<div dir="ltr"><div dir="ltr"><div><br></div><div>no averaging: edep is deposited at a given point position, then summed with all other edep in the voxel that include this point position. The output of the DoseActor is edep (or dose) in each voxel volume. Those voxel are the ones defined by the user in the DoseActor, sometimes called dosels or scoring voxels (NOT the voxels of an underlying CT image for example).</div><div dir="ltr"><br></div><div dir="ltr">More detail in the source code : <br><div><a href="https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateDoseActor.cc#L463">https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateDoseActor.cc#L463</a><br></div><div><br></div><div>or line : <a href="https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateDoseActor.cc#L549">https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateDoseActor.cc#L549</a></div><div><br></div><div>David</div><div><br></div></div></div></div><br><div class="gmail_quote"><div dir="ltr">On Tue, Jan 15, 2019 at 9:30 PM Josh Knowland <<a href="mailto:jknowland@lucernodynamics.com">jknowland@lucernodynamics.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div lang="EN-US">
<div class="gmail-m_-8566409208314345211WordSection1">
<p class="MsoNormal">All, I have made progress in using the dose output from the doseActor, but I still have a question about the overall use of it.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">If I have my 100mm x 100mm x 100mm cube of water and let’s say 1 Joule of energy is deposited into the first 50mm of one side. The dose for the entire cube would be 1J/1kg = 1 Gy.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Now, if I split the cube into two voxels, all the energy deposits into the first voxel and none into the second. Now the dose is:<u></u><u></u></p>
<p class="MsoNormal">1J/.5kg + 0J/.5kg = 2Gy+0Gy. Obviously, this sum of doses needs to be averaged over all the voxels.
<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">My question is, is this averaging already done by Gate in the doseActor? And if so, does it use all the voxels in the doseActor or only those which fall within the orgam geometry?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I do get different total dose for different voxel sizes, so I fear it is averaging over all the voxels.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thank you,<u></u><u></u></p>
<p class="MsoNormal">Josh<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><b>From:</b> Josh Knowland <br>
<b>Sent:</b> Tuesday, January 15, 2019 12:05 PM<br>
<b>To:</b> <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a><br>
<b>Subject:</b> RE: [Gate-users] Dose Actor Voxels?<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thank you David,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I think I am finally making sense of it. The problem, I believe, was that I was attempting to do this: (sum of all Edep) / (sum of all mass). It is not the same as calculating the dose for each voxel and then adding those.
<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I am getting agreement in calculations now, thank you!<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Josh<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><b>From:</b> David Sarrut <<a href="mailto:David.Sarrut@creatis.insa-lyon.fr" target="_blank">David.Sarrut@creatis.insa-lyon.fr</a>>
<br>
<b>Sent:</b> Tuesday, January 15, 2019 11:46 AM<br>
<b>To:</b> Ben Kopchick <<a href="mailto:kopchickbp@email.gwu.edu" target="_blank">kopchickbp@email.gwu.edu</a>><br>
<b>Cc:</b> Josh Knowland <<a href="mailto:jknowland@lucernodynamics.com" target="_blank">jknowland@lucernodynamics.com</a>>;
<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a><br>
<b>Subject:</b> Re: [Gate-users] Dose Actor Voxels?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<div>
<p class="MsoNormal">Hello<u></u><u></u></p>
</div>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">The dose actor do not consider anything except edep and mass in the given voxel, whatever the volume.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Dose is edep divided by mass. Consider edep to better understand your results ...<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">HTH,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">David <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
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<div>
<p class="MsoNormal">Le mar. 15 jans. 2019 à 17:34, Ben Kopchick <<a href="mailto:kopchickbp@email.gwu.edu" target="_blank">kopchickbp@email.gwu.edu</a>> a écrit :<u></u><u></u></p>
</div>
<blockquote style="border-top:none;border-right:none;border-bottom:none;border-left:1pt solid rgb(204,204,204);padding:0in 0in 0in 6pt;margin:5pt 0in 5pt 4.8pt">
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<p class="MsoNormal">Hi Josh,<u></u><u></u></p>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">In your original test, if you average the dose of the 1000 voxels do you get the same dose as the single voxel? I believe this should be the test as Dose (Gy) is dependent on the mass of the material.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Best,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Benjamin Kopchick<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<div>
<p class="MsoNormal">On Tue, Jan 15, 2019 at 11:25 AM Josh Knowland <<a href="mailto:jknowland@lucernodynamics.com" target="_blank">jknowland@lucernodynamics.com</a>> wrote:<u></u><u></u></p>
</div>
<blockquote style="border-top:none;border-right:none;border-bottom:none;border-left:1pt solid rgb(204,204,204);padding:0in 0in 0in 6pt;margin:5pt 0in 5pt 4.8pt">
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<div>
<p class="MsoNormal">To continue what I have found –
<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">The correct dose is not simply dividing by the total number of voxels in the doseActor. In fact, I have to divide by the total number of voxels in the union of the doseActor and
the geometry volume its attached to.<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">For instance, if I make my cube of water 100mm on a side, but make the doseActor 125mm on a side, I will only register dose within the volume of the cube. This makes sense – I should
register zero dose for those voxels outside of the water cube.<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">However, during dose calculation, the doseActor multiplies by the number of voxels that fell within the water cube. When using complex geometry from STL files, I can’t know this
number.<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">It seems the calculation would be fine if the doseActor is contained completely within your geometry, but how can you encompass an entire geometry (say, a liver organ modeled in
STL) using the rectangular solid doseActor? I can’t know exactly how many doseActor voxels actually fall within the liver.<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(225,225,225);padding:3pt 0in 0in">
<p class="MsoNormal"><b>From:</b> Josh Knowland
<br>
<b>Sent:</b> Tuesday, January 15, 2019 11:06 AM<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> RE: Dose Actor Voxels?<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Sorry, I had a typo. I meant:<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<ul type="disc">
<li class="gmail-m_-8566409208314345211m2523834079435268121gmail-m-5600038502538389230msolistparagraph">
Dose from doseActor seems to always <b>multiply</b> by the number of doseActor voxels. If I sum the dose output and then
<b>divide</b> by the number of voxels, I get the same as if I calculate dose from Edep.<u></u><u></u></li></ul>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(225,225,225);padding:3pt 0in 0in">
<p class="MsoNormal"><b>From:</b> Gate-users <<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>>
<b>On Behalf Of </b>Josh Knowland<br>
<b>Sent:</b> Tuesday, January 15, 2019 11:03 AM<br>
<b>To:</b> <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">
gate-users@lists.opengatecollaboration.org</a><br>
<b>Subject:</b> Re: [Gate-users] Dose Actor Voxels?<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Hi Matthew, thank you for the reply.<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Here is what I have done to try to verify the calculations:<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<ul type="disc">
<li class="gmail-m_-8566409208314345211m2523834079435268121gmail-m-5600038502538389230msolistparagraph">
Simulation of 1 liter of water hit with F18 positrons.<u></u><u></u></li><li class="gmail-m_-8566409208314345211m2523834079435268121gmail-m-5600038502538389230msolistparagraph">
Calculated dose three ways: <u></u><u></u></li></ul>
<ul type="disc">
<ul type="circle">
<li class="gmail-m_-8566409208314345211m2523834079435268121gmail-m-5600038502538389230msolistparagraph">
Summing Edep from Singles output and converting to Gray.<u></u><u></u></li><li class="gmail-m_-8566409208314345211m2523834079435268121gmail-m-5600038502538389230msolistparagraph">
Summing Edep from doseActor and converting to Gray.<u></u><u></u></li><li class="gmail-m_-8566409208314345211m2523834079435268121gmail-m-5600038502538389230msolistparagraph">
Summing dose from doseActor (already Gray).<u></u><u></u></li></ul>
</ul>
<ul type="disc">
<li class="gmail-m_-8566409208314345211m2523834079435268121gmail-m-5600038502538389230msolistparagraph">
Edep from Singles and summed Edep from doseActor always agree.<u></u><u></u></li><li class="gmail-m_-8566409208314345211m2523834079435268121gmail-m-5600038502538389230msolistparagraph">
Dose from doseActor seems to always divided by the number of doseActor voxels. If I sum the dose output and then multiply by the number of voxels, I get the same as if I calculate dose from Edep.<u></u><u></u></li></ul>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Can anyone explain this? When the dose map is already divided by voxel, why can’t I just sum all the voxels? I get the same results using VolumeWeighting or MassWeighting (of course,
I’m using 1 liter of water, so that’s the same.)<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Thank you all,<u></u><u></u></p>
<p class="MsoNormal">Josh<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(225,225,225);padding:3pt 0in 0in">
<p class="MsoNormal"><b>From:</b> Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" target="_blank">matthew.strugari@dal.ca</a>>
<br>
<b>Sent:</b> Tuesday, January 15, 2019 10:22 AM<br>
<b>To:</b> Josh Knowland <<a href="mailto:jknowland@lucernodynamics.com" target="_blank">jknowland@lucernodynamics.com</a>>;
<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a><br>
<b>Subject:</b> Re: Dose Actor Voxels?<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<div id="gmail-m_-8566409208314345211m_2523834079435268121gmail-m_-5600038502538389230divtagdefaultwrapper">
<p><span style="font-size:12pt;color:black">Hi Josh,</span><u></u><u></u></p>
<p><span style="font-size:12pt;color:black"> </span><u></u><u></u></p>
<p><span style="font-size:12pt;color:black">I am not entirely familiar on the behaviour of the doseActor, but it appears that the output dose is given as the dose per voxel. Hence, the same dose is deposited after integration in each case.</span><u></u><u></u></p>
<div id="gmail-m_-8566409208314345211m_2523834079435268121gmail-m_-5600038502538389230Signature">
<div id="gmail-m_-8566409208314345211m_2523834079435268121gmail-m_-5600038502538389230divtagdefaultwrapper">
<p style="background:white"><span style="font-size:12pt;color:black"><br>
Matthew</span><u></u><u></u></p>
</div>
</div>
</div>
<div class="MsoNormal" align="center" style="text-align:center">
<hr size="2" width="98%" align="center">
</div>
<div id="gmail-m_-8566409208314345211m_2523834079435268121gmail-m_-5600038502538389230divRplyFwdMsg">
<p class="MsoNormal"><b><span style="color:black">From:</span></b><span style="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 Josh Knowland <<a href="mailto:jknowland@lucernodynamics.com" target="_blank">jknowland@lucernodynamics.com</a>><br>
<b>Sent:</b> January 14, 2019 2:53:48 PM<br>
<b>To:</b> <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">
gate-users@lists.opengatecollaboration.org</a><br>
<b>Subject:</b> [Gate-users] Dose Actor Voxels?</span> <u></u><u></u></p>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
</div>
<div>
<div>
<p class="gmail-m_-8566409208314345211m2523834079435268121gmail-m-5600038502538389230xmsonormal">All,<u></u><u></u></p>
<p class="gmail-m_-8566409208314345211m2523834079435268121gmail-m-5600038502538389230xmsonormal"> <u></u><u></u></p>
<p class="gmail-m_-8566409208314345211m2523834079435268121gmail-m-5600038502538389230xmsonormal">Can you explain how the voxel size and number impacts the calculated dose by the doseActor?<u></u><u></u></p>
<p class="gmail-m_-8566409208314345211m2523834079435268121gmail-m-5600038502538389230xmsonormal">I have simulated a 1 liter cube of water containing 0.01 mCi of 18F positrons. When I enable the doseActor using 1000 voxels each 1cm^3, I get a total of
<b><span style="color:black">2.43E-05 Gy.</span></b><span style="color:black"> However, if I enable the doseActor using only 1 voxel of size 10cm^3, I get a dose of
<b>2.43E-02 Gy.</b> </span><u></u><u></u></p>
<p class="gmail-m_-8566409208314345211m2523834079435268121gmail-m-5600038502538389230xmsonormal"><span style="color:black"> </span><u></u><u></u></p>
<p class="gmail-m_-8566409208314345211m2523834079435268121gmail-m-5600038502538389230xmsonormal"><span style="color:black">I get the same total energy deposited no matter the voxel size and number, why not dose?</span><u></u><u></u></p>
</div>
</div>
</div>
</div>
<p class="MsoNormal">_______________________________________________<br>
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</blockquote>
</div>
<p class="MsoNormal">_______________________________________________<br>
Gate-users mailing list<br>
<a href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank">Gate-users@lists.opengatecollaboration.org</a><br>
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</blockquote>
</div>
</div>
<p class="MsoNormal">-- <u></u><u></u></p>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal">David Sarrut, Phd<br>
Directeur de recherche CNRS<br>
CREATIS, UMR CNRS 5220, Inserm U1206<u></u><u></u></p>
<div>
<p class="MsoNormal">Centre de lutte contre le cancer Léon Bérard<br>
28 rue Laënnec, 69373 Lyon cedex 08<br>
Tel : 04 78 78 51 51 / 06 74 72 05 42<br>
<a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a><br>
_________________________________<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> "2 + 2 = 5, for extremely large values of 2"<br>
_________________________________<u></u><u></u></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
_______________________________________________<br>
Gate-users mailing list<br>
<a href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank">Gate-users@lists.opengatecollaboration.org</a><br>
<a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" rel="noreferrer" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">David Sarrut, Phd<br>Directeur de recherche CNRS<br>CREATIS, UMR CNRS 5220, Inserm U1206<div>Centre de lutte contre le cancer Léon Bérard<br>28 rue Laënnec, 69373 Lyon cedex 08<br>Tel : 04 78 78 51 51 / 06 74 72 05 42<br><a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a><br>_________________________________</div><div> "2 + 2 = 5, for extremely large values of 2"<br>_________________________________</div></div></div></div></div></div></div>