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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Hi David
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">I’m still seeing the same effect even with a single core. I’ve attached the output files for a 150000 event I ran, plus my initial
mac files (for the single core). Obviously, the actual data is too big to send via email, but I can provide a link to the original CT/PET data and also the output MHA files if needed.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><img width="747" height="389" style="width:7.7812in;height:4.052in" id="Picture_x0020_1" src="cid:image001.png@01D7ECDD.9D01FE00"></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Thank you<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">Mark Baker<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">Principal Clinical Scientist (Interim)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">Imaging Physics (Ionising)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">The Clatterbridge Cancer Centre NHS Foundation Trust<o:p></o:p></span></p>
<p class="MsoNormal"><i><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">(he, him)<o:p></o:p></span></i></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">CCCW Tel: 0151 556 5030
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">CCCL Tel: 0151 318 8438<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">Email:
</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#4472C4"><a href="mailto:mark.baker23@nhs.net"><span style="color:#4472C4">mark.baker23@nhs.net</span></a></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#4472C4"><a href="https://teams.microsoft.com/l/chat/0/0?users=mark.baker23@nhs.net"><span style="color:#4472C4">Microsoft Teams (click here)</span></a></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Gate-users <gate-users-bounces@lists.opengatecollaboration.org>
<b>On Behalf Of </b>BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST)<br>
<b>Sent:</b> 08 December 2021 15:37<br>
<b>To:</b> David Sarrut <david.sarrut@creatis.insa-lyon.fr><br>
<b>Cc:</b> gate-users@lists.opengatecollaboration.org<br>
<b>Subject:</b> Re: [Gate-users] Weird Blips in F18 data<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Hi David<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Sorry for the delay in responding. I’m away from my machine at the moment, but I will try a single core tomorrow. However, the images
showed these effects on the root files of the individual cores (i.e. before they were merged) and I think this would be the same as running a single core (to my limited knowledge). I will do one to confirm however.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Thank you<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">Mark Baker<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">Principal Clinical Scientist (Interim)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">Imaging Physics (Ionising)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">The Clatterbridge Cancer Centre NHS Foundation Trust<o:p></o:p></span></p>
<p class="MsoNormal"><i><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">(he, him)<o:p></o:p></span></i></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">CCCW Tel: 0151 556 5030
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">CCCL Tel: 0151 318 8438<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">Email:
</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#4472C4"><a href="mailto:mark.baker23@nhs.net"><span style="color:#4472C4">mark.baker23@nhs.net</span></a></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#4472C4"><a href="https://teams.microsoft.com/l/chat/0/0?users=mark.baker23@nhs.net"><span style="color:#4472C4">Microsoft Teams (click here)</span></a><o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> David Sarrut <<a href="mailto:david.sarrut@creatis.insa-lyon.fr">david.sarrut@creatis.insa-lyon.fr</a>>
<br>
<b>Sent:</b> 07 December 2021 07:15<br>
<b>To:</b> BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <<a href="mailto:mark.baker23@nhs.net">mark.baker23@nhs.net</a>><br>
<b>Cc:</b> <a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a><br>
<b>Subject:</b> Re: [Gate-users] Weird Blips in F18 data<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hello Mark, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">can you try with a single core (no merging), even with a "low" statistics, to see if it also occurs ? <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">thanks<o:p></o:p></p>
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<div>
<p class="MsoNormal">David<o:p></o:p></p>
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</div>
<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">On Thu, Dec 2, 2021 at 4:52 PM BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <<a href="mailto:mark.baker23@nhs.net">mark.baker23@nhs.net</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi everyone<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I’m running a relatively simple simulation of a NEMA IQ phantom, looking at the dose deposited within it by F18. My sim has a CT scan loaded as the geometry (with HU determined
from the StoichHU example) and the F18 scan as the source. Physics are loaded as GQSP_BERT_EMV. The macro is split into 4 to run on 4 separate cores, then merged together afterwards using hadd for the root files. My source definition is Fluor18 with e+ particle,
6585s setforcedhalflife and true for setforcedunstableflag (unfortunately my code is on a different machine to my emails so I can’t cope and paste directly).
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I’m getting some interesting results in my tracklength and edepspectrum root files (see attached). The tracklength seems to get a little bit of a blip at pretty much 1mm, which
I’m finding hard to explain. Additionally, on the Edep there appears to be an event (or possibly several) which deposits 20GeV from an energy of around 0.5MeV. The reason that I think it might be several events is that the same point is visible on the individual
root files as well as the merged file. My actual edep and dose images look pretty good.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">These examples are from merged root files from 4x25000 events so probably not amazing statistically but are quick enough for me to run and trouble shoot. I’ve ran slightly more
events and still see the same effects, but I will run a longer simulation (4x200M or something) overnight to see if I get the same effects (and rule out a statistics related issue).<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Does anyone have any clues or suggests are to where to look to troubleshoot this?<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thank you<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="color:#006871">Mark Baker</span></b><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#006871">Principal Clinical Scientist (Interim)</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#006871">Imaging Physics (Ionising)</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#006871">The Clatterbridge Cancer Centre NHS Foundation Trust</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><i><span style="color:#006871">(he, him)</span></i><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="color:#006871"> </span></b><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#006871">CCCW Tel: 0151 556 5030
</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#006871">CCCL Tel: 0151 318 8438</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#006871">Email:
</span><span style="color:#4472C4"><a href="mailto:mark.baker23@nhs.net">mark.baker23@nhs.net</a></span><span style="color:#006871">
</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#4472C4">Microsoft Teams (click here)</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><i><span style="color:#006871">Honorary Lecturer, Dept. of Physics</span></i><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><i><span style="color:#006871">University of Liverpool</span></i><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#006871"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><o:p> </o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
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<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">-- <o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black">David Sarrut, Phd</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black">Directeur de recherche CNRS</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black">CREATIS, UMR CNRS 5220, Inserm U1294</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black">Centre de lutte contre le cancer Léon Bérard</span><o:p></o:p></p>
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<div>
<p class="MsoNormal"><span style="color:black">28 rue Laënnec, 69373 Lyon cedex 08</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black">Tel : 04 78 78 51 51 / 06 74 72 05 42</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black"><a href="http://dsarrut.github.io" target="_blank">http://dsarrut.github.io</a></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black">_________________________________</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black"> "2 + 2 = 5, for extremely large values of 2"</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black">_________________________________</span><o:p></o:p></p>
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i) inform the sender that you have received the message in error before deleting it; and
<br>
ii) do not disclose, copy or distribute information in this e-mail or take any action in relation to its content (to do so is strictly prohibited and may be unlawful).
<br>
Thank you for your co-operation.<br>
<br>
NHSmail is the secure email, collaboration and directory service available for all NHS staff in England. NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and other accredited email services.<br>
<br>
For more information and to find out how you can switch visit <a href="https://support.nhs.net/article-categories/joining-nhsmail/">
Joining NHSmail – NHSmail Support</a><br>
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