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<p>Dear Suguru,</p>
<p><br>
</p>
<p>Simply use the "-atn" option in castor-recon to give it the attenuation image you created.</p>
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</p>
<p>In a very general manner, to get help for all options, just launch castor-recon without arguments.</p>
<p>Then it provides all specific options to get specific help about many themes.</p>
<p>For you, "castor-recon -help-in" provides helps for all options about input files.</p>
<p><br>
</p>
<p>Best</p>
<p>Simon</p>
<p><br>
</p>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>De :</b> Castor-users <castor-users-bounces@lists.castor-project.org> de la part de Suguru Katsube <sug.katsu@gmail.com><br>
<b>Envoyé :</b> mercredi 15 juillet 2020 12:29<br>
<b>À :</b> tmerlin<br>
<b>Cc :</b> castor-users@lists.castor-project.org<br>
<b>Objet :</b> Re: [Castor-users] How to apply attenuation correction for PET reconstruction using GATE root data</font>
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<div dir="ltr">Dear Thibaut Merlin,
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<div>Thank you for your quick response. <br>
</div>
<div>Successfully, I made the attenuation image. Then, I made **.cdh and **.cdf with attenuaton correrction using castor-GATERootToCastor (This is list-mode format for reconstructing with scatter and random correction).
<br>
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<div>When I run castor-recon, the message below was displayed.</div>
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<div><b>***** oSensitivityGenerator::InitializeAttenuationFiles() -> Attenuation correction is included in the data file while it is not in the sensitivity computation !<br>
***** oSensitivityGenerator::Initialize() -> A problem occurred while initializing the attenuation files !<br>
***** castor-recon() -> A problem occurred while initializing the sensitivity generator !<br>
</b></div>
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<div>I know that the attenuation image MUST be providen to the castor-recon exe as well, in order to perform sensitivity image computation for PET list-mode. How should I provide attenuation image to reconstruct the data?<br>
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<div>Thank you in advance.</div>
<div>Best regards,</div>
<div><br>
</div>
<div>Suguru</div>
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<div dir="ltr" class="gmail_attr">2020年6月30日(火) 0:00 tmerlin <<a href="mailto:Thibaut.Merlin@univ-brest.fr" target="_blank">Thibaut.Merlin@univ-brest.fr</a>>:<br>
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<p>Hi Suguru,</p>
<p>Attenuation image must be in interfile format, and must be in cm-1. The dimensions/voxel sizes will be interpolated to the reconstruction image dimensions, so you don't need to provide an image with the exact same dimensions than for the reconstruction.
Additionally, you should make sure that the reconstruction image dimensions are large enough to include all attenuated materials of the attenuation image, otherwise the attenuation correction will be incorrect. </p>
<p>Regarding the image itself, you should generate it from the geometry of the phantom you use in the GATE simulation, or derive it directly from the phantom image if you used a voxelized phantom.</p>
<p>Hope this helps,</p>
<p>Thibaut<br>
</p>
<p><br>
</p>
<div>On 29/06/2020 09:57, Suguru Katsube wrote:<br>
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<div dir="ltr">Hi all,
<div><br>
</div>
<div>I am trying to reconstruct a GATE root file (PET).<br>
I want to apply attenuation correction and reconstruct it. The manual states I need an attenuation image, how do I create it ? The phantom was designed on a GATE and no CT images were acquired. There are many unclear points such as image format, number of pixels,
number of slices, alignment, etc. Can I create the attenuation image using a root file or mac file?</div>
<div><br>
Any advice is appreciated.<br clear="all">
<div><br>
</div>
<div>Best regards, </div>
<div><br>
</div>
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<div><font face="arial, sans-serif">○●----------------------------------------------------------●○</font></div>
<div><font face="arial, sans-serif"> 勝部 俊（Suguru Katsube）</font></div>
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<p style="margin:0px; line-height:normal"><font face="arial, sans-serif"><font color="#000000"> 九州大学大学院</font><span style="color:rgb(0,0,0)">医学系学府保健学専攻</span></font></p>
<p style="margin:0px; line-height:normal"><font face="arial, sans-serif" color="#000000"> 医用量子線科学分野 修士課程2年</font></p>
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</font></p>
<p style="margin:0px; line-height:normal"><font face="arial, sans-serif" color="#000000"> Medical Quantum Radiation Science Course<span style="line-height:normal">,</span></font></p>
<p style="margin:0px; line-height:normal"><font face="arial, sans-serif" color="#000000"> Department of Health Sciences<span style="line-height:normal">,</span></font></p>
<p style="margin:0px; line-height:normal"><font face="arial, sans-serif" color="#000000"> Graduate School of Medical Sciences<span style="line-height:normal">,</span> </font></p>
<p style="margin:0px; line-height:normal"><font face="arial, sans-serif" color="#000000"> Kyushu University<span style="line-height:normal">,</span> Fukuoka<span style="line-height:normal">,</span> Japan</font></p>
<p style="margin:0px; line-height:normal"><font face="arial, sans-serif"><font color="#000000"> E-mail: </font><a href="mailto:E-mail%3Aymmk88kmmy@gmail.com" target="_blank" style="color:rgb(17,85,204)">sug.katsu@gmail.com</a></font></p>
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<pre>_______________________________________________
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</pre>
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<pre cols="72">--
Thibaut MERLIN -- PhD
Docteur en Imagerie Médicale au Laboratoire de Traitement de l'Information Medicale (LaTIM - INSERM UMR 1101)
Institut Brestois de recherche en Bio-Santé (IBRBS)
12 Avenue Foch, 29200 Brest, FRANCE
Tel: 06.75.12.24.90</pre>
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<div><font face="arial, sans-serif">○●----------------------------------------------------------●○</font></div>
<div><font face="arial, sans-serif"> 勝部 俊（Suguru Katsube）</font></div>
<div>
<p style="margin:0px; line-height:normal"><font face="arial, sans-serif"><font color="#000000"> 九州大学大学院</font><span style="color:rgb(0,0,0)">医学系学府保健学専攻</span></font></p>
<p style="margin:0px; line-height:normal"><font face="arial, sans-serif" color="#000000"> 医用量子線科学分野 修士課程2年</font></p>
<p style="margin:0px; line-height:normal; min-height:14px"><font face="arial, sans-serif" color="#000000"><br>
</font></p>
<p style="margin:0px; line-height:normal"><font face="arial, sans-serif" color="#000000"> Medical Quantum Radiation Science Course<span style="line-height:normal">,</span></font></p>
<p style="margin:0px; line-height:normal"><font face="arial, sans-serif" color="#000000"> Department of Health Sciences<span style="line-height:normal">,</span></font></p>
<p style="margin:0px; line-height:normal"><font face="arial, sans-serif" color="#000000"> Graduate School of Medical Sciences<span style="line-height:normal">,</span> </font></p>
<p style="margin:0px; line-height:normal"><font face="arial, sans-serif" color="#000000"> Kyushu University<span style="line-height:normal">,</span> Fukuoka<span style="line-height:normal">,</span> Japan</font></p>
<p style="margin:0px; line-height:normal"><font face="arial, sans-serif"><font color="#000000"> E-mail: </font><a href="mailto:E-mail%3Aymmk88kmmy@gmail.com" target="_blank" style="color:rgb(17,85,204)">sug.katsu@gmail.com</a></font></p>
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