[Gate-users] calculation of photon specific absorbed fraction

Matthew Strugari matthew.strugari at dal.ca
Wed Mar 16 18:48:09 CET 2022

What have you attempted so far? And are you using the Digimouse F-18/FDG source distribution or your own distribution? This will determine how you setup your source macro.

Given that the USC group<https://neuroimage.usc.edu/neuro/Digimouse> provides PET, CT, cryosection, and atlas data for the Digimouse, you have a couple of options centered around a voxelized source distribution<https://opengate.readthedocs.io/en/latest/voxelized_source_and_phantom.html?highlight=voxel%20source#example-of-voxelized-source-description-macro>. The hyperlinked source description includes lines for setting up your monoenergetic emissions.

  1.  The PET distribution could be used as your source distribution if you were interested in calculating the SAFs for the specific Digimouse PET acquisition. This would require inserting the PET image for your source then utilizing the linear translator to scale all PET voxel values directly into activities.
  2.  If you were using your own source distribution, and assuming a uniform distribution in your organ of interest, you could use the atlas to define your source organs. This would require inserting the atlas image for your source then utilizing the range translator to convert discretized intervals, i.e. an organ of interest, into activities. You would then need to run a simulation considering the activity in each organ independently.

For determining energy deposition, you’ll need to record your particle interactions in your phantom which requires a similar approach for importing a voxelized phantom<https://opengate.readthedocs.io/en/latest/voxelized_source_and_phantom.html?highlight=voxelized#example-of-voxelized-phantom-description-macro>.

  1.  The CT image could be used as your phantom. This would require inserting the CT image and providing an HUToMaterial file to convert CT values to materials. This can get pretty hairy when accurately converting the CT values to a specific material.
  2.  The atlas could be used as your phantom. This would be the simplest approach given that the atlas is already nicely segmented. Here, you would use a RangeToMaterial file to convert discretized intervals, i.e. an organ of interest, into a material. The Digimouse webpage already categorizes the atlas tissues into the material types suitable for simulation.

>From there, you would likely want to use the DoseActor<https://opengate.readthedocs.io/en/latest/tools_to_interact_with_the_simulation_actors.html?highlight=doseactor#dose-measurement-doseactor> to score the energy deposited. Altogether, this would provide you with all the info necessary for calculating the SAFs.


Matthew Strugari
PhD Candidate at Biomedical Translational Imaging Centre - BIOTIC,
5890 University Ave, Halifax, NS, B3K 6R8

From: ABDELLAH KITANI <abdellah.kitani at etu.uae.ac.ma>
Date: Wednesday, March 16, 2022 at 13:18
To: Matthew Strugari <matthew.strugari at dal.ca>
Subject: Re: [Gate-users] calculation of photon specific absorbed fraction
CAUTION: The Sender of this email is not from within Dalhousie.
Thank you very much. I use digimouse phantom , but i need to reapply the example on gate but my problem is with the source , what should i do in the file source.mac ,, the organs  cible are the same as the organs cible ,

Le mer. 16 mars 2022 à 14:46, Matthew Strugari <matthew.strugari at dal.ca<mailto:matthew.strugari at dal.ca>> a écrit :

If you’re only after the SAF values, I would take a look at OpenDose<https://opendose.org/>. You can find SAFs (and other great information) for the ICRP 110 adult phantoms there which were already calculated with GATE. I’m not sure of your specific application but this would be the fastest route, unless you wanted to setup your own simulations to calculate SAFs for some other custom use case. Then I would checkout the GATE docs and the methods used by the OpenDose collaboration for your application.


From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org<mailto:gate-users-bounces at lists.opengatecollaboration.org>> on behalf of ABDELLAH KITANI <abdellah.kitani at etu.uae.ac.ma<mailto:abdellah.kitani at etu.uae.ac.ma>>
Date: Monday, March 14, 2022 at 11:13
To: gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org> <gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>>
Subject: [Gate-users] calculation of photon specific absorbed fraction
CAUTION: The Sender of this email is not from within Dalhousie.
Hello, dear users .

I need to apply this example on Gate if anyone can help. I need to calculat the  SAF values for monoenergetic photons of energies 25, 30, 200, 500  and 2000 keV were evaluated for the voxel ghost embedded in the Monte Carlo code. The source organs considered in this study were the lungs, skeleton, spleen, pancreas, adrenals, eyes and brain. The target organs considered were the lungs, the skeleton, the spleen, the pancreas, the adrenals and the brain. The eye was considered as the target organ only for the eye as the source organ

thank you so much
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