<div dir="ltr">Hi Maxime, <div><br></div><div>Thanks for reading my email and looking into it. Thanks for confirming the legitimacy of my doubt. I wish it would allow users to use TakeEnergyCentroid. </div><div><br></div><div>Please allow me to rephrase my sentences as follows:</div><div>In my system, each crystal is coupled to a single readout channel. In order to align my simulated system with my real system, I wanted to register the center of each crystal in Gate then to compare it with that of my real system, for which I have already got the data. The way I can think of to achieve the measurement of crystal center location in Gate is by using TakeEnergyCentroid and setting readout depth to crystal level. </div><div><br></div><div>To be short, Yes, I want the spatial position of my crystals. </div><div><br></div><div><br></div><div>Thanks for your time and wisdom. </div><div><br></div><div>Warmest regards,</div><div>Zhengzhi </div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Mar 11, 2020 at 8:43 AM Maxime Toussaint <<a href="mailto:Maxime.Toussaint@usherbrooke.ca">Maxime.Toussaint@usherbrooke.ca</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 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)">
Greetings,</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)">
The documentation claim that this policy is applied relative to a "crystal" component. Since PetScanner configuration do not possess that component, it make sense that it will not work. W<span style="font-size:12pt">hen in doupt, the code can't(Most of the
time) lie. In [1], you can see that the "crystal" component is required. I have no idea why, however.</span></div>
<div style="background-color:rgb(255,255,255);color:rgb(0,0,0)"><font face="Calibri, Arial, Helvetica, sans-serif"><span style="font-size:12pt"><br>
</span></font></div>
<div style="background-color:rgb(255,255,255);color:rgb(0,0,0)"><font face="Calibri, Arial, Helvetica, sans-serif"><span style="font-size:12pt">Also, i am not sure I understand the following: "<span style="font-size:15px;color:rgb(0,0,0);background-color:rgb(255,255,255);display:inline">Basically,
what I am trying to achieve is to measure the location of each crystal center since each crystal is coupled to a single readout PMT/readout channel in my design.</span>" You want to know the spatial position of your crystals?</span></font></div>
<div style="background-color:rgb(255,255,255);color:rgb(0,0,0)"><font face="Calibri, Arial, Helvetica, sans-serif"><span style="font-size:12pt"><br>
</span></font></div>
<div style="background-color:rgb(255,255,255);color:rgb(0,0,0)"><font face="Calibri, Arial, Helvetica, sans-serif"><span style="font-size:12pt">Have a nice day,</span></font></div>
<div style="background-color:rgb(255,255,255);color:rgb(0,0,0)"><font face="Calibri, Arial, Helvetica, sans-serif"><span style="font-size:12pt">Maxime Toussaint</span></font></div>
<div style="background-color:rgb(255,255,255);color:rgb(0,0,0)"><font face="Calibri, Arial, Helvetica, sans-serif"><span style="font-size:12pt"><br>
</span></font></div>
<div style="background-color:rgb(255,255,255);color:rgb(0,0,0)"><font face="Calibri, Arial, Helvetica, sans-serif"><span style="font-size:12pt"><br>
</span></font></div>
<div style="background-color:rgb(255,255,255);color:rgb(0,0,0)"><font face="Calibri, Arial, Helvetica, sans-serif"><span style="font-size:12pt">[1] <a href="https://github.com/OpenGATE/Gate/blob/f2d9a5e19d568c71fe11b64a05d4f6037a208841/source/digits_hits/src/GateReadout.cc" target="_blank">https://github.com/OpenGATE/Gate/blob/f2d9a5e19d568c71fe11b64a05d4f6037a208841/source/digits_hits/src/GateReadout.cc</a></span></font></div>
<div style="background-color:rgb(255,255,255);color:rgb(0,0,0)"><font face="Calibri, Arial, Helvetica, sans-serif"><br>
</font></div>
<div id="gmail-m_-3475326582305663163appendonsend"></div>
<hr style="display:inline-block;width:98%">
<div id="gmail-m_-3475326582305663163divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>De :</b> Zhengzhi Liu <<a href="mailto:zliu36@stanford.edu" target="_blank">zliu36@stanford.edu</a>><br>
<b>Envoyé :</b> 9 mars 2020 20:34<br>
<b>À :</b> 강한규 <<a href="mailto:lovehangulp@naver.com" target="_blank">lovehangulp@naver.com</a>>; Maxime Toussaint <Maxime.Toussaint@USherbrooke.ca><br>
<b>Cc :</b> gate-users <<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
<b>Objet :</b> Re: [Gate-users] Report of GATEv8.2 bugs (PETscanner "level5" is NOT working)</font>
<div> </div>
</div>
<div>
<div dir="ltr">A follow-up question, does PETScanner work with TakeEnergyCentroid policy?
<div><br>
</div>
<div>In my simulation using the PETScanner system, everything works fine and it has been validated to a certain degree. However, soon as I switched to TakeEnergyCentroid policy, no matter what the readout depth is, the core dumped. The error message is shown
in the screenshot below. According to the error message, it looks like it was trying to find the system component "crystal", however, "crystal" is not defined in the PETScanner/scanner as shown in its hierarchy below. </div>
<div><br>
</div>
<div>Basically, what I am trying to achieve is to measure the location of each crystal center since each crystal is coupled to a single readout PMT/readout channel in my design. The way I can think of is setting the readout depth to crystal level and using
TakeEnergyCentroid policy, however, it crashes in the PETScanner system. </div>
<div><br>
</div>
<div>Any suggestions? Is PETScanner compatible with akeEnergyCentroid policy? Or I have messed something up.</div>
<div><br>
</div>
<div>Thank you very much for help.</div>
<div><br>
</div>
<div>Zhengzhi </div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
<br>
<div>
<div dir="ltr">On Sat, Mar 7, 2020 at 2:48 PM Zhengzhi Liu <<a href="mailto:zliu36@stanford.edu" target="_blank">zliu36@stanford.edu</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">Dr. Han Gyu,
<div><br>
</div>
<div>Thank you for your detailed explanation and for showing us your excellent work. You have been a great help to many GATE users (like me) in this community. </div>
<div>Thank you very much and look forward to meeting you in person in future conferences.</div>
<div><br>
</div>
<div>Sincerely,</div>
<div>Zhengzhi </div>
</div>
<br>
<div>
<div dir="ltr">On Fri, Mar 6, 2020 at 10:25 PM 강한규 <<a href="mailto:lovehangulp@naver.com" target="_blank">lovehangulp@naver.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>
<div style="font-size:10pt;font-family:Gulim,sans-serif">
<p>Dear Zhengzhi and Maxime,</p>
<p> </p>
<p>Recently, I have been busy so I was not able to answer your questions.</p>
<p><span style="font-size:10pt"> </span></p>
<p><span style="font-size:10pt">I also experienced that the <b>"level5" is NOT working for "PETscanner" in GATEv6.2</b>.(slide#3-4)</span> </p>
<p>The solution was <b>to attach the "layer1"</b> to the 4th layer crystal as Maxime mentioned.</p>
<p> </p>
<p>Attached is my work about GATEv6.2 simulation for <b>staggered 4-layer DOI PET scanner</b>.</p>
<p><img src="cid:170ca4b3647a87ef7d24"> </p>
<p> </p>
<p> </p>
<p>After GATE simulation and image reconstruction, I obtained the PET image successfully.(slide#5-11)</p>
<p>The GATE output and crystal ID information are summarized.(slide#12-18)</p>
<p> </p>
<p>By the way, if you want more layers, then you can use just "genericRepeater". </p>
<p>In doing so you can place the crystal array whatever you like.</p>
<p>In this case, you need two system attachments as below.</p>
<p>-level1 (for PET block)</p>
<p>-level2 (for crystal with genericRepeater)</p>
<p> </p>
<p>Hopefully, my answer would be helpful for your works.</p>
<p> </p>
<p>Best regards,</p>
<p> </p>
<p>Han Gyu</p>
<p> </p>
<p> </p>
--------Han Gyu Kang, Ph.D, Researcher<br>
<br>
National Institute of Radiological Sciences (NIRS)<br>
National Institutes for Quantum and Radiological Science and Technology (QST)<br>
4-9-1 Anagawa, Inage-ku, Chiba 263-8555, JAPAN
<p> </p>
<p style="font-size:10pt;font-family:sans-serif;padding:0px 0px 0px 10pt"><span>-----Original Message-----</span><br>
<b>From:</b> "Maxime Toussaint"<Maxime.Toussaint@USherbrooke.ca> <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>Cc:</b> <br>
<b>Sent:</b> 2020-03-07 (토) 12:46:38 (GMT+09:00)<br>
<b>Subject:</b> Re: [Gate-users] Report of GATEv8.2 bugs<br>
</p>
<u></u>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Greetings,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Sorry, I explained myself poorly. level1 to level4 are okay. What I meant was to change level5 to either layer0 or layer1.</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
</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>
<hr style="display:inline-block;width:98%">
<div dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>De :</b> Zhengzhi Liu <<a href="mailto:zliu36@stanford.edu" target="_blank">zliu36@stanford.edu</a>><br>
<b>Envoyé :</b> 6 mars 2020 22:39<br>
<b>À :</b> Maxime Toussaint <Maxime.Toussaint@USherbrooke.ca><br>
<b>Objet :</b> Re: [Gate-users] Report of GATEv8.2 bugs</font>
<div> </div>
</div>
<div>
<div dir="ltr">Hi Maxime,
<div> </div>
<div>Thank you very much as well. I tried your suggestion of replacing level1 to level5 with layer0 to layer4 in PETScaner. It failed at layer2 and does not allow me to add layer2 and later layers. It worked fine with 2layers. Could you please verify this with
your code by adding some simple dummy layers to your code? </div>
<div>Here is the errormsg: </div>
<div>
<div><img alt="Screenshot from 2020-03-06 19-37-02.png" width="472" height="122" src="cid:170ca4b3647684830c63"><br>
</div>
</div>
<div> </div>
<div>Thank you very much sincerely.</div>
<div> </div>
<div>Zhengzhi </div>
</div>
<br>
<div>
<div dir="ltr">On Fri, Mar 6, 2020 at 7:04 PM Maxime Toussaint <<a href="mailto:Maxime.Toussaint@usherbrooke.ca" rel="noreferrer noopener" 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)">
Greetings,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
I quickly looked at the code and I think I found the problem. In short, the documentation is correct for the current version of the Gate code on github but not for Gate 8.2.</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
If we look at [1], we see that a change was made from having PETscanner/scanner system with components called layer0/layer1 to one called level5. That change was committed the 9th of May 2019 while Gate 8.2 seems to be a Februray 2019 version of the code.</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
I tried using layer0 (and later layer1) and Gate did not produce any warning nor bug. Note that this does not prove that the resulting system work. </div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Also, "PETscanner" is a valid system definition. I will propose a modification of the table 1.2 to make it more explicit.</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
This situation does highlight a little problem. From my understanding, the current version of the user guide follow the code on github but it is also used for the current stable version of Gate (8.2 at the moment). If I am correct, I would propose that a version
of the user guide, extracted at the same time as the official version, be saved separately from the "latest" and a note added saying something like "correction to the user guide are only applied on the latest version". After all, we can't expect anyone to
adapt all versions of the user guide each time the user guide is enhanced. </div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Hope that I could help and have a nice day,</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)">
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
[1] <a href="https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FOpenGATE%2FGate%2Fblame%2Fcbe7ffb1c3222b5c1801eb7bc8b703253540e6b1%2Fsource%2Fgeometry%2Fsrc%2FGateScannerSystem.cc&data=02%7C01%7CMaxime.Toussaint%40usherbrooke.ca%7C7c194e0ad8b8458980d208d7c48ae8d6%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637193973212126017&sdata=L%2B6wmzXNj%2BY5CEAxtwyT9T5QLqOgteVaFv3O%2FhIfdcA%3D&reserved=0" rel="noreferrer noopener" target="_blank">https://github.com/OpenGATE/Gate/blame/cbe7ffb1c3222b5c1801eb7bc8b703253540e6b1/source/geometry/src/GateScannerSystem.cc</a></div>
<hr style="display:inline-block;width:98%">
<div dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>De :</b> Gate-users <<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" rel="noreferrer noopener" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>>
de la part de Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" rel="noreferrer noopener" target="_blank">matthew.strugari@dal.ca</a>><br>
<b>Envoyé :</b> 6 mars 2020 20:57<br>
<b>À :</b> Zhengzhi Liu <<a href="mailto:zliu36@stanford.edu" rel="noreferrer noopener" target="_blank">zliu36@stanford.edu</a>>; gate-users <<a href="mailto:gate-users@lists.opengatecollaboration.org" rel="noreferrer noopener" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
<b>Objet :</b> Re: [Gate-users] Report of GATEv8.2 bugs</font>
<div> </div>
</div>
<div lang="EN-CA">
<div>
<p><span lang="EN-US">Hi Zhengzhi,</span></p>
<p><span lang="EN-US"> </span></p>
<p><span lang="EN-US">According to the user manual (Section 1.5.1 </span><a href="https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fopengate.readthedocs.io%2Fen%2Flatest%2Fdefining_a_system_scanner_ct_pet_spect_optical.html%23defining-the-systems&data=02%7C01%7CMaxime.Toussaint%40usherbrooke.ca%7C7c194e0ad8b8458980d208d7c48ae8d6%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637193973212126017&sdata=pKVc7m0txcRWujIUCIAbhUzqmwyonTNuM9ToKD7MbFo%3D&reserved=0" rel="noreferrer noopener" target="_blank">https://opengate.readthedocs.io/en/latest/defining_a_system_scanner_ct_pet_spect_optical.html#defining-the-systems</a>),
the system name must be one of those available in Table 1.1. In the image you provided, this would be Table 4.1. I’m not sure which version of the user manual you are referring to, but the most up to date information can be found on readthedocs. Nonetheless,
your error of COMMAND NOT FOUND shows that you defined the system name to be PETscanner which is not a valid system name. Replace “PETscanner” with “scanner” and you should be able to assign level5 with the defined functionality.</p>
<p> </p>
<p>Regards,</p>
<p>Matthew</p>
<p><span lang="EN-US"> </span></p>
<div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(181,196,223);padding:3pt 0cm 0cm">
<p><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" rel="noreferrer noopener" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>>
on behalf of Zhengzhi Liu <<a href="mailto:zliu36@stanford.edu" rel="noreferrer noopener" target="_blank">zliu36@stanford.edu</a>><br>
<b>Date: </b>Friday, March 6, 2020 at 7:30 PM<br>
<b>To: </b>gate-users <<a href="mailto:gate-users@lists.opengatecollaboration.org" rel="noreferrer noopener" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
<b>Subject: </b>Re: [Gate-users] Report of GATEv8.2 bugs</span></p>
</div>
<div>
<p> </p>
</div>
<div>
<p>According to the user manual, 5 levels can be attached. However, I am not able to attach any 5th level. Please share your thoughts if you have some experience. Thanks a lot.
</p>
<div>
<p> </p>
</div>
<div>
<p> </p>
<div>
<p><img border="0" width="471" height="195" style="width: 4.9062in; height: 2.0312in;" src="cid:170ca4b36464cff311"></p>
</div>
</div>
</div>
<p> </p>
<div>
<div>
<p>On Fri, Mar 6, 2020 at 3:17 PM Zhengzhi Liu <<a href="mailto:zliu36@stanford.edu" rel="noreferrer noopener" target="_blank">zliu36@stanford.edu</a>> wrote:</p>
</div>
<blockquote style="border-top:none;border-right:none;border-bottom:none;border-left:1pt solid rgb(204,204,204);padding:0cm 0cm 0cm 6pt;margin-left:4.8pt;margin-right:0cm">
<div>
<p>Report of a potential bug: </p>
<div>
<p> </p>
</div>
<div>
<p>It looks PETScanner only allows 4 layers to be attached, whenever I tried to attach the 5th layer (no matter what the geometry is), it throws the errormsg. Has anyone been able to attach a 5 level to PETScanner? My understanding is Gate doesn't recognize
the keyword <b>level5</b>. </p>
</div>
<div>
<p> </p>
</div>
<div>
<p><img border="0" width="472" height="219" style="width: 4.9166in; height: 2.2812in;" src="cid:170ca4b36475b16b22"></p>
</div>
<div>
<p>Thanks for reading.</p>
</div>
<div>
<p> </p>
</div>
<div>
<p>Sincere greetings,</p>
</div>
<div>
<p>Zhengzhi</p>
</div>
</div>
</blockquote>
</div>
</div>
</div>
</div>
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