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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 Chris,<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 lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">when loading voxelized sources in GATE, they’re placed in the first quarter of the coordinate system. You can find details
 in the manual (<a href="https://opengate.readthedocs.io/en/latest/voxelized_source_and_phantom.html#voxelized-sources">https://opengate.readthedocs.io/en/latest/voxelized_source_and_phantom.html#voxelized-sources</a>)  under â€œ7.3.2 Position”. There is also
 an example provided, explaining how you need to shift your voxelized source accordingly.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" 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 lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Try the command below instead
</span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F4E79;mso-style-textfill-fill-color:#1F4E79;mso-style-textfill-fill-alpha:100.0%;mso-fareast-language:EN-US">of â€œ</span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F4E79;mso-style-textfill-fill-color:#1F4E79;mso-style-textfill-fill-alpha:100.0%">/gate/source/thyroid_Phantom/gps/centre
 0. 35. 0. Mm“ and adjust the shift â€žXX“ according to half of your image size. This command line is also in your example on page 146 of the v8.0 manual version.</span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F4E79;mso-style-textfill-fill-color:#1F4E79;mso-style-textfill-fill-alpha:100.0%;mso-fareast-language:EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F4E79;mso-style-textfill-fill-color:#1F4E79;mso-style-textfill-fill-alpha:100.0%;mso-fareast-language:EN-US">/gate/source/</span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F4E79;mso-style-textfill-fill-color:#1F4E79;mso-style-textfill-fill-alpha:100.0%">
 thyroid_Phantom</span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F4E79;mso-style-textfill-fill-color:#1F4E79;mso-style-textfill-fill-alpha:100.0%;mso-fareast-language:EN-US"> /setPosition â€“XX â€“XX â€“XX mm<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F4E79;mso-style-textfill-fill-color:#1F4E79;mso-style-textfill-fill-alpha:100.0%;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F4E79;mso-style-textfill-fill-color:#1F4E79;mso-style-textfill-fill-alpha:100.0%;mso-fareast-language:EN-US">I hope this helps you to place your source
 in the right position. <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F4E79;mso-style-textfill-fill-color:#1F4E79;mso-style-textfill-fill-alpha:100.0%;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F4E79;mso-style-textfill-fill-color:#1F4E79;mso-style-textfill-fill-alpha:100.0%;mso-fareast-language:EN-US">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F4E79;mso-style-textfill-fill-color:#1F4E79;mso-style-textfill-fill-alpha:100.0%;mso-fareast-language:EN-US">Julia<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Von:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Gate-users <gate-users-bounces@lists.opengatecollaboration.org>
<b>Im Auftrag von </b>Christopher Watanabe<br>
<b>Gesendet:</b> Dienstag, 19. November 2019 22:53<br>
<b>An:</b> gate-users@lists.opengatecollaboration.org<br>
<b>Betreff:</b> [Gate-users] Voxelized Source Problem<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Hi all, <o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">I'm facing problems importing a voxelized source into my simulation. My code below is very close to the code in the Gate Users' Manual V8.0, page 146.
<br>
<br>
# Inserting Voxelized Source<br>
/gate/source/addSource                       thyroid_Phantom voxel<br>
/gate/source/thyroid_Phantom/reader/insert     image<br>
/gate/source/thyroid_Phantom/imageReader/translator/insert     linear<br>
/gate/source/thyroid_Phantom/imageReader/linearTranslator/setScale      2 Bq<br>
/gate/source/thyroid_Phantom/imageReader/readFile ./data/thyroidPhantom/metaimage2.mhd<br>
/gate/source/thyroid_Phantom/imageReader/verbose 1<br>
<br>
/gate/source/thyroid_Phantom/gps/centre 0. 35. 0. mm<br>
<br>
/gate/source/voxel/gps/particle gamma<br>
/gate/source/voxel/gps/energytype Mono<br>
/gate/source/voxel/gps/monoenergy 140.5 keV<br>
/gate/source/voxel/gps/angtype iso<br>
/gate/source/voxel/gps/mintheta                 0. deg<br>
/gate/source/voxel/gps/maxtheta 90. deg<br>
/gate/source/voxel/gps/minphi                0. deg<br>
/gate/source/voxel/gps/maxphi                360. deg<br>
/gate/source/voxel/gps/confine NULL<br>
/gate/source/voxel/setForcedUnstableFlag true<br>
/gate/source/voxel/setForcedHalfLife    21636 s<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Where metaimage2.mhd is a binary mask of a thyroid scan. (0 background, 1 thyroid).
<o:p></o:p></p>
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<p class="MsoNormal">Despite this, I'm getting very strange visualization results from the simulation:
<o:p></o:p></p>
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<p class="MsoNormal"><img border="0" width="541" height="306" style="width:5.6354in;height:3.1875in" id="_x0000_i1025" src="cid:image002.png@01D59F7E.56128E50" alt="image.png"><o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Strangely, the source doesn't move when I change the
<i>/gate/source/thyroid_Phantom/gps/centre</i> coordinates. I'm a bit at a loss of how to solve this problem.
<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Has anyone had similar experiences with this? Is it a GATE issue, or is this more likely something that would originate from a faulty .mhd file formatting?
<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Thank you! <o:p></o:p></p>
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<p class="MsoNormal">Chris<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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