[Gate-users] Filling an imported STL volume with a radionuclide

maxime maxime.chauvin at inserm.fr
Wed May 13 18:39:22 CEST 2020 

You’re welcome !

Nice, I had forgotten to tell you about the _phys :)

> On 13 May 2020, at 04:35, Steven Marsh <steven.marsh at canterbury.ac.nz> wrote:
> 
> Dear Maxime
>  
> Thank you for your response – it is much appreciated.
>  
> Based on your reply I have modified my code and it seems to be running well.  I include it below for others to use if needed or to comment on if necessary.  Please note, I likely need to more accurately place the encapsulating volume around the heart for my simulation – but the code should at least give others the idea.
>  
> Best wishes
> Steve
>  
> /gate/source/addSource src_Heart
> /gate/source/src_Heart/gps/energytype UserSpectrum
> /gate/source/src_Heart/gps/setSpectrumFile data/energy_spectrum_Tc99m.txt
> /gate/source/src_Heart/setForcedHalfLife  21624.12 s  #6.0 hrs
> /gate/source/src_Heart/setForcedUnstableFlag true
> /gate/source/src_Heart/setForcedHalfLife 21624.12 s
> /gate/source/src_Heart/setActivity 1.0 MBq
>  
> #Following defines a box which needs to encapsulate the heart
> /gate/source/src_Heart/gps/pos/type Volume
> /gate/source/src_Heart/gps/pos/shape Para
> /gate/source/src_Heart/attachTo heart  #Only really necessary if heart moving during simulation
> /gate/source/src_Heart/gps/pos/centre 0.000 0.000 0.000 mm 
> /gate/source/src_Heart/gps/pos/halfx 10.000 cm 
> /gate/source/src_Heart/gps/pos/halfy 30.000 cm 
> /gate/source/src_Heart/gps/pos/halfz 10.000 cm 
> # now confine this box shaped source to the heart.  (_phys essential in next line)
> /gate/source/src_Heart/gps/pos/confine heart_phys
>  
> /gate/source/src_Heart/gps/ang/type iso
>  
> From: maxime <maxime.chauvin at inserm.fr> 
> Sent: Tuesday, 12 May 2020 11:37 PM
> To: Steven Marsh <steven.marsh at canterbury.ac.nz>
> Cc: gate-users at lists.opengatecollaboration.org
> Subject: Re: [Gate-users] Filling an imported STL volume with a radionuclide
>  
> Dear Steven,
>  
> First, you are using correctly the stl to create a tesselated geometry of a heart.
>  
> But you are using a voxel source. A voxel source is intended for voxel geometries.
>  
> Instead here is what you should do:
> - use a GPS source with, shape, volume, energy, etc… For example a simple cube
> - attach it to the heart as you did (you can skip this if your heart will not move during the simulation)
> - place it correctly with respect to the STL coordinates (check with visu like OGL)
> - confine the source to heart: this final step is a trick to restrict the shape (cube) to the exact heart STL shape. So it is important that your simple shape (Cube, Sphere) is as close as possible but bigger than your heart.
>  
> For your second question, it could take a lot of time due to a side effect of your not correct source definition.
>  
> Best regards,
>   Maxime Chauvin
> 
> 
> On 12 May 2020, at 06:24, Steven Marsh <steven.marsh at canterbury.ac.nz> wrote:
>  
> Hi
>  
> Perhaps one of you can assist me…
>  
> My aim is to import, into my simulation, anatomy (in stl format – though I can change this if necessary) and fill the heart with Tc-99m. I want to assign a total amount of activity to the heart volume – i.e. ideally GATE will evenly spread the activity within the heart.
>  
> I have imported the anatomy - via the following:
>   
> /gate/phantom/daughters/name heart
> /gate/phantom/daughters/insert tessellated
> /gate/heart/geometry/setPathToSTLFile data/Heart.stl
> /gate/heart/setMaterial        Heart
>  
>  
> And I have hopefully filled the heart with Tc-99m via the following:
>  
> /gate/source/addSource source voxel
> /gate/source/source/gps/particle gamma
> /gate/source/source/gps/type Volume
> /gate/source/source/gps/angtype iso
> /gate/source/source/gps/energytype UserSpectrum
> /gate/source/source/gps/setSpectrumFile data/energy_spectrum_Tc99m.txt
> /gate/source/source/setForcedHalfLife  21624.12 s  #6.0 hrs
> /gate/source/source/setActivity 0.001 MBq
> /gate/source/source/attachTo heart
>  
> This (in addition to other code not given above) runs.
>  
> My questions are:
>  
> Firstly - is the above doing what I am hoping it will do?  Will this spread 0.001MBq evenly throughout the heart volume? 
>  
> Secondly - my code is running - though it is taking a very long time and is reporting it is up to run 4973100 with an elapsed time of 0.01 or so- does this relate to the release of primary photons - ie appx 5e6 photons have been released and tracked??
>  
> Any advice much appreciated
>  
> Best wishes
> Steve
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.opengatecollaboration.org
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>  
> 
> 
> On 12 May 2020, at 06:24, Steven Marsh <steven.marsh at canterbury.ac.nz> wrote:
>  
> Hi
>  
> Perhaps one of you can assist me…
>  
> My aim is to import, into my simulation, anatomy (in stl format – though I can change this if necessary) and fill the heart with Tc-99m. I want to assign a total amount of activity to the heart volume – i.e. ideally GATE will evenly spread the activity within the heart.
>  
> I have imported the anatomy - via the following:
>   
> /gate/phantom/daughters/name heart
> /gate/phantom/daughters/insert tessellated
> /gate/heart/geometry/setPathToSTLFile data/Heart.stl
> /gate/heart/setMaterial        Heart
>  
>  
> And I have hopefully filled the heart with Tc-99m via the following:
>  
> /gate/source/addSource source voxel
> /gate/source/source/gps/particle gamma
> /gate/source/source/gps/type Volume
> /gate/source/source/gps/angtype iso
> /gate/source/source/gps/energytype UserSpectrum
> /gate/source/source/gps/setSpectrumFile data/energy_spectrum_Tc99m.txt
> /gate/source/source/setForcedHalfLife  21624.12 s  #6.0 hrs
> /gate/source/source/setActivity 0.001 MBq
> /gate/source/source/attachTo heart
>  
> This (in addition to other code not given above) runs.
>  
> My questions are:
>  
> Firstly - is the above doing what I am hoping it will do?  Will this spread 0.001MBq evenly throughout the heart volume? 
>  
> Secondly - my code is running - though it is taking a very long time and is reporting it is up to run 4973100 with an elapsed time of 0.01 or so- does this relate to the release of primary photons - ie appx 5e6 photons have been released and tracked??
>  
> Any advice much appreciated
>  
> Best wishes
> Steve
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.opengatecollaboration.org
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users

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