/source/Y90Source/gps/hist/point 1.1991 0.0657<br>/gate/source/Y90Source/gps/hist/point 1.3133 0.0619<br>/gate/source/Y90Source/gps/hist/point 1.4275 0.0569<br>/gate/source/Y90Source/gps/hist/point 1.5417 0.0507<br>/gate/source/Y90Source/gps/hist/point 1.6559 0.0430<br>/gate/source/Y90Source/gps/hist/point 1.7701 0.0342<br>/gate/source/Y90Source/gps/hist/point 1.8843 0.0246<br>/gate/source/Y90Source/gps/hist/point 1.9985 0.0150<br>/gate/source/Y90Source/gps/hist/point 2.1127 0.00643<br>/gate/source/Y90Source/gps/hist/point 2.2269 0.00113<br>/gate/source/Y90Source/gps/hist/inter Lin<br>/gate/source/Y90Source/gps/pos/type Point<br>/gate/source/Y90Source/gps/angtype iso<br>/gate/source/Y90Source/setForcedUnstableFlag true<br>/gate/source/Y90Source/setForcedHalfLife 230760. s</span></div><div><span name="陈戈飞"><br></span></div><div><span name="陈戈飞">Thank you so much for your help again!</span></div><div><span name="陈戈飞"><br></span></div><div><span name="陈戈飞">Maria<br></span></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Ashok Tiwari <<a href="mailto:tiwarias@yahoo.com" target="_blank">tiwarias@yahoo.com</a>> escreveu no dia terça, 9/02/2021 à(s) 16:49:<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><div style="font-family:"Helvetica Neue",Helvetica,Arial,sans-serif;font-size:16px"><div></div>
<div dir="ltr">Hi Maria, </div><div dir="ltr"><br></div><div dir="ltr">You could start a simulation by setting a total number of primaries instead of time. Based on my experience with GATEv8.1, the transport of 20 million particles was found to provide sufficient statistical precision. See details in: <a href="https://meridian.allenpress.com/radiation-research/article-abstract/193/6/531/436368/The-Impact-of-Tissue-Type-and-Density-on-Dose?redirectedFrom=fulltext" rel="noreferrer noopener" target="_blank">The Impact of Tissue Type and Density on Dose Point Kernels for Patient-Specific Voxel-Wise Dosimetry: A Monte Carlo Investigation | Radiation Research | Allen Press</a></div><div><br></div><div id="gmail-m_6121459375416126408gmail-m_-6831884351991350653gmail-m_-2011264584781472718ydp3b9ead41enhancr_card_3691519457" style="max-width:400px;font-family:YahooSans,"Helvetica Neue","Segoe UI",Helvetica,Arial,sans-serif"><a href="https://meridian.allenpress.com/radiation-research/article-abstract/193/6/531/436368/The-Impact-of-Tissue-Type-and-Density-on-Dose?redirectedFrom=fulltext" style="text-decoration:none;color:rgb(0,0,0)" rel="noreferrer noopener" target="_blank"><table style="max-width:400px" cellspacing="0" cellpadding="0" border="0"><tbody><tr><td width="400"><table style="max-width:400px;border-width:1px;border-style:solid;border-color:rgb(224,228,233);border-radius:2px" width="100%" cellspacing="0" cellpadding="0" border="0"><tbody><tr><td><table style="background:rgb(255,255,255) none repeat scroll 0% 0%;width:100%;max-width:400px;border-radius:0px 0px 2px 2px;border-top:1px solid rgb(224,228,233)" cellspacing="0" cellpadding="0" border="0"><tbody><tr><td style="background-color:rgb(255,255,255);padding:16px 0px 16px 12px;vertical-align:top;border-radius:0px 0px 0px 2px"></td><td style="vertical-align:middle;padding:12px 24px 16px 12px;width:99%;font-family:YahooSans,"Helvetica Neue","Segoe UI",Helvetica,Arial,sans-serif;border-radius:0px 0px 2px"><h2 style="font-size:14px;line-height:19px;margin:0px 0px 6px;font-family:YahooSans,"Helvetica Neue","Segoe UI",Helvetica,Arial,sans-serif;color:rgb(38,40,42);max-width:314px">The Impact of Tissue Type and Density on Dose Point Kernels for Patient-...</h2><p style="font-size:12px;line-height:16px;margin:0px;color:rgb(151,155,167)"></p></td></tr></tbody></table></td></tr></tbody></table></td></tr></tbody></table></a></div><div><br></div><div dir="ltr">Also, I recommend using ~1 keV energy cuts in dose point kernel simulations. Cuts can be set by using:</div><div dir="ltr"><br></div><div dir="ltr"><div><div>/gate/physics/Gamma/SetCutInRegion world ... mm</div><div>/gate/physics/Electron/SetCutInRegion world ... mm</div><div><br></div><div>/gate/physics/Gamma/SetCutInRegion my_phantom ... mm </div><div>/gate/physics/Electron/SetCutInRegion my_phantom .. mm</div><div><br></div><div dir="ltr">Another important thing is an steplimiter, you could set it by using:</div><div dir="ltr"><br></div><div>/gate/physics/SetMaxStepSizeInRegion my_phantom ... mm</div><div>/gate/physics/ActivateStepLimiter e-</div><div><br></div></div><div dir="ltr">All other infos are described in the paper.</div><div dir="ltr"><br></div><div dir="ltr">Regards,</div><div dir="ltr">Ashok</div><br></div>
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On Tuesday, 9 February 2021, 09:19:23 am GMT-6, Maria Inês Ribeiro <<a href="mailto:mid.ribeiro@campus.fct.unl.pt" target="_blank">mid.ribeiro@campus.fct.unl.pt</a>> wrote:
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<div><div id="gmail-m_6121459375416126408gmail-m_-6831884351991350653gmail-m_-2011264584781472718yiv8564264232"><div dir="ltr">Thank you so much. <div><br></div><div>It was supposed to be 100000 s. I just killed the simulation because it was taking too long. </div><div>I swapped to the normal ion source definition since fastY90 can't be used for dosimetry. </div><div><br></div><div>Do you recommend decreasing cut energy for photons and electrons?</div><div><br></div><div>Kind regards, </div><div>Maria </div></div><br><div><div dir="ltr">陈戈飞 <<a href="mailto:xiaofeizaina@126.com" rel="noreferrer noopener" target="_blank">xiaofeizaina@126.com</a>> escreveu no dia terça, 9/02/2021 à(s) 15:13:<br></div><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div id="gmail-m_6121459375416126408gmail-m_-6831884351991350653gmail-m_-2011264584781472718yiv8564264232gmail-m_-973855092368961664contentDescription" style="line-height:1.5;text-align:justify">
<div id="gmail-m_6121459375416126408gmail-m_-6831884351991350653gmail-m_-2011264584781472718yiv8564264232gmail-m_-973855092368961664imail_extraContent">Hi maria
<br>The total time of your simulations is 10000s，right? If so, you only need to multiply by 1000(Gy->mGy) and divide 10000(time to 1s).
<br>And I recommend setting cut energy for beta and photon. Default is 10 mm.
<br>You'd better recheck the definition of fastY90. It can't be used for dose purposes.
<br>Thank you
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<div style="background-color:rgb(242,242,242);color:black;padding-top:6px;padding-bottom:6px;border-radius:3px;margin-top:45px;margin-bottom:20px"><div style="font-size:14px;line-height:1.5;margin-left:10px;margin-right:10px">On <span>02/09/2021 22:38</span>, <a style="text-decoration:none;color:rgb(42,151,255)" href="mailto:mid.ribeiro@campus.fct.unl.pt" rel="noreferrer noopener" target="_blank">Maria Inês Ribeiro</a> wrote: </div></div><blockquote id="gmail-m_6121459375416126408gmail-m_-6831884351991350653gmail-m_-2011264584781472718yiv8564264232gmail-m_-973855092368961664ntes-iosmail-quote" style="margin:0px"><div dir="ltr">Hi everyone, <div><br></div><div>I am attempting to compute a dose point kernel in soft tissue for a point source of Y90. I am using the fastY90 with an activity of 1 MBq. </div><div>I then ran 40.000 slices of 1 second and stored the dose. </div><div><br></div><div>My question is how do I convert my dose map (Gy) into the s values (mGy/(MBq.s)) for each voxel? </div><div><br></div><div>Here is my could in case it could help to support my question:</div><div><br></div><div>#===============================================================================<br># GEOMETRY<br>#===============================================================================<br><br>/gate/geometry/setMaterialDatabase data/GateMaterials.db<br><br>#WORLD ======================================<br>/gate/world/setMaterial Air<br>/gate/world/geometry/setXLength 50 mm<br>/gate/world/geometry/setYLength 50 mm<br>/gate/world/geometry/setZLength 50 mm<br><br>#LIVER ======================================<br>/gate/world/daughters/name liverPhantom<br>/gate/world/daughters/insert box<br>/gate/liverPhantom/setMaterial Liver<br>/gate/liverPhantom/geometry/setXLength 24.31 mm<br>/gate/liverPhantom/geometry/setYLength 24.31 mm<br>/gate/liverPhantom/geometry/setZLength 24.31 mm<br><br>#===============================================================================<br># PHYSICS<br>#===============================================================================<br><br>/gate/physics/addPhysicsList emstandard_opt3<br><br>#===============================================================================<br># DETECTORS<br>#===============================================================================<br><br>#DOSE ACTOR ==============================<br>#builds 3D images of:<br># - the energy deposited (edep in MeV)<br># - dose deposited (Gy)<br># - the number of hits in a volume<br><br>/gate/actor/addActor DoseActor VSV<br>/gate/actor/VSV/attachTo liverPhantom<br>/gate/actor/VSV/stepHitType random<br>/gate/actor/VSV/setSize 24.31 24.31 24.31 mm<br>/gate/actor/VSV/setPosition 0 0 0 cm<br>/gate/actor/VSV/setResolution 11 11 11<br>/gate/actor/VSV/enableEdep true<br>/gate/actor/VSV/enableUncertaintyEdep true<br>/gate/actor/VSV/enableSquaredEdep true<br>/gate/actor/VSV/enableDose true<br>/gate/actor/VSV/enableUncertaintyDose true<br>/gate/actor/VSV/enableSquaredDose true<br>/gate/actor/VSV/enableNumberOfHits true<br>/gate/actor/VSV/save output/VSV.mhd<br><br>#SIMULATION STATISTIC =====================<br>#this actos counts the number of steps, tracks, events, runs in the simulation<br><br>/gate/actor/addActor SimulationStatisticActor stat<br>/gate/actor/stat/save output/stat-VSV.txt<br>/gate/actor/stat/saveEveryNSeconds 60<br><br><br>#===============================================================================<br># INITIALISATION<br>#===============================================================================<br><br>/gate/run/initialize<br><br>/gate/random/setEngineName MersenneTwister<br>/gate/random/setEngineSeed auto<br><br>#===========================================================<br># SOURCE <br>#===========================================================<br><br># fastY90<br>/gate/source/addSource y90 fastY90<br>/gate/source/y90/setActivity 1. MBq<br><br>#=====================================================<br># START<br>#=====================================================<br><br>/gate/application/setTimeSlice 1. s<br>/gate/application/setTimeStart 0. s<br>/gate/application/setTimeStop 1000000. s <br>/gate/application/start<br></div><div><br></div><div><br></div><div>Thanks a lot for your attention, </div><div><br></div><div>Maria Inês</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div></div>
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