[Gate-users] S-values simulation
Maria Inês Ribeiro
mid.ribeiro at campus.fct.unl.pt
Thu Feb 11 14:45:06 CET 2021
Hi,
Thank you for your tips!
The simulation gave me better results by changing the source to a volume
source and by reviewing the b- spectrum.
Nevertheless, further from the source, the s-values decrease faster than
the ones in the reference.
I think the authors did not make any energy cut so I do not understand what
else could be wrong.
Attached, I send you an example of the comparison between my values and the
reference ones, as well as my code.
Thank you in advance
陈戈飞 <xiaofeizaina at 126.com> escreveu no dia quarta, 10/02/2021 à(s) 17:18:
> Hi
> 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.
> As for matlab, maybe it's too small to show. Try to plot it with logarithm
> scale.
>
> Regards
>
> At 2021-02-11 00:30:37, "Maria Inês Ribeiro" <
> mid.ribeiro at campus.fct.unl.pt> wrote:
>
> Hello 陈戈飞 and Ashok,
>
> I tried my best to implement your suggestions (thank you sooo much). I
> found reasonable s-values comparing to the one indicates at medphys.it
> For example, my center voxel s-value is of 4.5 mGy/(MBq s) and theirs is 3
> mGy/(MBq s).
> However, 2 things seem a bit strange:
> 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.
> 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....
> A simulates my source as follows:
>
> /gate/source/addSource Y90Source
> /gate/source/Y90Source/setActivity 1 MBq
> /gate/source/Y90Source/gps/particle e-
> /gate/source/Y90Source/gps/energytype Arb
> /gate/source/Y90Source/gps/hist/type arb
> /gate/source/Y90Source/gps/hist/point 0.0571 0.0426
> /gate/source/Y90Source/gps/hist/point 0.1713 0.0518
> /gate/source/Y90Source/gps/hist/point 0.2855 0.0594
> /gate/source/Y90Source/gps/hist/point 0.3997 0.0649
> /gate/source/Y90Source/gps/hist/point 0.5139 0.0686
> /gate/source/Y90Source/gps/hist/point 0.6281 0.0708
> /gate/source/Y90Source/gps/hist/point 0.7423 0.0717
> /gate/source/Y90Source/gps/hist/point 0.8565 0.0715
> /gate/source/Y90Source/gps/hist/point 0.9707 0.0704
> /gate/source/Y90Source/gps/hist/point 1.0849 0.0685
> /gate/source/Y90Source/gps/hist/point 1.1991 0.0657
> /gate/source/Y90Source/gps/hist/point 1.3133 0.0619
> /gate/source/Y90Source/gps/hist/point 1.4275 0.0569
> /gate/source/Y90Source/gps/hist/point 1.5417 0.0507
> /gate/source/Y90Source/gps/hist/point 1.6559 0.0430
> /gate/source/Y90Source/gps/hist/point 1.7701 0.0342
> /gate/source/Y90Source/gps/hist/point 1.8843 0.0246
> /gate/source/Y90Source/gps/hist/point 1.9985 0.0150
> /gate/source/Y90Source/gps/hist/point 2.1127 0.00643
> /gate/source/Y90Source/gps/hist/point 2.2269 0.00113
> /gate/source/Y90Source/gps/hist/inter Lin
> /gate/source/Y90Source/gps/pos/type Point
> /gate/source/Y90Source/gps/angtype iso
> /gate/source/Y90Source/setForcedUnstableFlag true
> /gate/source/Y90Source/setForcedHalfLife 230760. s
>
> Thank you so much for your help again!
>
> Maria
>
> Ashok Tiwari <tiwarias at yahoo.com> escreveu no dia terça, 9/02/2021 à(s)
> 16:49:
>
>> Hi Maria,
>>
>> 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: 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
>> <https://meridian.allenpress.com/radiation-research/article-abstract/193/6/531/436368/The-Impact-of-Tissue-Type-and-Density-on-Dose?redirectedFrom=fulltext>
>>
>> The Impact of Tissue Type and Density on Dose Point Kernels for
>> Patient-...
>>
>>
>> <https://meridian.allenpress.com/radiation-research/article-abstract/193/6/531/436368/The-Impact-of-Tissue-Type-and-Density-on-Dose?redirectedFrom=fulltext>
>>
>> Also, I recommend using ~1 keV energy cuts in dose point kernel
>> simulations. Cuts can be set by using:
>>
>> /gate/physics/Gamma/SetCutInRegion world ... mm
>> /gate/physics/Electron/SetCutInRegion world ... mm
>>
>> /gate/physics/Gamma/SetCutInRegion my_phantom ... mm
>> /gate/physics/Electron/SetCutInRegion my_phantom .. mm
>>
>> Another important thing is an steplimiter, you could set it by using:
>>
>> /gate/physics/SetMaxStepSizeInRegion my_phantom ... mm
>> /gate/physics/ActivateStepLimiter e-
>>
>> All other infos are described in the paper.
>>
>> Regards,
>> Ashok
>>
>> On Tuesday, 9 February 2021, 09:19:23 am GMT-6, Maria Inês Ribeiro <
>> mid.ribeiro at campus.fct.unl.pt> wrote:
>>
>>
>> Thank you so much.
>>
>> It was supposed to be 100000 s. I just killed the simulation because it
>> was taking too long.
>> I swapped to the normal ion source definition since fastY90 can't be used
>> for dosimetry.
>>
>> Do you recommend decreasing cut energy for photons and electrons?
>>
>> Kind regards,
>> Maria
>>
>> 陈戈飞 <xiaofeizaina at 126.com> escreveu no dia terça, 9/02/2021 à(s) 15:13:
>>
>> Hi maria
>> 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).
>> And I recommend setting cut energy for beta and photon. Default is 10 mm.
>> You'd better recheck the definition of fastY90. It can't be used for dose
>> purposes.
>> Thank you
>>
>>
>> 陈戈飞
>> 邮箱：xiaofeizaina at 126.com
>>
>> <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fqiyelogo%2FdefaultAvatar.png&name=%E9%99%88%E6%88%88%E9%A3%9E&uid=example%40163.com&ftlId=3&items=%5B%22%E9%82%AE%E7%AE%B1%EF%BC%9Axiaofeizaina%40126.com%22%5D>
>>
>> 签名由 网易邮箱大师 <https://mail.163.com/dashi/dlpro.html?from=mail88> 定制
>> On 02/09/2021 22:38, Maria Inês Ribeiro <mid.ribeiro at campus.fct.unl.pt>
>> wrote:
>>
>> Hi everyone,
>>
>> 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.
>> I then ran 40.000 slices of 1 second and stored the dose.
>>
>> My question is how do I convert my dose map (Gy) into the s values
>> (mGy/(MBq.s)) for each voxel?
>>
>> Here is my could in case it could help to support my question:
>>
>>
>> #===============================================================================
>> # GEOMETRY
>>
>> #===============================================================================
>>
>> /gate/geometry/setMaterialDatabase
>> data/GateMaterials.db
>>
>> #WORLD ======================================
>> /gate/world/setMaterial Air
>> /gate/world/geometry/setXLength 50 mm
>> /gate/world/geometry/setYLength 50 mm
>> /gate/world/geometry/setZLength 50 mm
>>
>> #LIVER ======================================
>> /gate/world/daughters/name liverPhantom
>> /gate/world/daughters/insert box
>> /gate/liverPhantom/setMaterial Liver
>> /gate/liverPhantom/geometry/setXLength 24.31 mm
>> /gate/liverPhantom/geometry/setYLength 24.31 mm
>> /gate/liverPhantom/geometry/setZLength 24.31 mm
>>
>>
>> #===============================================================================
>> # PHYSICS
>>
>> #===============================================================================
>>
>> /gate/physics/addPhysicsList emstandard_opt3
>>
>>
>> #===============================================================================
>> # DETECTORS
>>
>> #===============================================================================
>>
>> #DOSE ACTOR ==============================
>> #builds 3D images of:
>> # - the energy deposited (edep in MeV)
>> # - dose deposited (Gy)
>> # - the number of hits in a volume
>>
>> /gate/actor/addActor DoseActor VSV
>> /gate/actor/VSV/attachTo liverPhantom
>> /gate/actor/VSV/stepHitType random
>> /gate/actor/VSV/setSize 24.31 24.31 24.31 mm
>> /gate/actor/VSV/setPosition 0 0 0 cm
>> /gate/actor/VSV/setResolution 11 11 11
>> /gate/actor/VSV/enableEdep true
>> /gate/actor/VSV/enableUncertaintyEdep true
>> /gate/actor/VSV/enableSquaredEdep true
>> /gate/actor/VSV/enableDose true
>> /gate/actor/VSV/enableUncertaintyDose true
>> /gate/actor/VSV/enableSquaredDose true
>> /gate/actor/VSV/enableNumberOfHits true
>> /gate/actor/VSV/save output/VSV.mhd
>>
>> #SIMULATION STATISTIC =====================
>> #this actos counts the number of steps, tracks, events, runs in the
>> simulation
>>
>> /gate/actor/addActor
>> SimulationStatisticActor stat
>> /gate/actor/stat/save output/stat-VSV.txt
>> /gate/actor/stat/saveEveryNSeconds 60
>>
>>
>>
>> #===============================================================================
>> # INITIALISATION
>>
>> #===============================================================================
>>
>> /gate/run/initialize
>>
>> /gate/random/setEngineName MersenneTwister
>> /gate/random/setEngineSeed auto
>>
>> #===========================================================
>> # SOURCE
>> #===========================================================
>>
>> # fastY90
>> /gate/source/addSource y90 fastY90
>> /gate/source/y90/setActivity 1. MBq
>>
>> #=====================================================
>> # START
>> #=====================================================
>>
>> /gate/application/setTimeSlice 1. s
>> /gate/application/setTimeStart 0. s
>> /gate/application/setTimeStop 1000000. s
>>
>> /gate/application/start
>>
>>
>> Thanks a lot for your attention,
>>
>> Maria Inês
>>
>>
>>
>>
>>
>> _______________________________________________
>> Gate-users mailing list
>> Gate-users at lists.opengatecollaboration.org
>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>
>
>
>
>
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