<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> <html> <head> <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type"> </head> <body bgcolor="#ffffff" text="#000000"> Dear Yi I agree with you and the rest of the users. This  warning message has been reported before many times. On 23rd of November of this year we have confirmed at the GATE users mailing list the conclusion you have just made. Indeed, the source code clearly indicates that a size of 1 for the photon ID vector is strange because it means that a positron was generated and then only 1 gamma photon was generated. Normally after a positron is emiited there are two possibilities. Either the positron will be annihilated or not. If Positron Annihilation takes place then 2 gamma photons should be produced (photon vector size = 2). On the other hand if no annihilation takes place then we should have no gamma photons and the size of the photon vector should be 0. When only 1 gamma photon is tracked (photon vector size =1) we have an unexpected case which has to be investigated. However we have observed that this warning message is caused when a) the source volume is not surrounded by a phantom volume thick enough to ensure the annihilation of the emitted positrons or b) the source volume or some part of it is not surrounded entirely by a phantom volume. In this case some positrons will escape the attenuation phantom volumes without interacting and then eventually escape the world. As soon as they escape the world and no interaction is recorded then GATE produces a similar warning message with photon vector size value of 0. The reason you do not see this warning message is because you have probably set the verbose value to 0. Verbose 0 does not produce warning message for this case because it is an expected scenario (photon escapes the world without annihilation). When verbose is 0 you only see warning messages where the photon vector size of 1 because GATE considers this case strange and wants to notify the user about this. However those two warning messages are strongly related to each other. When the one is produced the other is also generated. When the geometry is designed in such a way that the phantom volumes surround entirely the source volumes then you should not see any of these warning messages. Please check the relative positions of your source and phantom volumes.Does the phantom volumes surround your source entirely?Is the surrounding area thick enough (larger than the positron range of your source) to ensure annihilation of the emitted positrons? These warnings are also observed in the previous versions of GATE. Best regards Nicolas Nicolas Karakatsanis PhD Candidate Biomedical Simulations and Imaging Laboratory School of Electrical and Computer Engineer National Technical University of Athens, Greece Su, Yi wrote: <blockquote cite="mid:D0674FCAA0917E439E7F2B65BEF2ED61FF56D201EA@RAD-VMSRVEXV1.rad.wustl.edu" type="cite"> <meta http-equiv="Content-Type" content="text/html; "> <meta name="Generator" content="Microsoft Word 12 (filtered medium)">  <style>  </style> <div class="Section1"> I studied the Reference manual a little bit, and it appears that in the source code it acknowledged that this is a strange case, since the photonID vector size is 1, instead of 0 or 2. If the positron escaped without annihilation, the photonID vector should be 0. <o:p></o:p> <o:p> </o:p> Does this happen in earlier version of GATE at all (I am using version 3.1.2)?<o:p></o:p> <o:p> </o:p> Yi<o:p></o:p> <o:p> </o:p> <div style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0in 0in;"> From: <a class="moz-txt-link-abbreviated" href="mailto:yuxuan.zhang@di.mdacc.tmc.edu">yuxuan.zhang@di.mdacc.tmc.edu</a> [<a class="moz-txt-link-freetext" href="mailto:yuxuan.zhang@di.mdacc.tmc.edu">mailto:yuxuan.zhang@di.mdacc.tmc.edu</a>] Sent: Friday, January 04, 2008 3:44 PM To: Su, Yi Cc: '<a class="moz-txt-link-abbreviated" href="mailto:gate-users@lists.healthgrid.org">gate-users@lists.healthgrid.org</a>'; <a class="moz-txt-link-abbreviated" href="mailto:gate-users-bounces@lists.healthgrid.org">gate-users-bounces@lists.healthgrid.org</a> Subject: Re: [Gate-users] GATE running problem--WARNING : positron found and photonID vector size 1<o:p></o:p> </div> <o:p> </o:p> Usually it is because that the size of your phantom is not big enough therefore some positron can escape from the phantom without annihilation. If there are not a lot of warning messages, (less than a few per second) then that's fine. Otherwise you need to check your phantom and source definition. The common error is that the part of the source is outside the phantom. yuxuan <o:p></o:p> <table class="MsoNormalTable" style="width: 100%;" border="0" cellpadding="0" width="100%"> <tbody> <tr> <td style="padding: 0.75pt;" valign="top"> </td> <td style="padding: 0.75pt;" valign="top"> "Su, Yi" <a class="moz-txt-link-rfc2396E" href="mailto:suy@mir.wustl.edu"><suy@mir.wustl.edu></a> Sent by: <a class="moz-txt-link-abbreviated" href="mailto:gate-users-bounces@lists.healthgrid.org">gate-users-bounces@lists.healthgrid.org</a> <o:p></o:p> 01/04/2008 01:31 PM <o:p></o:p> </td> <td style="padding: 0.75pt;" valign="top">                 To:        <a class="moz-txt-link-rfc2396E" href="mailto:'gate-users@lists.healthgrid.org'">"'gate-users@lists.healthgrid.org'"</a> <a class="moz-txt-link-rfc2396E" href="mailto:gate-users@lists.healthgrid.org"><gate-users@lists.healthgrid.org></a>         cc:                 Subject:        [Gate-users] GATE running problem--WARNING : positron found and photonID vector size 1<o:p></o:p> </td> </tr> </tbody> </table> Hi there,   I am running a GATE simulation and the following warning message keeps popping up:   [GateTrajectoryNavigator::FindAnnihilationGammasTrackID]  WARNING : positron found and photonID vector size: 1   Does anyone know what is going on, and what might be the problem? I am using Gate 3.1.2 and I am simulating an ecat system with a simple cylinder phantom and source.   Thanks a lot,   Yi __________________________________________ Yi Su, PhD Division of Radiological Sciences Mallinckrodt Institute of Radiology Washington University School of Medicine Campus Box 8225 510 S. Kingshighway Blvd St. Louis MO 63110 Phone: 314-362-8363 Fax:       314-362-9940 Email: <a class="moz-txt-link-abbreviated" href="mailto:suy@mir.wustl.edu">suy@mir.wustl.edu</a>   <o:p></o:p> <o:p> </o:p> <div class="MsoNormal" style="text-align: center;" align="center"> <hr align="center" size="2" width="100%"></div> The materials in this message are private and may contain Protected Healthcare Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.<tt>_______________________________________________</tt> <tt>Gate-users mailing list</tt> <tt><a class="moz-txt-link-abbreviated" href="mailto:Gate-users@lists.healthgrid.org">Gate-users@lists.healthgrid.org</a></tt> <tt><a class="moz-txt-link-freetext" href="http://lists.healthgrid.org/mailman/listinfo/gate-users">http://lists.healthgrid.org/mailman/listinfo/gate-users</a></tt><o:p></o:p> </div> <hr> The materials in this message are private and may contain Protected Healthcare Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. __________ NOD32 2765 (20080104) Information __________ This message was checked by NOD32 antivirus system. <a moz-do-not-send="true" href="http://www.eset.com">http://www.eset.com</a> <pre wrap=""> <hr size="4" width="90%"> _______________________________________________ Gate-users mailing list <a class="moz-txt-link-abbreviated" href="mailto:Gate-users@lists.healthgrid.org">Gate-users@lists.healthgrid.org</a> <a class="moz-txt-link-freetext" href="http://lists.healthgrid.org/mailman/listinfo/gate-users">http://lists.healthgrid.org/mailman/listinfo/gate-users</a> __________ NOD32 2765 (20080104) Information __________ This message was checked by NOD32 antivirus system. <a class="moz-txt-link-freetext" href="http://www.eset.com">http://www.eset.com</a> </pre> </blockquote> </body> </html>