<div dir="ltr">Hi Uwe and thanks for the suggestion!<div> </div><div>Unfortunately it didn't solve the problem, the source is still only partially confined. I've also tried making a cold volume (in this case the lower half of the cylinder. I only want activity in the top half) and forbid activity in that region, but that doesn't seem to work either. I still get coincidences (and source visualization) in regions where I shouldn't. </div> </div><div class="gmail_extra"> <div class="gmail_quote">On Mon, Mar 10, 2014 at 10:11 PM, Pietrzyk, Uwe <<a href="mailto:u.pietrzyk@fz-juelich.de" target="_blank">u.pietrzyk@fz-juelich.de</a>> wrote: <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> Hi Ida, we once ran into a similar problem and the solution was to use (now for your example) the line /gate/source/F18_upper/gps/confine upperinterior instead of your original /gate/source/F18_upper/gps/confine upperinterior_P Hence, simply remove the "_P". We checked it and it works for our examples Kind regards and best wishes, Uwe Pietrzyk /---------------------------------------------------------------------- Prof. Dr. Uwe Pietrzyk Diplom-Physiker Institut für Neurowissenschaften und Medizin / INM-4 Forschungszentrum Jülich GmbH 52425 Jülich Tel: <a href="tel:%2B49-2461-61%204763" value="+492461614763">+49-2461-61 4763</a> Fax: <a href="tel:%2B49-2461-61%202820" value="+492461612820">+49-2461-61 2820</a> Mobil: <a href="tel:%2B49-162-103-4871" value="+491621034871">+49-162-103-4871</a> eMail: <a href="mailto:U.Pietrzyk@fz-juelich.de">U.Pietrzyk@fz-juelich.de</a><mailto:<a href="mailto:U.Pietrzyk@fz-juelich.de">U.Pietrzyk@fz-juelich.de</a>> <a href="http://www.fz-juelich.de/inm" target="_blank">http://www.fz-juelich.de/inm</a><<a href="http://www.fz-juelich.de/inb/inb-3/" target="_blank">http://www.fz-juelich.de/inb/inb-3/</a>> & Bergische Universität Wuppertal Fachbereich C - Physik / D.08.01 Gaußstr. 20 42097 Wuppertal Tel: <a href="tel:%2B49-%280%29202-439-3523" value="+492024393523">+49-(0)202-439-3523</a> Fax: <a href="tel:%2B49-%280%29202-439-2811" value="+492024392811">+49-(0)202-439-2811</a> eMail: <a href="mailto:Uwe.Pietrzyk@physik.uni-wuppertal.de">Uwe.Pietrzyk@physik.uni-wuppertal.de</a><mailto:<a href="mailto:Uwe.Pietrzyk@physik.uni-wuppertal.de">Uwe.Pietrzyk@physik.uni-wuppertal.de</a>> <a href="http://www.medizinphysik.uni-wuppertal.de" target="_blank">http://www.medizinphysik.uni-wuppertal.de</a><<a href="http://www.medizinphysik.uni-wuppertal.de/" target="_blank">http://www.medizinphysik.uni-wuppertal.de/</a>> ----------------------------------------------------------------------/ <div class=""> On 10.03.2014, at 20:52, Ida Häggström wrote: Hello and thanks for your reply! 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. If I can't find a solution I guess I'm left with doing a voxelized source... Thanks again! Ida </div><div class="">On Mon, Mar 10, 2014 at 6:34 PM, Marc Chamberland <<a href="mailto:MarcChamberland@cmail.carleton.ca">MarcChamberland@cmail.carleton.ca</a><mailto:<a href="mailto:MarcChamberland@cmail.carleton.ca">MarcChamberland@cmail.carleton.ca</a>>> wrote: Hi Ida, 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.) 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> My first instinct is that this may be related. Marc __________________________ Marc Chamberland, MSc PhD candidate Department of Physics Carleton University Ottawa (ON) </div><div><div class="h5">On Mar 10, 2014, at 11:34, Ida Häggström <<a href="mailto:ida.haggstrom@radfys.umu.se">ida.haggstrom@radfys.umu.se</a><mailto:<a href="mailto:ida.haggstrom@radfys.umu.se">ida.haggstrom@radfys.umu.se</a>><mailto:<a href="mailto:ida.haggstrom@radfys.umu.se">ida.haggstrom@radfys.umu.se</a><mailto:<a href="mailto:ida.haggstrom@radfys.umu.se">ida.haggstrom@radfys.umu.se</a>>>> wrote: Hello! 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. Any ideas how to solve this? Thank you in advance! Sincerely, Ida # P H A N T O M /gate/world/daughters/name upperinterior /gate/world/daughters/insert cylinder /gate/upperinterior/placement/setTranslation 0.0 -3.5 -3.7 cm /gate/upperinterior/geometry/setRmax 14.7 cm /gate/upperinterior/geometry/setRmin 0.0 cm /gate/upperinterior/geometry/setHeight 21.4 cm /gate/upperinterior/geometry/setPhiStart 0. deg /gate/upperinterior/geometry/setDeltaPhi 180. deg /gate/upperinterior/setMaterial Water /gate/upperinterior/vis/forceWireframe /gate/upperinterior/vis/setColor blue # S O U R C E /gate/source/addSource F18_upper /gate/source/F18_upper/setActivity 1 becquerel /gate/source/F18_upper/gps/particle e+ /gate/source/F18_upper/setForcedUnstableFlag true /gate/source/F18_upper/setForcedHalfLife 6586.2 s /gate/source/F18_upper/gps/energytype Fluor18 /gate/source/F18_upper/gps/type Volume /gate/source/F18_upper/gps/shape Cylinder /gate/source/F18_upper/gps/radius 14.7 cm /gate/source/F18_upper/gps/halfz 10.7 cm /gate/source/F18_upper/gps/angtype iso /gate/source/F18_upper/gps/centre 0.0 -3.5 -3.7 cm /gate/source/F18_upper/gps/confine upperinterior_P /gate/source/F18_upper/visualize 1000 cyan 2 <source_confinement.PNG>_______________________________________________ Gate-users mailing list </div></div><a href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a><mailto:<a href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a>><mailto:<a href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a><mailto:<a href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a>>> <div class=""><a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> _______________________________________________ Gate-users mailing list <a href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a><mailto:<a href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a>> <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> </div>------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. 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