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You’re welcome. Make sure to keep gate-users in the thread when responding to emails so information does not get lost.
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<div>I would recommend the voxelized source as outlined in my previous email. </div>
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<div>Good luck with GATE! Let us know if you have any other questions.<br>
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<div dir="ltr">Matthew</div>
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<blockquote type="cite">On Mar 16, 2022, at 5:37 PM, KHAOULA LAAZOUZI <khaoula.laazouzi@etu.uae.ac.ma> wrote:<br>
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<div dir="ltr">actually we are trying to reapply an <a href="https://www.sciencedirect.com/science/article/abs/pii/S0969806X21000104">
article</a> with openGate ,, we are beginners ,, right now we could use the <font size="2">
<span class="gmail-markedContent" id="gmail-page39R_mcid0"><span style="font-family:sans-serif" role="presentation" dir="ltr">Atlas Digimouse phantom</span></span></font> and we used density and materials of each organ from icrp110 ,, but for the source we
don't know what should we do in this part , thank you so much for you time <br>
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<div dir="ltr" class="gmail_attr">Le mer. 16 mars 2022 à 18:48, Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca">matthew.strugari@dal.ca</a>> a écrit :<br>
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<p class="MsoNormal"><span lang="EN-US">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.
<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">Given that the <a href="https://neuroimage.usc.edu/neuro/Digimouse" target="_blank">
USC group</a> provides PET, CT, cryosection, and atlas data for the Digimouse, you have a couple of options centered around a
<a href="https://opengate.readthedocs.io/en/latest/voxelized_source_and_phantom.html?highlight=voxel%20source#example-of-voxelized-source-description-macro" target="_blank">
voxelized source distribution</a>. The hyperlinked source description includes lines for setting up your monoenergetic emissions.<u></u><u></u></span></p>
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<li class="gmail-m_-3958571401283202876MsoListParagraph" style="margin-left:0cm">
<span lang="EN-US">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.<u></u><u></u></span></li><li class="gmail-m_-3958571401283202876MsoListParagraph" style="margin-left:0cm">
<span lang="EN-US">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.<u></u><u></u></span></li></ol>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">For determining energy deposition, you’ll need to record your particle interactions in your phantom which requires a similar approach for importing a
<a href="https://opengate.readthedocs.io/en/latest/voxelized_source_and_phantom.html?highlight=voxelized#example-of-voxelized-phantom-description-macro" target="_blank">
voxelized phantom</a>.<u></u><u></u></span></p>
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<li class="gmail-m_-3958571401283202876MsoListParagraph" style="margin-left:0cm">
<span lang="EN-US">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.<u></u><u></u></span></li><li class="gmail-m_-3958571401283202876MsoListParagraph" style="margin-left:0cm">
<span lang="EN-US">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.<u></u><u></u></span></li></ol>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">From there, you would likely want to use the
<a href="https://opengate.readthedocs.io/en/latest/tools_to_interact_with_the_simulation_actors.html?highlight=doseactor#dose-measurement-doseactor" target="_blank">
DoseActor</a> to score the energy deposited. Altogether, this would provide you with all the info necessary for calculating the SAFs.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">Regards,<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">Matthew</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:-webkit-standard;color:black"> </span><span style="color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:-webkit-standard;color:black">--</span><span style="color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:-webkit-standard;color:black">Matthew Strugari<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:-webkit-standard;color:black">PhD Candidate</span><span style="color:black"> at
</span><span style="font-size:10.5pt;font-family:-webkit-standard;color:black" lang="EN-US">Biomedical Translational Imaging Centre - BIOTIC,<br>
5890 University Ave, Halifax, NS, B3K 6R8</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
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<p class="MsoNormal" style="margin-bottom:12pt"><b><span style="font-size:12pt;color:black">From:
</span></b><span style="font-size:12pt;color:black">ABDELLAH KITANI <<a href="mailto:abdellah.kitani@etu.uae.ac.ma" target="_blank">abdellah.kitani@etu.uae.ac.ma</a>><br>
<b>Date: </b>Wednesday, March 16, 2022 at 13:18<br>
<b>To: </b>Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" target="_blank">matthew.strugari@dal.ca</a>><br>
<b>Subject: </b>Re: [Gate-users] calculation of photon specific absorbed fraction<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="color:white">Thank you very much. I use digimouse phantom , but i need to reapply the example on gate but my problem is with the sou</span>rce , what should i do in the file source.mac ,, the organs cible are the same as the
organs cible , <u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Le mer. 16 mars 2022 à 14:46, Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" target="_blank">matthew.strugari@dal.ca</a>> a écrit :<u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:10pt;font-family:"Arial",sans-serif;color:black">Hello,</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:10pt;font-family:"Arial",sans-serif;color:black"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:10pt;font-family:"Arial",sans-serif;color:black">If you’re only after the SAF values, I would take a look at
<a href="https://opendose.org/" target="_blank">OpenDose</a>. 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.</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:10pt;font-family:"Arial",sans-serif;color:black"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:10pt;font-family:"Arial",sans-serif;color:black">Cheers,</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:10pt;font-family:"Arial",sans-serif;color:black">Matthew</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US"> </span><u></u><u></u></p>
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<p class="MsoNormal" style="margin-bottom:12pt"><b><span style="font-size:12pt;color:black">From:
</span></b><span style="font-size:12pt;color:black">Gate-users <<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>> on behalf of ABDELLAH KITANI <<a href="mailto:abdellah.kitani@etu.uae.ac.ma" target="_blank">abdellah.kitani@etu.uae.ac.ma</a>><br>
<b>Date: </b>Monday, March 14, 2022 at 11:13<br>
<b>To: </b><a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a> <<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
<b>Subject: </b>[Gate-users] calculation of photon specific absorbed fraction</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="color:white">Hello, dear users . </span><br>
<br>
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 <br>
<br>
thank you so much <u></u><u></u></p>
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