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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 “7.3.2 Positionâ€. 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 “</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 „XX“ 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 –XX –XX –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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