<html> <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> </head> <body style="word-wrap:break-word"> <div><br> </div> <div>Hi Ida,</div> <div><br> </div> <div>we once ran into a similar problem and the solution was</div> <div>to use (now for your example) the line</div> <div><br> </div> <div>/gate/source/F18_upper/gps/confine upperinterior</div> <div><br> </div> <div>instead of your original</div> <div>/gate/source/F18_upper/gps/confine upperinterior_P</div> <div><br> </div> Hence, simply remove the "_P". We checked it and it <div>works for our examples</div> <div><br> </div> <div>Kind regards and best wishes,</div> <div><br> </div> <div>Uwe Pietrzyk<br> <div><span class="Apple-style-span" style="border-collapse:separate; color:rgb(0,0,0); font-family:'Lucida Grande'; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; orphans:2; text-indent:0px; text-transform:none; white-space:normal; widows:2; word-spacing:0px; font-size:medium"><span class="Apple-style-span" style="border-collapse:separate; color:rgb(0,0,0); font-family:Helvetica; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; orphans:2; text-indent:0px; text-transform:none; white-space:normal; widows:2; word-spacing:0px; font-size:medium"> <div style="word-wrap:break-word"><span class="Apple-style-span" style="border-collapse:separate; color:rgb(0,0,0); font-family:Helvetica; font-size:medium; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; orphans:2; text-indent:0px; text-transform:none; white-space:normal; widows:2; word-spacing:0px"> <div style="word-wrap:break-word"><span class="Apple-style-span" style="border-collapse:separate; color:rgb(0,0,0); font-family:Helvetica; font-size:medium; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; orphans:2; text-indent:0px; text-transform:none; white-space:normal; widows:2; word-spacing:0px"> <div style="word-wrap:break-word"><span class="Apple-style-span" style="border-collapse:separate; color:rgb(0,0,0); font-family:Helvetica; font-size:12px; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; orphans:2; text-indent:0px; text-transform:none; white-space:normal; widows:2; word-spacing:0px"> <div style="word-wrap:break-word"><span class="Apple-style-span" style="border-collapse:separate; color:rgb(0,0,0); font-family:Helvetica; font-size:12px; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; orphans:2; text-indent:0px; text-transform:none; white-space:normal; widows:2; word-spacing:0px"> <div style="word-wrap:break-word"><span class="Apple-style-span" style="border-collapse:separate; color:rgb(0,0,0); font-family:Helvetica; font-size:12px; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; orphans:2; text-indent:0px; text-transform:none; white-space:normal; widows:2; word-spacing:0px"> <div style="word-wrap:break-word"><span class="Apple-style-span" style="border-collapse:separate; color:rgb(0,0,0); font-family:Helvetica; font-size:12px; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; orphans:2; text-indent:0px; text-transform:none; white-space:normal; widows:2; word-spacing:0px"> <div style="word-wrap:break-word"> <div> <div style="word-wrap:break-word"> <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> ----------------------------------------------------------------------/</div> <div><br> </div> </div> </div> </div> </span></div> </span></div> </span></div> </span></div> </span></div> </span></div> </span></span></div> <br> <div> <div>On 10.03.2014, at 20:52, Ida Häggström wrote:</div> <br class="Apple-interchange-newline"> <div dir="ltr">Hello and thanks for your reply! <div><br> </div> <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> <div><br> </div> <div>If I can't find a solution I guess I'm left with doing a voxelized source...</div> <div><br> </div> <div>Thanks again!</div> <div>Ida</div> <div><br> </div> <div class="gmail_extra"><br> <br> <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> <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left-width:1px; border-left-color:rgb(204,204,204); border-left-style:solid; padding-left:1ex"> 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> <br> <br> <br> __________________________<br> <br> Marc Chamberland, MSc<br> PhD candidate<br> Department of Physics<br> Carleton University<br> Ottawa (ON)<br> <div> <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> <br> </div> </div> <source_confinement.PNG>_______________________________________________<br> Gate-users mailing list<br> <a href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank">Gate-users@lists.opengatecollaboration.org</a><mailto:<a href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank">Gate-users@lists.opengatecollaboration.org</a>><br> <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><br> <br> </blockquote> </div> <br> </div> </div> _______________________________________________<br> Gate-users mailing list<br> <a href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a><br> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</div> <br> </div> <br> <font face="Arial" color="Black" size="1"><br> ------------------------------------------------------------------------------------------------<br> ------------------------------------------------------------------------------------------------<br> Forschungszentrum Juelich GmbH<br> 52425 Juelich<br> Sitz der Gesellschaft: Juelich<br> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. 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