<html> <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> </head> <body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""> Hi, <div class=""> </div> <div class="">Ah, my apologies. I believe GatePet2Stir and the c code only works on cylindricalPET systems in Gate, then. Those systems are made up of components rsector, module, submodule, and crystal in Gate, whereas the ecat system only has components block and crystal.</div> <div class=""> </div> <div class="">At this point, modifying the c code probably is your best option. </div> <div class=""> </div> <div class=""> <div apple-content-edited="true" class=""><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-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "> <div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; " class=""> <div class="">Marc</div> <div class=""> </div> <div class=""> </div> <div class=""> </div> </div> </div> <div> <blockquote type="cite" class=""> <div class="">On Nov 28, 2014, at 07:49, Kris Thielemans <<a href="mailto:kris.f.thielemans@gmail.com" class="">kris.f.thielemans@gmail.com</a>> wrote:</div> <div class="">Hi This file gives us the same problems as GatePet2Stir. A closer look shows that this c file is looking for module and submodule info in the root file, while in our root file there is only block info. Indeed, in the Gate 7.0 ecat macro, there is no info on modules at all. I think I can modify the C code accordingly but if anyone can provide pointers, or tell us why this happened, this would be great. Kris <blockquote type="cite" class="">-----Original Message----- From: Marc Chamberland [<a href="mailto:MarcChamberland@cmail.carleton.ca" class="">mailto:MarcChamberland@cmail.carleton.ca</a>] Sent: 27 November 2014 12:42 To: Kris Thielemans Cc: Ana Margarida Mota; Gate Users Subject: Re: [Gate-users] Sinogram from Root file Hi Kris, hi Ana, I’ve never used the DigiGate option, but it might work. However, it only works if you have saved the Hits (and not just the coincidences or the singles) in your Root output. You would then just use the -d (or --d? I'll check and correct the Gate wiki, if needed) option, with the same macro you used before (but adding the sinogram output). Again, I'm not sure if that would work, but it's worth a try. Another possibility is to use Ross Schmidtlein and Sadek Nehmeh's code for generating projection data from Root output: <a href="http://www.opengatecollaboration.org/sites/opengatecollaboration.org/file" class="">http://www.opengatecollaboration.org/sites/opengatecollaboration.org/file</a> s/Bin_GATE_v1.0.c That's the code I've used before (and my personal preferred way of going from Gate to STIR). You just need to put in the correct values for your scanner. Cheers, Marc __________________________ Marc Chamberland, MSc PhD candidate Department of Physics Carleton University Ottawa (ON) <blockquote type="cite" class="">On Nov 26, 2014, at 17:37, Kris Thielemans <kris.f.thielemans@gmail.com> </blockquote> wrote: <blockquote type="cite" class=""> Hi Marc Ana is currently visiting UCL, so we do know about STIR utilities :-) We tried gatepet2stir, but it didn't seem to like the GATE 7.0 output (it </blockquote> complained about some Root fields not being recognised) and gave no output. Ana will have the error messages so hopefully she'll find the time to send those to this list, but she's quite pressed in time right now. <blockquote type="cite" class=""> So, instead, what we tried is to use the ecat sinogram output via /gate/output/sinogram/enable /gate/output/sinogram/setFileName MySinogramFileName That outputs the 3D sinogram as raw floats. There's then a STIR utility (that </blockquote> needed fixing for the data-type) to create the corresponding Interfile header. So Ana is currently running simulations with both Root and ecat sinogram output. That seems to work ok. <blockquote type="cite" class=""> However, now we're wondering if we can use an existing Root file, read </blockquote> that into GATE, and use the above macro to get the corresponding sinogram output. Is that possible? For instance, I see at <blockquote type="cite" class=""> </blockquote> http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:How_to _run_Gate#How_to_launch_DigiGate <blockquote type="cite" class=""> that DigiGate can read an existing root file by using "Gate -d < </blockquote> somemacro.mac" (or is it "Gate --d"?). Would that work here as well? What would the appropriate contents of that macro then be (the same as the original one with the sinogram output enabled?). I can't seem to find any documentation on the -d option, but then I don't know Gate really. <blockquote type="cite" class=""> Thanks Kris Thielemans Senior Lecturer at University College London, Institute of Nuclear Medicine, UCL Hospital From: gate-users-bounces@lists.opengatecollaboration.org [mailto:gate- </blockquote> users-bounces@lists.opengatecollaboration.org] On Behalf Of Marc Chamberland <blockquote type="cite" class="">Sent: 26 November 2014 18:25 To: Ana Margarida Mota Cc: Gate Users Subject: Re: [Gate-users] Sinogram from Root file Hi Ana, Sorta. A couple of people have written tools over the years to convert the </blockquote> Root output to projection data readable by STIR (for image reconstruction) and STIR provides a utility to extract sinograms from the projection data. <blockquote type="cite" class=""> This program generates projection data readable by STIR: </blockquote> http://sourceforge.net/projects/gatepet2stir/ <blockquote type="cite" class="">You can get STIR from here: http://stir.sourceforge.net The utility extract_segments from STIR allows you to extract the sinograms </blockquote> (in Interfile format, so you’ll to use Amide or a similar to program to display them). <blockquote type="cite" class=""> Cheers, Marc __________________________ Marc Chamberland, MSc PhD candidate Department of Physics Carleton University Ottawa (ON) On Nov 26, 2014, at 12:35, Ana Margarida Mota <ninimota87@gmail.com> </blockquote> wrote: <blockquote type="cite" class=""> Dear Gate users, I would like to know if there is any way to have a sinogram from the root </blockquote> file?? <blockquote type="cite" class=""> I know we can have directly the sinogram as output, but that's not the </blockquote> question. <blockquote type="cite" class="">My simulation is still running and I it would be good to analyze the </blockquote> sinogram from data obtained so far. <blockquote type="cite" class=""> Thanks in advance!! Regards, Ana Margarida _______________________________________________ Gate-users mailing list Gate-users@lists.opengatecollaboration.org http://lists.opengatecollaboration.org/mailman/listinfo/gate-users </blockquote> </blockquote> </div> </blockquote> </div> </div> </body> </html>