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Greetings,</div>
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Sorry, I explained myself poorly. level1 to level4 are okay. What I meant was to change level5 to either layer0 or layer1.</div>
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Bests,</div>
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Maxime Toussaint</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>De :</b> Zhengzhi Liu <zliu36@stanford.edu><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>
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<div dir="ltr">Hi Maxime,
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<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>
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<div><img alt="Screenshot from 2020-03-06 19-37-02.png" width="472" height="122" data-outlook-trace="F:1|T:1" src="cid:ii_k7h24whn2"><br>
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<div>Thank you very much sincerely.</div>
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<div>Zhengzhi </div>
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<div dir="ltr" class="x_gmail_attr">On Fri, Mar 6, 2020 at 7:04 PM Maxime Toussaint <<a href="mailto:Maxime.Toussaint@usherbrooke.ca">Maxime.Toussaint@usherbrooke.ca</a>> wrote:<br>
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Greetings,</div>
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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>
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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>
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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>
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Also, "PETscanner" is a valid system definition. I will propose a modification of the table 1.2 to make it more explicit.</div>
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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>
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Hope that I could help and have a nice day,</div>
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Maxime Toussaint</div>
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[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%7Ca971d6afd43c4d17ddde08d7c24949ce%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637191492338352392&sdata=0tnuCu9tvsChRVm3SDxUCDOJ9SpRttb70TPFsZ5VJaM%3D&reserved=0" originalsrc="https://github.com/OpenGATE/Gate/blame/cbe7ffb1c3222b5c1801eb7bc8b703253540e6b1/source/geometry/src/GateScannerSystem.cc" shash="B3eSdG4LKJgoObk5X7ohyq2mGzvYqlaTwTDUUnHAQEk++MIwhu/9RLuoKae2UEM3116ZqrteeBrgj0BepqpIac2l0Hl6p1G6+GB8kpGoJOOUTlLBrRZLq83X5YI/q1PumoNvbhv2B2YUqaFikkK+DIiDm88zNBmZ3sKRHuIZBsE=" target="_blank">https://github.com/OpenGATE/Gate/blame/cbe7ffb1c3222b5c1801eb7bc8b703253540e6b1/source/geometry/src/GateScannerSystem.cc</a></div>
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<div id="x_gmail-m_4358644349878560984divRplyFwdMsg" 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" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>>
de la part de Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" 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" target="_blank">zliu36@stanford.edu</a>>; 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</font>
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<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%7Ca971d6afd43c4d17ddde08d7c24949ce%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637191492338352392&sdata=%2BOyRHqqtKsH6tb6OA12YUa9MelxQnO%2B2Od%2FVliHcntM%3D&reserved=0" originalsrc="https://opengate.readthedocs.io/en/latest/defining_a_system_scanner_ct_pet_spect_optical.html#defining-the-systems" shash="O8GhEWHNu8nJFAM3ROVeg3qOuK14FrwEKqnziLHjBeufEbAcQLpstqdBAQrESBnkscxXJHymCdpeCRAY4HWjOhSoWNpQnEvLBN3Hy1DFcDaaHVATOMsac6ob5iGdK/W7pdbvfdH0m2uzW289RGjcN9XKNXh7m6VfhD1zBfUNTcw=" 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>
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<p>Regards,</p>
<p>Matthew</p>
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<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" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>>
on behalf of Zhengzhi Liu <<a href="mailto:zliu36@stanford.edu" 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" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
<b>Subject: </b>Re: [Gate-users] Report of GATEv8.2 bugs</span></p>
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<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.
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<p><img border="0" width="471" height="195" id="x_gmail-m_4358644349878560984x__x0000_i1026" style="width:4.9062in; height:2.0312in" data-outlook-trace="F:1|T:1" src="cid:170b30e7e204cff311"></p>
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<p>On Fri, Mar 6, 2020 at 3:17 PM Zhengzhi Liu <<a href="mailto:zliu36@stanford.edu" target="_blank">zliu36@stanford.edu</a>> wrote:</p>
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<p>Report of a potential bug: </p>
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<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>
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<p><img border="0" width="472" height="219" id="x_gmail-m_4358644349878560984x__x0000_i1025" style="width:4.9166in; height:2.2812in" data-outlook-trace="F:1|T:1" src="cid:170b30e7e205b16b22"></p>
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<p>Thanks for reading.</p>
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<p>Sincere greetings,</p>
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<p>Zhengzhi</p>
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