[Gate-users] Regarding Voxelized Dosimetry
Arun Gupta
arunaiims1984 at gmail.com
Wed Jul 6 02:04:19 CEST 2016
Dear Loic,
Thank you for the reply. I am sorry that my reply was only sent to you.
Your advice is really appreciated.
Thank you.
Best Regards,
On Fri, Jul 1, 2016 at 7:03 PM, Grevillot Loic <loic.grevillot at medaustron.at
> wrote:
> Hello,
>
>
>
> Please always use the mailing-list so that everybody can benefit of the
> comments or provide new inputs.
>
> 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.
>
> At least I would do it like this…
>
> Does anyone has a better suggestion?
>
>
>
> Best,
>
> Loïc
>
>
>
>
>
>
>
> *From:* Arun Gupta [mailto:arunaiims1984 at gmail.com]
> *Sent:* Friday, July 01, 2016 11:14 AM
> *To:* Grevillot Loic
> *Subject:* Re: [Gate-users] Regarding Voxelized Dosimetry
>
>
>
> Dear Loic,
>
>
>
> Thank you very much for the reply.
>
> Actually I have used the Dose Actor for dose output file which is as
> follow.
>
>
> #=============================================================================
> # DOSE ACTOR
>
> #=============================================================================
>
> /gate/actor/addActor DoseActor doseDistribution
> /gate/actor/doseDistribution/attachTo mouse
> /gate/actor/doseDistribution/saveEveryNEvents 1000000
>
> /gate/actor/doseDistribution/stepHitType random
> /gate/actor/doseDistribution/setSize 43.86 43.86 95.03
> mm
> /gate/actor/doseDistribution/setPosition 0 0 0 cm
> /gate/actor/doseDistribution/setResolution 96 96 208
> /gate/actor/doseDistribution/enableEdep false
> /gate/actor/doseDistribution/enableUncertaintyEdep false
> /gate/actor/doseDistribution/enableSquaredEdep false
> /gate/actor/doseDistribution/enableDose true
> /gate/actor/doseDistribution/enableUncertaintyDose true
> /gate/actor/doseDistribution/enableSquaredDose false
> /gate/actor/doseDistribution/enableNumberOfHits false
> /gate/actor/doseDistribution/save output/mouse.hdr
>
> /gate/actor/addActor SimulationStatisticActor stat
> /gate/actor/stat/save output/stat-mouse1.txt
> /gate/actor/stat/saveEveryNSeconds 3600
>
> /gate/actor/resetAfterSaving 1
>
>
>
> The output as analyze file(.hdr/.img) for dose, Edep and uncertainty are
> obtained.
>
> 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.
>
> Then the total no. of ROs and the mean value per voxel were multiplied to
> get the absorbed dose of that organ in Gy.
>
> 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.
>
> 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?
>
> Is there ant other method for estimating the absorbed dose?
>
>
>
> Kindly give some suggestions.
>
>
>
> On Thu, Jun 30, 2016 at 8:22 PM, Grevillot Loic <
> loic.grevillot at medaustron.at> wrote:
>
> Hi,
>
>
>
> 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.
>
> If you score doses in none squared area, there might be some artifacts
> (not for energy).
>
> I never extracted doses to organs directly from Gate, but cannot you do
> that using some clinical software?
>
> Good luck,
>
> Loïc
>
>
>
> *From:* Gate-users [mailto:
> gate-users-bounces at lists.opengatecollaboration.org] *On Behalf Of *Arun
> Gupta
> *Sent:* Thursday, June 30, 2016 12:45 PM
> *To:* gate-users at lists.opengatecollaboration.org; sebastien.jan at cea.fr
> *Subject:* [Gate-users] Regarding Voxelized Dosimetry
>
>
>
> Dear all,
>
>
>
> 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. .
>
> 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.
>
> 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.
>
> 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.
>
> I used emstandard physics macro by defining the CUTS parameters but used
> manually.
>
> 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.
>
> I got the ouput dose map and uncertianity in dose for 8 simulations for 8
> PET scans.
>
> 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.
>
> 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.
>
> I would like to know how should I get the total absorbed dose of any organ
> in this case?
>
> The following are the macros I used.
>
> #===========================================================
> # VOXELIZED GEOMETRY
> #===========================================================
> # World
> /gate/world/geometry/setXLength 50 cm
> /gate/world/geometry/setYLength 50 cm
> /gate/world/geometry/setZLength 50 cm
> /gate/world/setMaterial Air
> #/gate/world/vis/setVisible 1
> #/gate/world/vis/forceWireframe
>
> ### Image Regular Parameterized volume
>
> /gate/world/daughters/name mouse
> /gate/world/daughters/insert ImageRegularParametrisedVolume
> /gate/mouse/geometry/setImage data/m000-CT_reorient.h33
> /gate/mouse/geometry/setRangeToMaterialFile data/Atten_Range.dat
>
> /gate/mouse/placement/setTranslation 0. 0. 0. mm
>
> /gate/mouse/attachPhantomSD
>
> #===========================================================
> # VOXELIZED SOURCE
> #===========================================================
>
> /gate/source/addSource PET_UCNP voxel
>
> /gate/source/PET_UCNP/reader/insert interfile
> /gate/source/PET_UCNP/interfileReader/translator/insert linear
> /gate/source/PET_UCNP/interfileReader/linearTranslator/setScale
> 0.0012725287 Bq
> /gate/source/PET_UCNP/interfileReader/readFile data/m003-UCNP_PET_1.h33
> /gate/source/PET_UCNP/setPosition -21.93 -21.93 -47.515 mm
>
> /gate/source/PET_UCNP/gps/particle ion
> /gate/source/PET_UCNP/gps/ion 29 64 0 0
> /gate/source/PET_UCNP/gps/energytype Mono
> /gate/source/PET_UCNP/gps/monoenergy 0. MeV
> /gate/source/PET_UCNP/setForcedUnstableFlag true
> /gate/source/PET_UCNP/setForcedHalfLife 45723.6 s
> /gate/source/PET_UCNP/dump 1
>
>
> ############################################################
> # PHYSICS
> ############################################################
>
> /gate/physics/addProcess PhotoElectric
> /gate/physics/processes/PhotoElectric/setModel StandardModel
>
> /gate/physics/addProcess Compton
> /gate/physics/processes/Compton/setModel StandardModel
>
> /gate/physics/addProcess RayleighScattering
> /gate/physics/processes/RayleighScattering/setModel PenelopeModel
>
> /gate/physics/addProcess GammaConversion
> /gate/physics/processes/GammaConversion/setModel StandardModel
>
> /gate/physics/addProcess ElectronIonisation
> /gate/physics/processes/ElectronIonisation/setModel StandardModel e-
> /gate/physics/processes/ElectronIonisation/setModel StandardModel e+
>
> /gate/physics/addProcess Bremsstrahlung
> /gate/physics/processes/Bremsstrahlung/setModel StandardModel e-
> /gate/physics/processes/Bremsstrahlung/setModel StandardModel e+
>
> /gate/physics/addProcess PositronAnnihilation
>
> /gate/physics/addProcess MultipleScattering e+
> /gate/physics/addProcess MultipleScattering e-
>
> ## In case of Ion source ##
>
> /gate/physics/addProcess IonIonisation
> /gate/physics/addProcess RadioactiveDecay
>
> /gate/physics/setEMin 0.1 keV
> /gate/physics/setEMax 10 GeV
>
> /gate/physics/processList Enabled
> /gate/physics/processList Initialized
>
> ############################################################
> # CUTS
> ############################################################
>
> /gate/physics/Gamma/SetCutInRegion world 0.1 mm
> /gate/physics/Electron/SetCutInRegion world 0.1 mm
> /gate/physics/Positron/SetCutInRegion world 0.1 mm
>
> /gate/physics/Gamma/SetCutInRegion mouse 0.01 mm
> /gate/physics/Electron/SetCutInRegion mouse 0.01 mm
> /gate/physics/Positron/SetCutInRegion mouse 0.01 mm
>
> /gate/physics/SetMaxStepSizeInRegion mouse 0.001 mm
>
> #===========================================================
> # RANDOM
> #===========================================================
>
> /gate/random/setEngineName MersenneTwister
>
> /gate/random/setEngineSeed default
> /gate/random/verbose 0
>
> #============================================================
> # START
> #===========================================================
>
> /gate/application/noGlobalOutput
>
> /gate/application/setTimeSlice 10 s
> /gate/application/setTimeStart 0 s
> /gate/application/setTimeStop 90 s
>
> /gate/application/startDAQ
>
> It will be highly appreciated if you help me in this case.
>
> Thank you.
>
>
>
> Arun Gupta
>
> Ph.D. Student
>
> Functional and Molecular Imaging System Lab
>
> Nuclear Medicine department
>
> College of Medicine
>
> Seoul National Univ. Hospital
>
> 103 Daehakro, Jongno-gu, Seoul, 110-799, Korea
>
>
>
>
>
> *Disclaimer:*
> Please notice our E-Mail Disclaimer
> http://www.medaustron.at/email-disclaimer/
>
>
>
>
>
>
> --
>
>
>
> Arun Gupta
>
> Ph.D. Student
>
> Functional and Molecular Imaging System Lab
>
> Nuclear Medicine department
>
> College of Medicine
>
> Seoul National Univ. Hospital
>
> 103 Daehakro, Jongno-gu, Seoul, 110-799, Korea
>
>
>
>
>
> *Disclaimer:*
> Please notice our E-Mail Disclaimer
> http://www.medaustron.at/email-disclaimer/
>
>
--
Arun Gupta
Ph.D. Student
Functional and Molecular Imaging System Lab
Nuclear Medicine department
College of Medicine
Seoul National Univ. Hospital
103 Daehakro, Jongno-gu, Seoul, 110-799, Korea
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