<div dir="ltr"><div><br></div>(I forward this because it can be of interest for others users)<br><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">---------- Forwarded message ---------<br>From: <strong class="gmail_sendername" dir="auto">David Sarrut</strong> <span dir="auto"><<a href="mailto:David.Sarrut@creatis.insa-lyon.fr">David.Sarrut@creatis.insa-lyon.fr</a>></span><br>Date: Wed, Jul 3, 2019 at 8:20 AM<br>Subject: Re: Question on GATE source geometry<br>To: Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca">matthew.strugari@dal.ca</a>><br></div><br><div dir="ltr">Hi Matthew, <div><br></div><div>there are two ways to define source shapes : 1) GPS, 2) voxelized source. Both work but have some interests and some flaws. </div><div><br></div><div>1) GPS (<a href="https://opengate.readthedocs.io/en/latest/source_and_particle_management.html?highlight=gps" target="_blank">https://opengate.readthedocs.io/en/latest/source_and_particle_management.html?highlight=gps</a>)</div><div>Only few simple shapes may be defined: Sphere, Ellipsoid, Cylinder, or Para. Warning: the doc is particularly misleading here (code have changed a lot in the past while changes were not all reflected in the docs). Best is to check with <a href="https://github.com/OpenGATE/Gate/blob/develop/source/physics/src/GateSingleParticleSourceMessenger.cc" target="_blank">https://github.com/OpenGATE/Gate/blob/develop/source/physics/src/GateSingleParticleSourceMessenger.cc</a></div><div><br></div><div>2) for more complex shapes, use voxelized source (<a href="https://opengate.readthedocs.io/en/latest/voxelized_source_and_phantom.html#voxelized-sources" target="_blank">https://opengate.readthedocs.io/en/latest/voxelized_source_and_phantom.html#voxelized-sources</a>)<br></div><div>You create an image, with pixel values representing the intensity. I recommend to ensure that the sum of pixel values is equal to 1 (normalization), such as is it then easy to specify the total activity. This vox source is a "virtual" volume you can superposed it with any other real shape in the simulation. Example : TRT in <a href="https://davidsarrut.pages.in2p3.fr/gate-exercices-site/docs/exercice5/" target="_blank">https://davidsarrut.pages.in2p3.fr/gate-exercices-site/docs/exercice5/</a> with the macros <a href="https://gitlab.in2p3.fr/davidsarrut/gate-exercices/tree/master/internal-rt/mac" target="_blank">https://gitlab.in2p3.fr/davidsarrut/gate-exercices/tree/master/internal-rt/mac</a> (see source-gps and source-vox). </div><div><br></div><div>If needed, you can always use several sources in the same simulation.</div><div><br></div><div>We plan to rewrite all documentation in the following months ...</div><div><br></div><div>have fun !</div><div>David</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Jul 2, 2019 at 10:15 PM Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" target="_blank">matthew.strugari@dal.ca</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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Hi David,</div>
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Thank you for the information at the GATE workshop in Montreal, I found it to be very useful!</div>
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I have a question regarding complex shapes when defining the shape of the source in GATE. I have modelled an Eppendorf tube to contain 4 ul of saline as defined by a semi-sphere attached to a truncated cone. Ideally, I would like to specify this volume to contain
Tc-99m as the source. Unfortunately, it appears that I do not have access to these same shapes when defining the source. Is it possible to define an object geometry as the source? Or is there someway that I could define the source to occupy the exact same
volume as the geometry in which it is contained? I can't seem to figure out a trick to define a semi-sphere and truncated cone as the source.</div>
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Cheers,</div>
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<p style="margin-top:0px;margin-bottom:0px"><span style="font-family:Calibri,Helvetica,sans-serif">Matthew</span></p>
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<p class="m_-7060096041675561791gmail-m_2796932213481823636x_MsoNormal" style="margin-top:0px;margin-bottom:0px"><span style="font-size:10.5pt;color:black;font-family:Calibri,Helvetica,sans-serif">--</span></p>
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<p class="m_-7060096041675561791gmail-m_2796932213481823636x_MsoNormal" style="margin-top:0px;margin-bottom:0px"><span style="font-size:10.5pt;color:black;font-family:Calibri,Helvetica,sans-serif">Matthew Strugari</span><span style="font-size:10.5pt;color:black"></span></p>
<span style="font-family:Calibri,Helvetica,sans-serif"></span><span style="font-size:10.5pt;color:black" lang="EN-US"><span style="font-family:Calibri,Helvetica,sans-serif">Biomedical Translational Imaging Centre -
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<span style="font-family:Calibri,Helvetica,sans-serif">5890 University Ave, </span><br>
<span style="font-family:Calibri,Helvetica,sans-serif">Halifax, NS, B3K 6R8</span></span><br>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="m_-7060096041675561791gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">David Sarrut, Phd<br>Directeur de recherche CNRS<br>CREATIS, UMR CNRS 5220, Inserm U1206<div>Centre de lutte contre le cancer Léon Bérard<br>28 rue Laënnec, 69373 Lyon cedex 08<br>Tel : 04 78 78 51 51 / 06 74 72 05 42<br><a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a><br>_________________________________</div><div> "2 + 2 = 5, for extremely large values of 2"<br>_________________________________</div></div></div></div></div></div></div>
</div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">David Sarrut, Phd<br>Directeur de recherche CNRS<br>CREATIS, UMR CNRS 5220, Inserm U1206<div>Centre de lutte contre le cancer Léon Bérard<br>28 rue Laënnec, 69373 Lyon cedex 08<br>Tel : 04 78 78 51 51 / 06 74 72 05 42<br><a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a><br>_________________________________</div><div> "2 + 2 = 5, for extremely large values of 2"<br>_________________________________</div></div></div></div></div></div></div></div>