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Thanks for the tip, Uwe!
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<div>I looked at the latest source code of Gate available to the public and I think the User's Guide is outdated about this command. You are right, no "_P" is needed at the end of the volume name for the confine (or forbid) command.</div>
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<div>(Technically, according to the source code, the user should add the tag "_phys" to the volume name for the confine command; but if you leave it out, the code adds the tag by itself, so...)</div>
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<div>Cheers,<br>
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<div>Marc</div>
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<div>__________________________</div>
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<div>Marc Chamberland, MSc</div>
PhD candidate<br>
Department of Physics<br>
Carleton University<br>
Ottawa (ON)</div>
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<div>On Mar 10, 2014, at 17:10, Pietrzyk, Uwe <<a href="mailto:u.pietrzyk@fz-juelich.de">u.pietrzyk@fz-juelich.de</a>> wrote:</div>
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<div>Hi Ida,</div>
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<div>we once ran into a similar problem and the solution was</div>
<div>to use (now for your example) the line</div>
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<div>/gate/source/F18_upper/gps/confine upperinterior</div>
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<div>instead of your original</div>
<div>/gate/source/F18_upper/gps/confine upperinterior_P</div>
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</div>
Hence, simply remove the "_P". We checked it and it
<div>works for our examples</div>
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<div>Kind regards and best wishes,</div>
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<div>Uwe Pietrzyk<br>
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<div>/----------------------------------------------------------------------</div>
<div>Prof. Dr. Uwe Pietrzyk<br>
Diplom-Physiker<br>
Institut für Neurowissenschaften und Medizin / INM-4<br>
Forschungszentrum Jülich GmbH<br>
52425 Jülich<br>
Tel: +49-2461-61 4763<br>
Fax: +49-2461-61 2820<br>
Mobil: +49-162-103-4871<br>
eMail: <a href="mailto:U.Pietrzyk@fz-juelich.de">U.Pietrzyk@fz-juelich.de</a><br>
<a href="http://www.fz-juelich.de/inb/inb-3/">http://www.fz-juelich.de/inm</a><br>
&<br>
Bergische Universität Wuppertal<br>
Fachbereich C - Physik / D.08.01<br>
Gaußstr. 20<br>
42097 Wuppertal<br>
Tel: +49-(0)202-439-3523<br>
Fax: +49-(0)202-439-2811<br>
eMail: <a href="mailto:Uwe.Pietrzyk@physik.uni-wuppertal.de">Uwe.Pietrzyk@physik.uni-wuppertal.de</a><br>
<a href="http://www.medizinphysik.uni-wuppertal.de/">http://www.medizinphysik.uni-wuppertal.de</a><br>
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<div>On 10.03.2014, at 20:52, Ida Häggström wrote:</div>
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<div dir="ltr">Hello and thanks for your reply!
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<div>Yes, I did run a short simulation (I also thought it might have been just the visualization), but unfortunately when looking at the *.raw output images it shows that the source has indeed spilled out. I get scattered and true coincidences originating from
the spilled out areas.</div>
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<div>If I can't find a solution I guess I'm left with doing a voxelized source...</div>
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<div>Thanks again!</div>
<div>Ida</div>
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<div class="gmail_quote">On Mon, Mar 10, 2014 at 6:34 PM, Marc Chamberland <span dir="ltr">
<<a href="mailto:MarcChamberland@cmail.carleton.ca" target="_blank">MarcChamberland@cmail.carleton.ca</a>></span> wrote:<br>
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Hi Ida,<br>
<br>
Did you try a short simulation with your macro and did you confirm that the source is not properly confined? (For example, by looking at the source position distribution in the Root output.)<br>
<br>
The reason I'm asking is that, in the past, I've found limitations in the Geant4 visualization code. For example, see this thread from the mailing list:
<a href="http://article.gmane.org/gmane.comp.science.opengate.user/3109/match=source+visualize" target="_blank">
http://article.gmane.org/gmane.comp.science.opengate.user/3109/match=source+visualize</a><br>
<br>
My first instinct is that this may be related.<br>
<br>
Marc<br>
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__________________________<br>
<br>
Marc Chamberland, MSc<br>
PhD candidate<br>
Department of Physics<br>
Carleton University<br>
Ottawa (ON)<br>
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<div><br>
On Mar 10, 2014, at 11:34, Ida Häggström <<a href="mailto:ida.haggstrom@radfys.umu.se" target="_blank">ida.haggstrom@radfys.umu.se</a><mailto:<a href="mailto:ida.haggstrom@radfys.umu.se" target="_blank">ida.haggstrom@radfys.umu.se</a>>> wrote:<br>
<br>
Hello!<br>
<br>
I'm trying to confine a source to a particular phantom geometry, but cannot get it to work properly. Part of the source spills out outside the confinement volume. Below are codes for the phantom + source and a visualization image where you can see the issue.<br>
<br>
Any ideas how to solve this?<br>
<br>
Thank you in advance! Sincerely,<br>
Ida<br>
<br>
# P H A N T O M<br>
/gate/world/daughters/name upperinterior<br>
/gate/world/daughters/insert cylinder<br>
/gate/upperinterior/placement/setTranslation 0.0 -3.5 -3.7 cm<br>
/gate/upperinterior/geometry/setRmax 14.7 cm<br>
/gate/upperinterior/geometry/setRmin 0.0 cm<br>
/gate/upperinterior/geometry/setHeight 21.4 cm<br>
/gate/upperinterior/geometry/setPhiStart 0. deg<br>
/gate/upperinterior/geometry/setDeltaPhi 180. deg<br>
/gate/upperinterior/setMaterial Water<br>
/gate/upperinterior/vis/forceWireframe<br>
/gate/upperinterior/vis/setColor blue<br>
<br>
# S O U R C E<br>
/gate/source/addSource F18_upper<br>
/gate/source/F18_upper/setActivity 1 becquerel<br>
/gate/source/F18_upper/gps/particle e+<br>
/gate/source/F18_upper/setForcedUnstableFlag true<br>
/gate/source/F18_upper/setForcedHalfLife 6586.2 s<br>
/gate/source/F18_upper/gps/energytype Fluor18<br>
/gate/source/F18_upper/gps/type Volume<br>
/gate/source/F18_upper/gps/shape Cylinder<br>
/gate/source/F18_upper/gps/radius 14.7 cm<br>
/gate/source/F18_upper/gps/halfz 10.7 cm<br>
/gate/source/F18_upper/gps/angtype iso<br>
/gate/source/F18_upper/gps/centre 0.0 -3.5 -3.7 cm<br>
/gate/source/F18_upper/gps/confine upperinterior_P<br>
/gate/source/F18_upper/visualize 1000 cyan 2<br>
<br>
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