Hello ! in Ascii Coincidenc.dat file certain columns like 4-6,9-11,27-29,32-34 represents XYZ position of the annihilation in world referential ? what does it mean? which are the columns one should consider to see the image of the simulation, thanks <div class="gmail_quote">On Thu, Dec 13, 2012 at 10:32 PM, <<a href="mailto:gate-users-request@lists.opengatecollaboration.org" target="_blank">gate-users-request@lists.opengatecollaboration.org</a>> wrote: <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Gate-users mailing list submissions to <a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a> To subscribe or unsubscribe via the World Wide Web, visit <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> or, via email, send a message with subject or body 'help' to <a href="mailto:gate-users-request@lists.opengatecollaboration.org">gate-users-request@lists.opengatecollaboration.org</a> You can reach the person managing the list at <a href="mailto:gate-users-owner@lists.opengatecollaboration.org">gate-users-owner@lists.opengatecollaboration.org</a> When replying, please edit your Subject line so it is more specific than "Re: Contents of Gate-users digest..." Today's Topics: 1. Re: about "Forbid" command in GATE simulation (?? ?) 2. Re: Voxelized source orientation (J?r?me Suhard) 3. Gate command menu (dme627b) 4. Re: Gate command menu (Carlos Uribe) ---------------------------------------------------------------------- Message: 1 Date: Thu, 13 Dec 2012 23:30:34 +0900 From: ?? ? <<a href="mailto:takuyama@med.hokudai.ac.jp">takuyama@med.hokudai.ac.jp</a>> To: Kaiyang Li <<a href="mailto:kl780@uowmail.edu.au">kl780@uowmail.edu.au</a>>, gate-users <<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>> Subject: Re: [Gate-users] about "Forbid" command in GATE simulation Message-ID: <CADb2yx9Vjttz8=<a href="mailto:NhQSVh%2BEJABf_2UWL5wdCOncqi2z2BKxnNOQ@mail.gmail.com">NhQSVh+EJABf_2UWL5wdCOncqi2z2BKxnNOQ@mail.gmail.com</a>> Content-Type: text/plain; charset="iso-2022-jp" Hello Kaiyang Li, I'm still struggling with "forbid". I tried the simple geometry, too, but my simulation stops with "***Break*** segmentation violation" and I cannot proceed to even see the reconstructed image... this didn't happen before... Anyway, it seems the command is working somehow. When I tried to forbid the whole source by surrounding with the "forbidding" volume and start simulation, GATE gave me the message of "primaries were always generated in forbidden volumes!" and the simulation was shut down. Also, you can visualize the source by /gate/source/FictiveSource/visualize "count" "color" "size" This command should reflect the "forbid" as well, so we are supposed to be able to see the "forbidden" source... but... You can check how the "forbid" command works in GATE in GateSPSPosDistribution.cc line:150 After all, I cannot give you any solution to this problem. I'll still work on with this, so if you find anything new, please let me know. Taku 2012/12/10 Kaiyang Li <<a href="mailto:kl780@uowmail.edu.au">kl780@uowmail.edu.au</a>> > Hi Taku, > > My name is Kaiyang Li, a GATE user. > I have the problem of using "forbid" in my simulation. It seems that the > forbid area is simply > not forbidden at all. > > I have read all other questions, including yours. Have you figure it out > yet? > I have used GATE for half a year and run some other complex simulations > successfully but for this forbid one, it seems something is wrong. > > Here is my simple code followed by the GATE instruction: > > /gate/world/daughters/name cold_area > /gate/world/daughters/insert cylinder > /gate/cold_area/vis/forceWireframe > /gate/cold_area/vis/setColor green > /gate/cold_area/geometry/setRmax 2.0 mm > /gate/cold_area/geometry/setHeight 0.3 mm > /gate/cold_area/setMaterial Water > > /gate/run/initialize > > /gate/source/addSource number1 > /gate/source/number1/setActivity 37000000. becquerel > /gate/source/number1/gps/particle gamma > /gate/source/number1/setType backtoback > /gate/source/number1/gps/monoenergy 511. keV > /gate/source/number1/setForcedUnstableFlag true > /gate/source/number1/setForcedHalfLife 6586 s > /gate/source/number1/gps/type Volume > /gate/source/number1/gps/shape Cylinder > /gate/source/number1/gps/radius 4. mm > /gate/source/number1/gps/halfz 0.15 mm > /gate/source/number1/gps/centre 0. 0. 0. mm > /gate/source/number1/gps/angtype iso > /gate/source/number1/gps/Forbid cold_area > /gate/source/number1/dump 1 > /gate/source/list > > The reconstructed image shows that there is no forbidden area. > Probably the forbidden command is not working, what do you think? > > > Kind Regards, > Kaiyang Li > -- Hokkaido University, Graduate school of medicine, medical physics and engineering D1 ????? ??? ????? ???????? D1 Taku Yamanaka ?? ? <a href="mailto:takuyama@med.hokudai.ac.jp">takuyama@med.hokudai.ac.jp</a> -- -------------- next part -------------- An HTML attachment was scrubbed... URL: <<a href="http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20121213/b6e4d5a9/attachment-0001.html" target="_blank">http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20121213/b6e4d5a9/attachment-0001.html</a>> ------------------------------ Message: 2 Date: Thu, 13 Dec 2012 17:19:25 +0100 From: J?r?me Suhard <<a href="mailto:jerome@suhard.fr">jerome@suhard.fr</a>> To: Tom Buitenhuis <<a href="mailto:hjt.buitenhuis@gmail.com">hjt.buitenhuis@gmail.com</a>> Cc: <a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a> Subject: Re: [Gate-users] Voxelized source orientation Message-ID: <CANCPmRcWPWs2Fvj_GBXUp+4D_nNmg_Q15=<a href="mailto:Khj%2BFauYPqOPK3Cw@mail.gmail.com">Khj+FauYPqOPK3Cw@mail.gmail.com</a>> Content-Type: text/plain; charset="iso-8859-1" Hi, 2012/12/13 Tom Buitenhuis <<a href="mailto:hjt.buitenhuis@gmail.com">hjt.buitenhuis@gmail.com</a>> > According to the documentation of these file formats, data is stored in > row-major order. For example, for the InterFile 3.3 format, the specs can > be found here: > <a href="http://www.nucmed.si.mahidol.ac.th/nucmed1/pip/interfil1.html" target="_blank">http://www.nucmed.si.mahidol.ac.th/nucmed1/pip/interfil1.html</a> > > Relevant section: > "I.5. IMAGE DATA > > A. Image arrays are to be arranged with the first value (in the binary > data) corresponding to the pixel in the top left corner and with the value > corresponding to the pixel in the bottom right corner occurring last. Image > arrays in V3.3 remain 2-D. The order of the pixel data shall increment by > column from left to right, and then (for each such row) by row, from top to > bottom. This is also known as row major order." > > more info on row-major order: <a href="http://en.wikipedia.org/wiki/Row-major_order" target="_blank">http://en.wikipedia.org/wiki/Row-major_order</a> > > However, when I simulate a voxelized source, the activity seems to have > the y-axis inverted, i.e. it seems that GATE ignores this row-major part of > the InterFile specification. An example of this can be seen in the attached > image. On the left, there is a window where I display the InterFile source > in AMIDE, which correctly interprets the specs. The top, white, part of the > source has an activity of 10 Bq, where the bottom, green, part has an > activity of 500 Bq. On the right of the image, I display the root output of > the source-position of simulated coincidences, where we can see that the > top-part now has the higher activity, instead of the bottom part. > > The same seems to hold for the Analyze 7.5 voxelized phantom. When we > center both the source and the phantom, this shouldn't be a problem in a > cylindrical symmetric PET-scanner, but when we translate one with respect > to the other, this could be problematic. The fix is ofcourse easy, i.e. > translate in the -y instead of the +y direction, but when this is > undocumented, incorrect simulations will be performed. > > Does anyone else have any experience with this? Am I making a mistake, or > is this a bug in the implementation of the file specs in GATE? > GATE doesn't conform to InterFile specs. It just parses some keys according to the function GateSourceVoxelInterfileReader::ReadKey(FILE* fp) in source/physics/src/GateSourceVoxelInterfileReader.cc . Here are the relevant portions: if ( key == "matrix size [1]" ) { sscanf(value,"%d",m_dim); } else if ( key == "matrix size [2]" ) { sscanf(value,"%d",m_dim+1); } else if ( ( key == "number of slices" ) || (key == "number of images") ) { sscanf(value,"%d",&m_numPlanes); } else if ( key == "scaling factor (mm/pixel) [1]" ) { sscanf(value,"%f",m_pixelSize); } else if ( key == "scaling factor (mm/pixel) [2]" ) { sscanf(value,"%f",m_pixelSize+1); } else if ( key == "slice thickness (pixels)" ) { sscanf(value,"%f",&m_planeThickness); } else if ( key == "name of data file" ) { m_dataFileName = std::string(value); } else if ( key == "number format" ) { if ( (strcmp(value,"float")==0) || (strcmp(value,"FLOAT")==0) ) m_dataTypeName = "FLOAT"; else if ( (strcmp(value,"unsigned integer")==0) || (strcmp(value,"UNSIGNED INTEGER")==0) ) m_dataTypeName = "UNSIGNED INTEGER"; else G4cout << "Unrecognised type name '" << value << "'" << G4endl; } else if (key == "imagedata byte order") { if ( strcmp(value,"BIGENDIAN") == 0 ) m_dataByteOrder = "BIGENDIAN"; else if ( strcmp(value,"LITTLEENDIAN") == 0) m_dataByteOrder = "LITTLEENDIAN"; else G4cerr << "Unrecognized data byte order '" + G4String(value) + "', assuming default BIGENDIAN\n" << G4endl; } else { // G4cout << "Key not processed: '" << key << "'" << G4endl; } Best regards, -- J?r?me Suhard -------------- next part -------------- An HTML attachment was scrubbed... URL: <<a href="http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20121213/01ad17f6/attachment-0001.html" target="_blank">http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20121213/01ad17f6/attachment-0001.html</a>> ------------------------------ Message: 3 Date: Thu, 13 Dec 2012 13:32:54 -0800 From: dme627b <<a href="mailto:dme627b@gmail.com">dme627b@gmail.com</a>> To: "<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>" <<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>> Subject: [Gate-users] Gate command menu Message-ID: <<a href="mailto:201212131332533900771@gmail.com">201212131332533900771@gmail.com</a>> Content-Type: text/plain; charset="us-ascii" Hi everyone, I am a new gate user. I do not know if there is a Gate command menu which includes all the gate command, because I think it will be very helpful. Any other document of Gate command is also appreciate. Can anyone help me? Thank you in advance. Best Regards, Jeremy -------------- next part -------------- An HTML attachment was scrubbed... URL: <<a href="http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20121213/7b6bd3a5/attachment-0001.html" target="_blank">http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20121213/7b6bd3a5/attachment-0001.html</a>> ------------------------------ Message: 4 Date: Thu, 13 Dec 2012 13:37:44 -0800 From: Carlos Uribe <<a href="mailto:carluri@phas.ubc.ca">carluri@phas.ubc.ca</a>> To: dme627b <<a href="mailto:dme627b@gmail.com">dme627b@gmail.com</a>> Cc: "<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>" <<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>> Subject: Re: [Gate-users] Gate command menu Message-ID: <<a href="mailto:CAPJy_1TQZ-9D1kVAretM%2B%2B14bnKnY%2B4AiYvbKrQHYPaNYXT03g@mail.gmail.com">CAPJy_1TQZ-9D1kVAretM++14bnKnY+4AiYvbKrQHYPaNYXT03g@mail.gmail.com</a>> Content-Type: text/plain; charset="iso-8859-1" Hi Jeremy, you can try typing "Gate" in your terminal then "help". does that work? On Thu, Dec 13, 2012 at 1:32 PM, dme627b <<a href="mailto:dme627b@gmail.com">dme627b@gmail.com</a>> wrote: > ** > Hi everyone, > > I am a new gate user. I do not know if there is a Gate command menu which > includes all the gate command, because I think it will be very helpful. Any > other document of Gate command is also appreciate. > > Can anyone help me? Thank you in advance. > > Best Regards, > > Jeremy > > _______________________________________________ > Gate-users mailing list > <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> > > -- > Carlos F Uribe > > -------------- next part -------------- An HTML attachment was scrubbed... URL: <<a href="http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20121213/c7de1876/attachment.html" target="_blank">http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20121213/c7de1876/attachment.html</a>> ------------------------------ _______________________________________________ Gate-users mailing list <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> End of Gate-users Digest, Vol 79, Issue 17 ****************************************** </blockquote></div>