First, let me copy my old email about this question in 2004, /***************************************************************************************** I spent some time read the source code of GATE recently and found out why the spectrum looks different. The GATE program first generates two gamma photons, let's say S0 and S1. Then GATE will traces down the two photons respectively, and generates a Hits list. After that, the program will generates Adder_list and Readout_list one after another before generates the Single_list. If you check the ASCII output files, you will find that in the Singles_Adder file, for each photon, if a Compton backscatter event happened, then the event of energy deposit after backscatter will be listed in front of all other events in the Adder_list. So for each photon-pair with one  Compton backscatter event, we should have two possible event lists as: Case 1: (1). S0 backscatter in detector B (or A), but deposits energy (0.17MeV) in detector A (or B) (2). S0 deposits remained energy (0.34MeV) in detector B (or A) (3). S1_photoelectric_absorption (0.511MeV) in detector A (or B) or Case 2: (1). S0_photoelectric_absorption (0.511MeV) in detector A (or B) (2). S1 backscatter in detector B (or A), but deposits energy (0.17MeV) in detector A (or B) (3). S1 deposits remained energy (0.34MeV) in detector B (or A) when GATE process the Adder_lsit, in Case1, it will add the energy from enevt3 to enevt1 and update the other information of event1 with event3, and keep the event2, then generates the Readout_list with two events: (1). S1 (energy 0.17+0.511MeV) in detector A (or B) (2). S0_remained_energy (0.34MeV) in detector B (or A) for Case2, GATE will add the energy from enevt2 to enevt1 and keep the original information of event1, then generates the Readout list as: (1). S0 (energy 0.17+0.511MeV) in detector A (or B) (2). S1_remained_energy (0.34MeV) in detector B (or A) Therefore, no matter the Compton backscatter event was happened with photon S0 or S1, or in detector A or detector B, in the Singles_Readout List, the high energy Single always comes first. Then later, this Single will appears in the first column in the coincidence list. Which means that the first and the second photons in the coincidence pairs do not always correspond with the original two gamma photons S0 and S1. ***********************************************************************************************/ 2. When GATE processing the data it will in the order of digitizer chain.    and it always like this:    hits -> adder -> readout -> (blur) -> coincidence                                      |                                       -> delay -> delaycoincidence  As what I explained in the old email, all these steps is happened in the process of "adder" when GATE was processing the Compton back scatter events. So whenever the "coincidence" or "delay" module began to process the singles list, the sequence of the singles was already fixed in the singles list, and cannot be changed. I don't know what's your meaning about "<tt>sort by detector or detector pair</tt>". Whenever you sort one detector, for example, detector0, it will appear both in the first column and second column, and you don't know which event belong to the gamma1 and which event belong to the gamma2. So all you can do is just add up all the events from column1 and column2 (and divide by 2 if you like), and that's the spectra for detector0. Dr. Yuxuan ZHANG Dept. Experimental Diagnostic Imaging Univ. Texas, MD Anderson Cancer Center 1515 Holcombe Blvd, Unit 217 Houston, TX 77030-4095 Tel: +1-713-745-1671 Fax: +1-713-745-1672 <table width=100%> <tr valign=top> <td> <td>Paul Vaska <vaska@bnl.gov> 08/27/2007 12:00 PM <td>                To:        yuxuan.zhang@di.mdacc.tmc.edu         cc:        Irčne Buvat <buvat@imed.jussieu.fr>, gate-users-bounces@lists.healthgrid.org, gate-users@lists.healthgrid.org, Wonho Lee <wlee@bnl.gov>, Sudeepti Southekal <southekal@bnl.gov>         Subject:        Re: [Gate-users] Fwd: FW: Difference in energy spectrum for first and second event in         cylindrical PET system</table> <tt>Hi Andrew, I don't really understand this answer.  We have found a different   pattern concerning the ordering in the coincidence output.  Maybe the   code has changed.  From looking at time difference spectra for a   given detector pair (i.e. time of det b minus time of det a, _not_   time of column 2 minus time of column 1) it appears that true and   random coincidences are treated differently.  For trues, it seems   that the order can be either way (don't know what determines the   order) but for randoms, the 2nd single is always the later one.   Given this, it is still disconcerting to me that the energy spectra   are different.  True and random coincidences can have different   energy spectra (due to different constraints on geometry) but I don't   see how this could explain your effect.   Hopefully if you sort by   detector or detector pair instead of the position of the data in the   file, the energy and time spectra would make sense. Paul Paul Vaska, Ph.D. Medical Department, Building 490 Brookhaven National Laboratory Upton, NY 11973 vaska@bnl.gov (631)344-6228 fax:(631)344-4146 On Aug 27, 2007, at 11:09 AM, yuxuan.zhang@di.mdacc.tmc.edu wrote: > > Hi, > > This effect is not something new. One or two years ago someone   > already found this and reported here. > At that time I was also curious about this so I spent some time   > looking into it. After reading the source > code, my conclusion is that this result is caused by the GATE code   > about how it processing the energy > deposit from hits. > > When two gamma ray photons travel inside the material, GATE records   > all the energy deposit in an array. > Then in the "adder" process, GATE will add up all the energy   > deposits from the same gamma photon and > stored in one of the cells in the same array. During this step, the   > gamma photon with a higher total deposited > energy will always stored in front of the other gamma photon (or   > after, I can remember clearly). So in > the output file the photon1 and photon2 are just a label, it does   > not represents the original photon1 or > photon2. > > So if you really want the spectrum of the coincidences, just add   > the photon1 and photon2 together. > > Yuxuan > > > > > Irčne Buvat <buvat@imed.jussieu.fr> > Sent by: gate-users-bounces@lists.healthgrid.org > 08/26/2007 09:19 AM > > >         To:        gate-users@lists.healthgrid.org >         cc: >         Subject:        [Gate-users] Fwd: FW: Difference in energy   > spectrum for first and second event in         cylindrical PET system > > > > X-Ids: 165 > X-Greylist: delayed 857 seconds by postgrey-1.21 at ns2919.ovh.net; >   Sat, 25 Aug 2007 00:17:05 CEST > X-IronPort-AV: E=Sophos;i="4.19,305,1183352400"; >  d="mac'?jpg'145?scan'145,208,217,145";a="310266" > Subject: FW: Difference in energy spectrum for first and second   > event in >        cylindrical PET system > Date: Fri, 24 Aug 2007 16:54:28 -0500 > Thread-Topic: Difference in energy spectrum for first and second   > event in >    cylindrical PET system > Thread-Index: Acfmlfu0s1jG3B4WQ1WCyGHMNxLkBQAAzp2w > From: "Andrew Goertzen" <AGoertzen2@exchange.hsc.mb.ca> > To: <gate-users-owner@lists.healthgrid.org> > X-OriginalArrivalTime: 24 Aug 2007 21:54:28.0267 (UTC) >        FILETIME=[57E9BFB0:01C7E699] > Sender: mailman-bounces@lists.healthgrid.org > X-Virus-Scanned: ClamAV 0.88.7/4054/Fri Aug 24 18:55:59 2007 on  </tt> <tt>> shiva.jussieu.fr > X-Virus-Status: Clean > X-Miltered: at shiva.jussieu.fr with ID 46CF5710.007 by Joe's j- > chkmail (http://j-chkmail.ensmp.fr)! > The following message was rejected by the address 'gate- > users@lists.healthgrid.org'.  Could you please post it on my behalf? > Thanks, > Andrew > > Hi All, > I am simulating a cylindrical PET system in GATE 3.0.0 with the   > geometry of a microPET R4 and I am hoping someone can help explain   > the behaviour I am seeing.  My source is a 1.25 MBq line source at   > the centre of the FOV.  Data is written to an ASCII text file.   > When I create an energy histogram from the coincidence data output   > file I notice that the events identified as 'single 1' in a   > coincidence event (i.e. columns 1-21 of a coincident event in ascii   > format as described in section 10.1 of the user manual) have a   > different energy spectrum than events identified as 'single 2'.  I   > have included an example of this in the attached jpg image.  I do   > not think it is time related because I get this behaviour with and   > without 1.5ns of time blurring.  Also, the timestamp for single 1   > is not always less than for single 2.  I do not think it is energy   > related because the energy of single 1 is neither always greater   > than or always less than single 2. > So I am hoping that someone can answer the following questions: > How does GATE determine the order of singles that make up a   > coincident event? > Has anyone else observed this sort of difference between the first   > and second single? > I have included the .mac file I am using. > Regards, > Andrew Goertzen > Department of Radiology > University of Manitoba > <<EnergyHistogram.jpg>> <<microPETR4.mac>> > > Content-Type: image/jpeg; >       name="EnergyHistogram.jpg" > Content-Description: EnergyHistogram.jpg > Content-Disposition: attachment; >      filename="EnergyHistogram.jpg" > > > Content-Type: application/octet-stream; >   name="microPETR4.mac" > Content-Description: microPETR4.mac > Content-Disposition: attachment; >        filename="microPETR4.mac" > > > This email and/or any documents in this transmission is intended   > for the > addressee(s) only and may contain legally privileged or   > confidential information.  Any unauthorized use, disclosure,   > distribution, copying or dissemination is strictly prohibited.  If   > you receive this transmission in error, please notify the sender   > immediately and return the original. > > Ce courriel et tout document dans cette transmission est destiné ŕ   > la personne ou aux personnes ŕ qui il est adressé. Il peut contenir   > des informations privilégiées ou confidentielles. Toute   > utilisation, divulgation, distribution, copie, ou diffusion non   > autorisée est strictement défendue. Si vous n'ętes pas le   > destinataire de ce message, veuillez en informer l'expéditeur   > immédiatement et lui remettre l'original. > > > -- > > Irene Buvat, PhD > Equipe "Imagerie de la perfusion et des échanges moléculaires" > U678 INSERM > CHU Pitié Salpętričre > 91 Boulevard de l'Hôpital > 75634 Paris Cedex 13 > France > Tel : 01 53 82 84 19 > Fax : 01 53 82 84 48 > email : buvat@imed.jussieu.fr > http://www.guillemet.org/ > irene_______________________________________________ > Gate-users mailing list > Gate-users@lists.healthgrid.org > http://lists.healthgrid.org/mailman/listinfo/gate-users > > > _______________________________________________ > Gate-users mailing list > Gate-users@lists.healthgrid.org > http://lists.healthgrid.org/mailman/listinfo/gate-users </tt>