<div dir="ltr">Hi ! <div><br></div><div>thanks for reporting on that. Could you please add a summary of your findings as an issued in the github, please? (you can copy parts of the emails of course). It helps us a lot to keep track and correct issues. </div><div><br></div><div>We run a monthly meeting to discuss issues, maintenance and new features. Hopefully, someone will look at this soon.</div><div><br></div><div>thanks again for reporting, </div><div>David</div><div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">---------- Forwarded message ---------<br>From: <strong class="gmail_sendername" dir="auto">Maxime Toussaint</strong> <span dir="auto"><<a href="mailto:Maxime.Toussaint@usherbrooke.ca">Maxime.Toussaint@usherbrooke.ca</a>></span><br>Date: Tue, Nov 10, 2020 at 5:57 PM<br>Subject: Re: [Gate-users] Setting accolinearity with back to back source<br>To: <a href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a> <<a href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a>><br></div><br><br>
<div dir="ltr">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Geetings,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
First, my apologies <span style="color:rgb(0,0,0);background-color:rgb(255,255,255);display:inline!important">
Zhengzhi </span>for the late response. The NssMic conference took most of my time!</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Now about acolinearity. From my limited testing, my current conclusion is that the acolinearity feature of back-to-back source should not be used since its behavior seems wrong. Since the current Gate documentation does not describe how to use this feature,
it is fair to suspect that it is not currently officialy supported. If this is confirmed by the Gate developers, I will suggest a modification to the current Gate documentation to highlight this since it was a feature described in the past.</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
About your results, I suspect that the non-zero angles are due to numerical error. Back-to-back source are not affected, by default, by acolinearity in Gate. The source of the error is due, I believe, to using the hits/coincidence file. If memory serves me
right, some of the floats precision is lost when converted for these files. Also, it might be better to reconsider neglecting the effect of acolinearity due to the presence of scatter. While you might be right in a given system, I expect that it is not always
the case.</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Thank you <span style="color:rgb(0,0,0);background-color:rgb(255,255,255);display:inline!important">Zhengzhi</span> for taking the time to consider the problem I presented in my first mail.</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Bests,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Maxime Toussaint</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<br>
</div>
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<br>
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<div id="m_-1292912161393133967appendonsend"></div>
<hr style="display:inline-block;width:98%">
<div id="m_-1292912161393133967divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>De :</b> Gate-users <<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>> de la part de Albert Grace Lieu <<a href="mailto:albertnew2018@gmail.com" target="_blank">albertnew2018@gmail.com</a>><br>
<b>Envoyé :</b> 27 octobre 2020 20:24<br>
<b>À :</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>Cc :</b> Peter Olcott <<a href="mailto:polcott@reflexion.com" target="_blank">polcott@reflexion.com</a>><br>
<b>Objet :</b> Re: [Gate-users] Setting accolinearity with back to back source</font>
<div> </div>
</div>
<div>
<div dir="ltr">Dear Gate users,
<div><br>
</div>
<div>I apologize for my earlier false result regarding the accolinearity of the back-to-back gamma generator. Maxime's finding is correct that back-to-back gamma source default is linear and accolinearity is not enabled by default. </div>
<div><br>
</div>
<div>The reason why I came to the wrong conclusion is that I used a real PET system in GATE to conduct the simulation which involving much scattering. Now I updated my simulation with an ideal PET system to repeat the simulation, the result is shown below: </div>
<div>
<div><img alt="back-to-back angle distribution.PNG" width="558" height="397" src="cid:175d4fa7085818837f92"><br>
</div>
</div>
<div><br>
</div>
<div>My understanding is that whether to simulate the accolinearity of annihilation gammas or not is not a big deal in simulation as it can easily be counteracted by scattering, which always happens in a real system. Just in case someone would be interested
in this, I shared my personal finding and understanding here as well. </div>
<div><br>
</div>
<div>Thanks, Maxime.</div>
<div><br>
</div>
<div><br>
</div>
<div>Zhengzhi </div>
</div>
<br>
<div>
<div dir="ltr">On Mon, Oct 26, 2020 at 3:22 PM Albert Grace Lieu <<a href="mailto:albertnew2018@gmail.com" target="_blank">albertnew2018@gmail.com</a>> wrote:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Hi Maxime,
<div><br>
</div>
<div>I did a simple simulation to verify whether a back-to-back gamma generator creates colinear or accolinear gamma pairs. I used a point source with a single emission direction to generate back to back gammas in a cylindrical PET system (in GATE 8.2). Then
I collected hits file and coincidences file. I used valid coincidence event IDs to find its first hit position registered by the PET system (ideal resolution). Please note that I did not use any following commands:</div>
<blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><span style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;margin:0px"> /gate/source/NAME/setAccolinearityFlag true</span></div>
<div><span style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;margin:0px"> /gate/source/NAME/setAccoValue 0.5 deg</span> </div>
</blockquote>
<div><br>
</div>
<div>Here is what I found: </div>
<div>It looks back-to-back gamma source has accolinearity enabled by default. The mean is 5.5 degrees with and a standard deviation of 4.2. </div>
<div><img alt="Screenshot from 2020-10-26 14-58-32.png" width="523" height="404" src="cid:175d4fa70859ba4645d1"><br>
</div>
<div><br>
</div>
<div>My question is whether back-to-back gamma source has accolinearity enabled by default? Maybe I shall have looked into GateBackToBack.cc, however, source code might have compiled with other flags which I don't know of. </div>
<div><br>
</div>
<div>Thanks for your precious time answering. </div>
<div><br>
</div>
<div>Zhengzhi</div>
<div> <br>
</div>
</div>
<br>
<div>
<div dir="ltr">On Mon, Oct 26, 2020 at 10:59 AM Albert Grace Lieu <<a href="mailto:albertnew2018@gmail.com" target="_blank">albertnew2018@gmail.com</a>> wrote:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Hi Maxime,
<div><br>
</div>
<div>Thanks for sharing your findings regarding this accolineraity feature associated with the back-to-back gamma source. I did not see "setAccolinearityFlag" command in the GATE 8 and 9 manual either and am skeptical about its validity. May I know your conclusion
on the usage of accolineraity feature in GATE? Is it still supported or dead? How can one still possibly use it correctly?</div>
<div><br>
</div>
<div>Thanks a lot. </div>
<div><br>
</div>
<div>Sincere wishes,</div>
<div><br>
</div>
<div>Zhengzhi </div>
</div>
<br>
<div>
<div dir="ltr">On Wed, Jul 1, 2020 at 11:39 AM Maxime Toussaint <<a href="mailto:Maxime.Toussaint@usherbrooke.ca" target="_blank">Maxime.Toussaint@usherbrooke.ca</a>> wrote:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<div style="background-color:white;color:black">
<div>
<div>
<div dir="ltr">
<div style="font-size:12pt;font-family:Calibri,Arial,Helvetica,sans-serif;background-color:white">
<div style="background-color:white;margin:0px">Greetings,<br>
</div>
<div style="background-color:white;margin:0px"><br>
</div>
<div style="background-color:white;margin:0px">If one look<span><span>s</span></span> into the mailing list or in the Gate code, one can find that there is an option to simulate accolinearity from back to back source. The commands to use are as follow:</div>
<div style="background-color:white;margin:0px"><span style="margin:0px"> /gate/source/NAME/setAccolinearityFlag true<br>
</span><span style="margin:0px"> /gate/source/NAME/setAccoValue 0.5 deg</span></div>
<div style="background-color:white;margin:0px"><span style="margin:0px"><br>
</span></div>
<div style="background-color:white;margin:0px"><span style="margin:0px">In short, is this feature validated and still supported?<br>
</span></div>
<div style="background-color:white;margin:0px"><span style="margin:0px"><br>
</span></div>
<div style="background-color:white;margin:0px"><span style="margin:0px">In the following, I detail what I found from my search on that feature.</span></div>
<div style="background-color:white;margin:0px"><span style="margin:0px"><br>
</span></div>
<div style="background-color:white;margin:0px"><span style="margin:0px">This feature is not mentioned in the current openGate wiki (or at least, it was not found with the wiki search tool). I did a quick "cntrl+f" search of "setAccolinearityFlag" for the userguides
available from v6.0 to the last available and I did not found a single mention</span> of that keyword. However, if we look at the mailing list, we can find the following:</div>
<div style="background-color:white;margin:0px">
<ul>
<li>A possible bug was found in 2011 for which the resulting thread does not provide a clear conclusion about if the bug was corrected or if it was a real bug [1].<br>
</li><li>Around two years later, the feature was proposed to a user [4].</li><li>This feature seems to be still used currently [2, 3]. In [3], the user asked for some tips on the feature which were not answered.<br>
</li><li>From Gate v5.0 to v6.0, a bug was found and corrected [5, 6, 7].<br>
</li></ul>
</div>
<div style="background-color:white;margin:0px">I did try to look into the available release note of Gate and the Gate github but I did not find a mention about that feature.<br>
</div>
<div style="background-color:white;margin:0px"><br>
</div>
<div style="background-color:white;margin:0px">Currently, the option to test Gate with accolinearity validation does not work out-of-the-box with that feature. When I tried to activate the accollinearity error graph creation, the resulting graph indicated
pure back-to-back events. I have built some tests by hand[*] and it showed that a Gaussian angular error was indeed simulated which is good. However, when I compared the accolinearity error resulting from that feature to when using a positron source[**], the
profile were clearly different. The latter being Gaussian-like, as expected. It would seems that something unexpected happens when the angular error is applied to the gamma pairs momentum with that feature. While I did try to make sense of the code in the
method "GenerateVertex" of GateBacktoBack.cc, I must admit I fail to comprehend all the steps it does.<br>
</div>
<div style="background-color:white;margin:0px"><br>
</div>
<div style="background-color:white;margin:0px">Thus, it seems that this feature might have some problems or that it is not completely supported. If it is indeed the case, I will propose a modification to the wiki such that it mention the existence of that
feature but warns the users that it might not work as intended. If it should work, I will try to make a MWE of my tests and ask for validation.<br>
</div>
<div style="background-color:white;margin:0px"><br>
</div>
<div style="background-color:white;margin:0px">Best,<br>
Maxime Toussaint</div>
<div style="background-color:white;margin:0px"><br>
</div>
<div style="background-color:white;margin:0px"><br>
</div>
<div style="background-color:white;margin:0px">[1]<span> </span><a href="https://can01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.opengatecollaboration.org%2Fpipermail%2Fgate-users%2F2011-February%2F004842.html&data=04%7C01%7Cmaxime.toussaint%40usherbrooke.ca%7C601c25b9ff6f45dc134908d87ad7f8f9%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637394415312830884%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=%2BPXRSL%2FAd5VeEMEhFanBzwxkCYbhoezw1br7c96e9Ak%3D&reserved=0" rel="noopener noreferrer" title="URL d'origine : http://lists.opengatecollaboration.org/pipermail/gate-users/2011-February/004842.html. Cliquez ou appuyez si vous faites confiance à ce lien." style="margin:0px" target="_blank">http://lists.opengatecollaboration.org/pipermail/gate-users/2011-February/004842.html</a></div>
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<div style="background-color:white;margin:0px">[5]<span> </span><a href="https://can01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.opengatecollaboration.org%2Fpipermail%2Fgate-users%2F2010-November%2F004684.html&data=04%7C01%7Cmaxime.toussaint%40usherbrooke.ca%7C601c25b9ff6f45dc134908d87ad7f8f9%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637394415312850876%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=j914Rj8W%2FZu8Cpqpsggmn%2BvVAa2gC06puuwXwDQDU9Y%3D&reserved=0" rel="noopener noreferrer" title="URL d'origine : http://lists.opengatecollaboration.org/pipermail/gate-users/2010-November/004684.html. Cliquez ou appuyez si vous faites confiance à ce lien." style="margin:0px" target="_blank">http://lists.opengatecollaboration.org/pipermail/gate-users/2010-November/004684.html</a><br>
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<div style="background-color:white;margin:0px">[6]<span> </span><a href="https://can01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.opengatecollaboration.org%2Fpipermail%2Fgate-users%2F2010-November%2F004683.html&data=04%7C01%7Cmaxime.toussaint%40usherbrooke.ca%7C601c25b9ff6f45dc134908d87ad7f8f9%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637394415312860870%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=MdgU3JTcfxRcrbVlRD1mBdKkyNmM4zJfrdArBnHb4v8%3D&reserved=0" rel="noopener noreferrer" title="URL d'origine : http://lists.opengatecollaboration.org/pipermail/gate-users/2010-November/004683.html. Cliquez ou appuyez si vous faites confiance à ce lien." style="margin:0px" target="_blank">http://lists.opengatecollaboration.org/pipermail/gate-users/2010-November/004683.html</a><br>
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<div style="background-color:white;margin:0px">[7]<span> </span><a href="https://can01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.opengatecollaboration.org%2Fpipermail%2Fgate-users%2F2010-October%2F004599.html&data=04%7C01%7Cmaxime.toussaint%40usherbrooke.ca%7C601c25b9ff6f45dc134908d87ad7f8f9%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637394415312870860%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=EC27VOQzN3dj5ELzF26QO2XMlvHPcCAtDQjebZa%2BWiQ%3D&reserved=0" rel="noopener noreferrer" title="URL d'origine : http://lists.opengatecollaboration.org/pipermail/gate-users/2010-October/004599.html. Cliquez ou appuyez si vous faites confiance à ce lien." style="margin:0px" target="_blank">http://lists.opengatecollaboration.org/pipermail/gate-users/2010-October/004599.html</a></div>
<div style="background-color:white;margin:0px"><br>
</div>
<div style="background-color:white;margin:0px">[*] Outputting the "dev" variable from the file GateBacktoBack.cc</div>
<div style="background-color:white;margin:0px">[**] Outputting the momentum from the file GateBacktoBack.cc and GatePositronAnnihilation.cc, and extracting the photon pairs accolinearity.</div>
</div>
</div>
</div>
</div>
</div>
<br>
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<a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" rel="noreferrer" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="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></div></div>