<div dir="ltr"><div><div><div>Hi, Also, you may want to use a navigator which is appropriate for imaging applications (meaning when you want to retrieve scatter information), as described in the documentation. The ImageNestedParameterizedVolume is used only for Radiotherapy Applications as it is included in the section entitled : "Alternative usage of voxelized geometry (radiation therapy applications)" </div>Use the regular navigator for example, it is as fast as the image nested one. </div>And by the way Yannick, good trick for attaching a nested volume as phantomSD :-) </div>Regards, Simon </div><div class="gmail_extra"> <div class="gmail_quote">On Thu, Mar 6, 2014 at 2:02 PM, Berker, Yannick <<a href="mailto:Yannick.Berker@philips.com" target="_blank">Yannick.Berker@philips.com</a>> wrote: <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> <div link="blue" vlink="purple" lang="EN-US"> <div> Hi Tom, which version of GATE are you using? I had my problems with early versions of GATE 6 (like 6.0 or 6.1), and I have managed to get seemingly correct values with GATE 6.2. First, I recall that for Rayleigh (not Compton) interactions, there was a bug in GATE 6.0 and 6.1 that was fixed in 6.2. In 6.0 and 6.1, an interaction from a “PenelopeRayleighScattering” (6.0/6.1) or “RayleighScattering” (6.1) process would not be counted as a Rayleigh interaction in the ROOT output since the code checks for a process name with “LowEnRayleigh” in it – this is due to these lines here: <a href="http://www.opengatecollaboration.org/lxr/source/6.0.0/source/digits_hits/src/GateAnalysis.cc#L278" target="_blank">http://www.opengatecollaboration.org/lxr/source/6.0.0/source/digits_hits/src/GateAnalysis.cc#L278</a> <a href="http://www.opengatecollaboration.org/lxr/source/6.1.0/source/digits_hits/src/GateAnalysis.cc#L281" target="_blank">http://www.opengatecollaboration.org/lxr/source/6.1.0/source/digits_hits/src/GateAnalysis.cc#L281</a> Here, is it fixed: <a href="http://www.opengatecollaboration.org/lxr/source/6.2.0/source/digits_hits/src/GateAnalysis.cc#L292" target="_blank">http://www.opengatecollaboration.org/lxr/source/6.2.0/source/digits_hits/src/GateAnalysis.cc#L292</a> Here are some physics processes which could have been affected by that bug: <a href="http://www.opengatecollaboration.org/lxr/source/6.0.0/source/physics/src/GateRayleighPenelopePB.cc" target="_blank">http://www.opengatecollaboration.org/lxr/source/6.0.0/source/physics/src/GateRayleighPenelopePB.cc</a> <a href="http://www.opengatecollaboration.org/lxr/source/6.1.0/source/physics/src/GateRayleighPenelopePB.cc" target="_blank">http://www.opengatecollaboration.org/lxr/source/6.1.0/source/physics/src/GateRayleighPenelopePB.cc</a> <a href="http://www.opengatecollaboration.org/lxr/source/6.1.0/source/physics/src/GateRayleighPB.cc" target="_blank">http://www.opengatecollaboration.org/lxr/source/6.1.0/source/physics/src/GateRayleighPB.cc</a> If you are already using GATE 6.2, the problem (or at least one solution) might be that you can attach the PhantomSD to the subvolumes which are created from your voxelized phantom. My current code contains this: /gate/patientAT_AG_SI1_31/attachPhantomSD […, 4 more] /gate/patientAT_AG_SI5_36/attachPhantomSD /gate/patientAir_0/attachPhantomSD /gate/patientAir_1/attachPhantomSD /gate/patientConnectiveTissue_40/attachPhantomSD /gate/patientLung_10/attachPhantomSD […, 27 more] /gate/patientLung_9/attachPhantomSD /gate/patientMarrow_Bone01_41/attachPhantomSD […, 13 more] /gate/patientMarrow_Bone08_55/attachPhantomSD /gate/patientSoftTissus_37/attachPhantomSD /gate/patientSoftTissus_38/attachPhantomSD /gate/patientSoftTissus_39/attachPhantomSD /gate/patientworldDefaultAir/attachPhantomSD The complete list depends on your phantom – you should include all subvolumes, but you may only include existing ones. I think the list of volumes generated is part of the GATE output, so you can grab this from your current simulation, prepend “/gate/patient” (or whatever your generating volume name is), append “/attachPhantomSD” and save this as the phantomSD.mac specific to that voxelized input and the volume-generation parameters. Should any of these change without yout re-generating the mac file, in the best case you lose one of the volumes you had in your the mac file before and your script returns an error message. In the worst case, you will get inaccurate results without noticing, for example, when only additional volumes are generated and you miss scatter interactions in those without getting any error message. Best regards Yannick <div> <div style="border:none;border-top:solid #e1e1e1 1.0pt;padding:3.0pt 0in 0in 0in"> From: Tom Buitenhuis [mailto:<a href="mailto:h.j.t.buitenhuis@rug.nl" target="_blank">h.j.t.buitenhuis@rug.nl</a>] Sent: Thursday, March 06, 2014 12:27 PM To: Berker, Yannick; <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a> Subject: No comptonPhantom or RayleighPhantom entries for voxelized phantom </div> </div><div><div class="h5"> <div> Dear GATE users, </div> <div> </div> <div> I am having the same problem as Yannick Berker described on 2011-10-21. I use the ImageNestedParametrisedVolume phantom for a PET simulation. The sources are described using interfiles. Everything seems to be working correctly, i.e. the sources and phantom are in the right place and coincidences are detected. The effect of phantom attenuation is also clearly visible. </div> <div> </div> <div> The problem that I’m having, is that in the ROOT coincidences tree there is no comptonPhantom and RayleighPhantom data. I cannot add the VoxelPhantomSD to the ImageNestedParametrisedVolume, because I get an error message saying the command is unavailable. I can add the ordinary PhantomSD, but this does not seem to add the comptonPhantom or RayleighPhantom information to the coincidence tree. The comptonCrystal and RayleighCrystal entries are correct, so I think the physics processes are registered and working correctly. </div> <div> </div> <div> I need the comptonPhantom and RayleighPhantom information to get scatter information on coincidences. </div> <div> </div> <div> Did anyone else come across this problem, and if so, how did you solve it? Or can anyone point me in the direction of a solution? </div> <div> </div> <div> Regards, </div> <div> </div> <div> Tom Buitenhuis </div> <div> </div> <div> PhD student </div> <div> KVI - Center for Advanced Radiation Technology </div> <div> University of Groningen </div> <div> The Netherlands </div> <blockquote style="margin-top:5.0pt;margin-bottom:5.0pt"> <div> <pre>Dear GATE users,</pre> <pre> </pre> <pre>I have some issues using the HounsfieldMaterialGenerator to simulate a PET scan of a patient. The</pre> <pre>simulation itself is running fine, but I am lacking two features that I am used to from other simulations,</pre> <pre>which are scatter information and color visualization. I mainly used the example from</pre> <pre><a href="http://www.creatis.insa-lyon.fr/gate/Example2/" target="_blank">http://www.creatis.insa-lyon.fr/gate/Example2/</a> to generate the following phantom:</pre> <pre> </pre> <pre>/gate/HounsfieldMaterialGenerator/SetMaterialTable CT/Schneider2000MaterialsTable.txt</pre> <pre>/gate/HounsfieldMaterialGenerator/SetDensityTable CT/Schneider2000DensitiesTable.txt</pre> <pre>/gate/HounsfieldMaterialGenerator/SetDensityTolerance 0.03 g/cm3</pre> <pre>/gate/HounsfieldMaterialGenerator/SetOutputMaterialDatabaseFilename CT/p971-HUmaterials.db</pre> <pre>/gate/HounsfieldMaterialGenerator/SetOutputHUMaterialFilename CT/p971-HU2mat.txt</pre> <pre>/gate/HounsfieldMaterialGenerator/Generate</pre> <pre>/gate/world/daughters/name patient</pre> <pre>/gate/world/daughters/insert ImageRegionalizedVolume</pre> <pre>/gate/geometry/setMaterialDatabase CT/p971-HUmaterials.db</pre> <pre>/gate/patient/geometry/SetHUToMaterialFile CT/p971-HU2mat.txt</pre> <pre>/gate/patient/geometry/SetImage CT/p971s3.hdr</pre> <pre>...</pre> <pre> </pre> <pre>The ROOT output shows me that the volume is placed correctly, and the distribution of detected</pre> <pre>coincidences also shows the effect of photon attenuation by the phantom. However, I cannot attach a</pre> <pre>VoxelPhantomSD to the patient - I receive an error message telling me that this command is unavailable:</pre> <pre>[G4-cerr] ***** COMMAND NOT FOUND </gate/patient/attachVoxelPhantomSD> *****</pre> <pre>Attaching an ordinary PhantomSD seems to work, but only generates 0 entries in ComptonPhantom and</pre> <pre>RayleighPhantom. I also tried using a ImageNestedParametrisedVolume, with no effect. ComptonCrystal</pre> <pre>entries, however, seem to be correct (>= 0).</pre> <pre> </pre> <pre>Apart from that, how can I visualize the voxelized phantom using colors? I was not able to add color</pre> <pre>attributes (like "true 0.5 0.5 0.5 1.0") to p971-HU2mat.txt manually, since this resulted in the</pre> <pre>following error message:</pre> <pre>src/<a href="http://GateVImageVolume.cc" target="_blank">GateVImageVolume.cc</a> (l.332): No Hounsfield material defined in the file</pre> <pre>CT/p971s3_ToSim_OneBP_HU2mat_Colors.txt. Abort</pre> <pre> </pre> <pre>Does anyone have knowledge in this area, or can point to some helpful documentation on this topic? The GATE</pre> <pre>User's Guide has a few, but only incomplete examples for the case of voxelized phantoms and sources.</pre> <pre> </pre> <pre>Best regards,</pre> <pre> </pre> <pre>Yannick Berker</pre> <pre> </pre> <pre>The information contained in this message may be confidential and legally protected under applicable</pre> <pre>law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are</pre> <pre>hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly</pre> <pre>prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return</pre> <pre>e-mail and destroy all copies of the original message.</pre> </div> </blockquote> <div> </div> </div></div></div> </div> _______________________________________________ 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> </blockquote></div> </div>