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<p class="MsoNormal"><span style="color:#1F497D">Hi Simon,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">I would appreciate your input on one additional task please. I want to reconstruct the LM data with a span>1? I am writing for every event all the possible crystal pairs, and in case the number of LOR’s is less
than “k” (as described in table 3) I write “garbage” with both ID1 and ID2 equal to zero. My norm file has the same format in addition to the normalization correction factor for each crystal pair. I also set the “Maximum number of lines per event” to the proper
maximum number of crystal pair in the .cdh file. Does this sound right?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Sadek<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b>From:</b> STUTE Simon <simon.stute@chu-nantes.fr> <br>
<b>Sent:</b> Thursday, October 22, 2020 7:29 AM<br>
<b>To:</b> Sadek Nehmeh <san2028@med.cornell.edu>; castor-users@lists.castor-project.org<br>
<b>Subject:</b> [EXTERNAL] RE: Normalization<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">OK thanks for this feedback, we will try to improve it.<o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">Simon<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="color:black">De :</span></b><span style="color:black"> Sadek Nehmeh <<a href="mailto:san2028@med.cornell.edu">san2028@med.cornell.edu</a>><br>
<b>Envoyé :</b> jeudi 22 octobre 2020 13:09<br>
<b>À :</b> STUTE Simon; <a href="mailto:castor-users@lists.castor-project.org">castor-users@lists.castor-project.org</a><br>
<b>Objet :</b> RE: Normalization</span><span style="font-size:12.0pt;color:#212121">
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:#212121"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#1F497D">Thank you Marina and Simon for your feedback.
</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">The way this is described in table 3 of the userguide sounds as if the user has the option to either pass the norm factors for each crystals pair within the LM file, or as a separate norm file, and then Castor
takes care of the rest; i.e. it has nothing to do with the MLEM equation. Thank you for the clarification.</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Regards,</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Sadek</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="color:#212121">From:</span></b><span style="color:#212121"> STUTE Simon <<a href="mailto:simon.stute@chu-nantes.fr">simon.stute@chu-nantes.fr</a>>
<br>
<b>Sent:</b> Thursday, October 22, 2020 4:41 AM<br>
<b>To:</b> Sadek Nehmeh <<a href="mailto:san2028@med.cornell.edu">san2028@med.cornell.edu</a>>;
<a href="mailto:castor-users@lists.castor-project.org">castor-users@lists.castor-project.org</a><br>
<b>Subject:</b> [EXTERNAL] RE: Normalization<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#212121"> <o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">Hi Sadek,</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">If you look at an MLEM equation, it does not make sense to include normalization factor in the system matrix in the right part of the equation but not in the left part (where the sensitivity is taken
into account).</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">When you perform a list-mode reconstruction, a sensitivity image has to be computed from all possible lines of response that may contribute to the list-mode file.</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">So there is a sensitivity image; either you provided it, or it is computed by looping on all crystal pairs or on events from a normalization datafile if provided.</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">If you include normalization correction factors in the list-mode file, it means that you are able to know the normalization correction factor for any possible crystal pair admissible in the list-mode
file.</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">From these normalization factors, you have to build a normalization datafile that contains the list of any admissible line of response with the associated normalization factor (this type of datafile
is described in the documentation).</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">Then you provide this normalization datafile using '-norm' option to castor, so that it will loop on it to compute the sensitivity image.</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">And the error message will disappear.</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">Simon</span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-family:"Calibri",sans-serif;color:#212121"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="color:black">De :</span></b><span style="color:black"> Castor-users <<a href="mailto:castor-users-bounces@lists.castor-project.org">castor-users-bounces@lists.castor-project.org</a>> de la part de Sadek Nehmeh <<a href="mailto:san2028@med.cornell.edu">san2028@med.cornell.edu</a>><br>
<b>Envoyé :</b> jeudi 22 octobre 2020 05:09<br>
<b>À :</b> <a href="mailto:castor-users@lists.castor-project.org">castor-users@lists.castor-project.org</a><br>
<b>Objet :</b> [Castor-users] Normalization</span><span style="font-size:12.0pt;color:#212121">
</span><span style="color:#212121"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:#212121"> </span><span style="color:#212121"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#212121">Hi All,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#212121"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#212121">I am trying to reconstruct a dataset with the normalization correction factors included in the listmode data. I am getting the following error when I submit for reconstruction:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#212121"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#212121">***** The following error message was issued by MPI instance 0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#212121">***** oSensitivityGenerator::InitializeNormalizationFiles() -> Normalization correction is included in the data file while it is not in the sensitivity computation !<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#212121"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#212121">Here is the reconstruction command:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#212121"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#212121">castor-recon -df LM_df.Cdh -opti MLEM -it 2:4 -proj joseph -dim 256,256,309 -vox 2.73,2.73,1.6 -dout my_images<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#212121"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#212121">Please notice that I don’t have a sensitivity image.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#212121"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#212121">Any help would be very appreciated.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#212121"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#212121">Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#212121">Sadek<o:p></o:p></span></p>
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