<div dir="ltr"><div class="gmail_attr" style="color:rgb(80,0,80)"><span style="color:rgb(0,0,0)">Hi Matthew,</span><br></div><div class="gmail_attr" style="color:rgb(80,0,80)"><span style="color:rgb(0,0,0)"><br></span></div><div class="gmail_attr"><font color="#000000">First, thank you very much for your suggestion. I am using Users Guide V8.0. I learned the system type <b>PETScanner</b> from previous gate user group correspondence which is forwarded below. Actually, PETScanner is a valid PET system in GATE. Because of the problem of coincidence with other types of PET system under certain conditions (I will raise this bug later separately), PETScanner is my only valid option. I have been using </font><b>PETScanner</b><font color="#000000"> for quite a while in GATE v8.2. The only problem I have with PETScanner is that it does not allow me to add any 5th level to the system. It looks like that level5 is not defined in PETScanner. </font></div><div class="gmail_attr"><font color="#000000"><br></font></div><div class="gmail_attr"><font color="#000000">As to changing PETScanner to <b>scanner</b>, it indeed allows me to add the 5th layer. However, it does not allow using any coincidence flags.</font><img src="cid:ii_k7h1dxts2" alt="Screenshot from 2020-03-06 19-16-16.png" width="472" height="129"></div><div class="gmail_attr">Unfortunately, I am desperate to need coincidence sorter and data. </div><div><br></div><div><br></div><div>Dear Dr. Kang, </div><div><br></div><div>Sincere I learned this initially from you, I was wondering whether you had been able to add a 5th level to PETScanner? Could you share your thoughts on this?</div><div>Thank you very much. </div><div><br></div><div class="gmail_attr" style="color:rgb(80,0,80)"><span style="color:rgb(0,0,0)">Zhengzhi </span></div><div class="gmail_attr" style="color:rgb(80,0,80)"><span style="color:rgb(0,0,0)"><br></span></div><div dir="ltr" class="gmail_attr" style="color:rgb(80,0,80)"><br></div><div dir="ltr" class="gmail_attr" style="color:rgb(80,0,80)"><br></div><div class="gmail_attr" style="color:rgb(80,0,80)">Forwarded message: </div><div dir="ltr" class="gmail_attr" style="color:rgb(80,0,80)"><br></div><div dir="ltr" class="gmail_attr" style="color:rgb(80,0,80)">On Mon, Jan 27, 2020 at 8:27 PM 강한규 <<a href="mailto:lovehangulp@naver.com" target="_blank">lovehangulp@naver.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="color:rgb(80,0,80);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 Christian,</p><p> </p><p><span style="font-size:10pt">As you already know, Christian (</span><a href="mailto:pommranz@astro.uni-tuebingen.de" rel="noreferrer noopener" style="font-family:arial,helvetica,sans-serif;font-size:small" target="_blank">pommranz@astro.uni-tuebingen.de</a><span style="font-size:10pt">) shared the git patch file to solve the coincidence output issue.</span> </p><p><a href="http://lists.opengatecollaboration.org/pipermail/gate-users/2019-February/010729.html" style="font-size:10pt" target="_blank">http://lists.opengatecollaboration.org/pipermail/gate-users/2019-February/010729.html</a></p><p> </p><p>I have also <b>succeeded </b>in acquiring coincidence output using <b>generic repeater</b> in<b> PETscanner </b>system with the patch file shared by Christian.</p><p>Below is an example of the detector arrangement with genericRepeater.</p><p>Thanks Christian for your great contribution~!</p><p><img src="cid:16feafef0c54ec9c9171" style="outline:0px"> </p><p> </p><p>Here is a brief manual how to apply the git patch in GATEv8.2.</p><p><span style="font-size:10pt">===========================================================================================================================</span></p><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small"><b><font color="#ff0000">Problem</font></b>: <font color="#ff0000"><b>No coincidence</b></font> in the "<b>PETscanner</b>" when <font color="#ff0000"><b>genericRepeater </b></font>was used.</div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small"><b><font color="#0000ff">Solution</font></b>: <b>Modify the GATEv8.2 source code</b> using a <b>git patch file</b> and <b>re-compile</b>.</div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small"> </div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small">GATE mailing list (Christian Pommranz <<a href="mailto:pommranz@astro.uni-tuebingen.de" rel="noreferrer noopener" target="_blank">pommranz@astro.uni-tuebingen.de</a>>) </div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small"><a href="http://lists.opengatecollaboration.org/pipermail/gate-users/2019-February/010729.html" rel="noreferrer noopener" target="_blank">http://lists.opengatecollaboration.org/pipermail/gate-users/2019-February/010729.html</a></div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small"> </div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small"><b>STEP1</b>> Download the git patch file in the mailing list.</div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small">Filename: <b>coincidences_for_generic_repeater.patch</b></div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small"> </div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small"><b>STEP2</b>> Apply the git patch file.</div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small">>cd /home/kanghg2/program/Gate-8.2</div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small">>git apply --ignore-space-change --ignore-whitespace coincidences_for_generic_repeater.patch</div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small"> </div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small"><b>STEP3</b>> Re-compile GATEv8.2</div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small">>cd /home/kanghg2/program/Gate-8.2-build</div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small">>ccmake ../Gate-8.2</div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small">[c] configure</div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small">[g] generate</div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small"> </div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small">>make</div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small"> </div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small"><b>STEP4</b>> Run the GATE PETscanner with genericRepeater.</div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:small"><b>Now coincidence output will be generated!</b></div><p><span style="font-size:10pt">===========================================================================================================================</span></p><div><p> </p><p><span style="font-size:10pt">Hopefully, you will be able to obtain coincidence output with genericRepeater.</span> </p></div><div><span style="font-size:10pt"> </span></div><p>Best regards,</p><p> </p><p>Han Gyu Kang, Ph.D.</p><p> </p><p>Imaging Physics Group, NIRS-QST, Japan.</p></div></div></blockquote></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Mar 6, 2020 at 5:57 PM Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" target="_blank">matthew.strugari@dal.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">
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<p class="MsoNormal"><span lang="EN-US">Hi Zhengzhi,<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">According to the user manual (Section 1.5.1
</span><a href="https://opengate.readthedocs.io/en/latest/defining_a_system_scanner_ct_pet_spect_optical.html#defining-the-systems" 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.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Regards,<u></u><u></u></p>
<p class="MsoNormal">Matthew<u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
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<p class="MsoNormal"><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<u></u><u></u></span></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">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.
<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><img border="0" width="471" height="195" style="width: 4.9062in; height: 2.0312in;" id="gmail-m_7869974751573777647gmail-m_3488737524990665659_x0000_i1026" src="cid:170b2f22e474cff311"><u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">On Fri, Mar 6, 2020 at 3:17 PM Zhengzhi Liu <<a href="mailto:zliu36@stanford.edu" target="_blank">zliu36@stanford.edu</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal">Report of a potential bug: <u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">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>. <u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><img border="0" width="472" height="219" style="width: 4.9166in; height: 2.2812in;" id="gmail-m_7869974751573777647gmail-m_3488737524990665659_x0000_i1025" src="cid:170b2f22e475b16b22"><u></u><u></u></p>
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<p class="MsoNormal">Thanks for reading.<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Sincere greetings,<u></u><u></u></p>
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<p class="MsoNormal">Zhengzhi<u></u><u></u></p>
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