<html xmlns="http://www.w3.org/1999/xhtml" xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office"><head><!--[if gte mso 9]><xml><o:OfficeDocumentSettings><o:AllowPNG/><o:PixelsPerInch>96</o:PixelsPerInch></o:OfficeDocumentSettings></xml><![endif]--></head><body><div style="color:#000; background-color:#fff; font-family:Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:13px"><div id="yui_3_16_0_ym19_1_1518620526477_4107"><span>Dear Ane,</span></div><div id="yui_3_16_0_ym19_1_1518620526477_4107"><span><br></span></div><div id="yui_3_16_0_ym19_1_1518620526477_4107"><span id="yui_3_16_0_ym19_1_1518620526477_4131">Thank you very much for your help.</span></div><div id="yui_3_16_0_ym19_1_1518620526477_4107"><br></div><div id="yui_3_16_0_ym19_1_1518620526477_4107">Happily, I have managed to implement the NEMA Image Quality phantom.</div><div id="yui_3_16_0_ym19_1_1518620526477_4107"><br></div><div id="yui_3_16_0_ym19_1_1518620526477_4107" dir="ltr">Following archive message written by Kaiyang Li in 2012 was very useful: <a href="http://lists.opengatecollaboration.org/pipermail/gate-users/2012-December/006145.html" class="enhancr2_3c809770-1908-3faa-fafc-04945ef65037" id="yui_3_16_0_ym19_1_1518620526477_4326">[Gate-users] cold area and "forbid" usage in GATE</a></div><div id="yui_3_16_0_ym19_1_1518620526477_4436"><br></div><div id="yui_3_16_0_ym19_1_1518620526477_4636">These are advices from the message:</div><div id="yui_3_16_0_ym19_1_1518620526477_4437"><br></div><div id="yui_3_16_0_ym19_1_1518620526477_4417">*1* cold area can not be overlapping with other volumes in the world (source is not a volume, so cold area can overlap with source). If you want to simulate a cold area in a water phantom. This cold area should be the daughter of the water phantom, not the daughter of the world.</div><div id="yui_3_16_0_ym19_1_1518620526477_4423">*2* initializing step should run after defining the cold area, before defining the source.</div><div id="yui_3_16_0_ym19_1_1518620526477_4427">*3* if forbid success, there should be two lines indicated by terminal (if you debug your codes one line by one line in the terminal) "Confirming activity forbidden in volume 'xxxx' Activity forbidden in volume 'xxx' confirmed"</div><div id="yui_3_16_0_ym19_1_1518620526477_4433">*4* The name of the cold area should longer than 5 characters.<br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1518620526477_4435"><br></div><div dir="ltr" id="yui_3_16_0_ym19_1_1518620526477_4435"><b id="yui_3_16_0_ym19_1_1518620526477_4683">Dear GATE Developers, please add these suggestions to the wiki.</b></div><div id="yui_3_16_0_ym19_1_1518620526477_4547"><br></div><div id="yui_3_16_0_ym19_1_1518620526477_4547" dir="ltr">In order to implement the source I had to modify the phantom macro (maybe it should be updated in the repository on github?). I had to change the name of volume IBox into name longer than 5 characters (boxinterior). I had to also add the cold volume NEMA_IQ_cold.</div><div id="yui_3_16_0_ym19_1_1518620526477_4547" dir="ltr">According to suggestion 1, cold volumes cannot overlap. Happily it is possible to use elements of the phantom (which are not overlapping) as cold areas.</div><div id="yui_3_16_0_ym19_1_1518620526477_4547" dir="ltr"><br></div><div id="yui_3_16_0_ym19_1_1518620526477_4547" dir="ltr">Sources activities were calculated using the attached spreedsheet assuming that the background activity concentration is 5.3 kBq/cc.</div><div id="yui_3_16_0_ym19_1_1518620526477_4547" dir="ltr"><br></div><div id="yui_3_16_0_ym19_1_1518620526477_4547" dir="ltr">You can find my phantom and source in attachment.</div><div id="yui_3_16_0_ym19_1_1518620526477_4547" dir="ltr"><br></div><div id="yui_3_16_0_ym19_1_1518620526477_4547" dir="ltr">These macros and their updates will be also available in the github repository: <a href="https://github.com/JPETTomography/j-pet-gate-tools" id="yui_3_16_0_ym19_1_1518620526477_5696">https://github.com/JPETTomography/j-pet-gate-tools</a> </div><div id="yui_3_16_0_ym19_1_1518620526477_4530"><br></div><div id="yui_3_16_0_ym19_1_1518620526477_4530">Best regards,</div><div id="yui_3_16_0_ym19_1_1518620526477_4530">Paweł Kowalski,</div><div id="yui_3_16_0_ym19_1_1518620526477_4530" dir="ltr">National Centre for Nuclear Research</div><div id="yui_3_16_0_ym19_1_1518620526477_5804"><br></div> <div class="qtdSeparateBR"><br><br></div><div class="yahoo_quoted" style="display: block;"> <div style="font-family: Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 13px;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div dir="ltr"><font size="2" face="Arial"> 11:30 środa, 2018-2-14, Ane Etxebeste <fplico817@gmail.com> napisał(a):<br></font></div> <br><br> <div class="y_msg_container"><div id="yiv4804944442"><div dir="ltr"><span style="white-space:nowrap;"><br></span><span style="white-space:nowrap;">Dear Pawe Kowalski,</span><br>
<br>
<span style="white-space:nowrap;">I have not looked carefully into your macro.</span><br>
<span style="white-space:nowrap;">But I have seen that you have applied Forbid command several times to</span><br>
<span style="white-space:nowrap;">the same volume without specifying it.<br><br></span>
<span style="white-space:nowrap;">For example, you have the following lines in your macro.</span><br>
<span style="white-space:nowrap;"> /gate/source/IBox_hot/gps/Forbid sphere22</span><br>
<span style="white-space:nowrap;"> /gate/source/IBox_hot/gps/Forbid sphere22in</span><br>
<span style="white-space:nowrap;"> /gate/source/IBox_hot/gps/Forbid fill22</span><br>
<span style="white-space:nowrap;"> /gate/source/IBox_hot/gps/Forbid fill22in</span><br>
<span style="white-space:nowrap;"> /gate/source/IBox_hot/gps/Forbid sphere28</span><br>
<span style="white-space:nowrap;"> /gate/source/IBox_hot/gps/Forbid sphere28in</span><br>
<span style="white-space:nowrap;"> /gate/source/IBox_hot/gps/Forbid fill28</span><br>
<span style="white-space:nowrap;"> /gate/source/IBox_hot/gps/Forbid fill28in<br><br></span>
<span style="white-space:nowrap;">In this case you have applied Forbid command 8 times to IBox_hot volume.</span><br>
<span style="white-space:nowrap;">Try adding the following command to specify the number of cold volumes</span><br>
<span style="white-space:nowrap;">you want to create inside IBox_hot volume</span><br>
<span style="white-space:nowrap;"> /gate/source/IBox_hot/dump 8</span><br>
<br>
<span style="white-space:nowrap;">I hope this helps you.</span><br>
<span style="white-space:nowrap;">Best regards,</span><br>
Ane Etxebeste<br>
<br>
<br>
<br>
<blockquote><span style="white-space:nowrap;">Quoting "Pawe Kowalski" <<a rel="nofollow" ymailto="mailto:pawkowalski@yahoo.com" target="_blank" href="mailto:pawkowalski@yahoo.com">pawkowalski@yahoo.com</a>>:</span><br>
<br>
<blockquote><span style="white-space:nowrap;">Dear GATE users,</span><br>
<span style="white-space:nowrap;">I am currently working on simulations of the NEMA characteristics of</span><br>
<span style="white-space:nowrap;">a PET scanner.</span><br>
While it is quite easy to implement phantoms and sources for spatial
resolution, scatter fraction and sensitivity characteristics, it is
challenging to implement the NEMA Image Quality phantom and the source.<br>
<span style="white-space:nowrap;">Happily, the macro for the phantom may be found at Github repository</span><br>
<span style="white-space:nowrap;">in path:</span><br>
GateContrib-master/imaging/PhantomSource/Analytical_Phantom/NEMA_IEC_2001.macUnfortunatelly
the phantom seems to be useless without the dedicated<br>
<span style="white-space:nowrap;">source.</span><br>
I have searched for many archive messeges from gate-users mailing list
and I have found no working macro with implementation of this source. It
is very strange for me because it seems that the Image Quality is a
quite important characteristic and many people try to perform such
simulations.<br>
Has noone really managed to implement the source for the NEMA IQ phantom?<br>
<span style="white-space:nowrap;">If someone managed to do it, please make it public.</span><br>
<span style="white-space:nowrap;">Using some examples that may be found in the network, I have been</span><br>
<span style="white-space:nowrap;">trying to implement this source by myself. Unfortunatelly I have</span><br>
<span style="white-space:nowrap;">some problems that I cannot solve (and it seems that they were not</span><br>
<span style="white-space:nowrap;">solved by the people that tried to implement the phantom in previous</span><br>
<span style="white-space:nowrap;">years).</span><br>
<span style="white-space:nowrap;">In the attachments there are my macros for the phantom, the source,</span><br>
<span style="white-space:nowrap;">and the test source which is a part of the whole source.</span><br>
Because of the fact that it is not possible to use gps source with
volume which is an angular part of the cylinder (for the phantom there
are commands: setPhiStart and setDeltaPhi) I have tried to implement
parts of the IQ source using cylindrical sources and cold regions.
Unortunatelly, it seems that the Forbid command does not work as it
should.There are some generations in regions, in which theoretically
they should not appear.<br>
<span style="white-space:nowrap;">The macro source_test.mac is a part of the source. The generations</span><br>
<span style="white-space:nowrap;">should be only between angles 270 and 360 but they are also in the</span><br>
<span style="white-space:nowrap;">rest of the region. I attach 2d histogram of sourcePosX and</span><br>
<span style="white-space:nowrap;">sourcePosY as a proof (for simulation with source_test.mac).</span><br>
<span style="white-space:nowrap;">What am I doing wrong? Please take a look at my macros. Maybe</span><br>
<span style="white-space:nowrap;">someone will know how to correct them in order to make them proper.</span><br>
<span style="white-space:nowrap;">I would be very grateful for your help and for any suggestions that</span><br>
<span style="white-space:nowrap;">would lead to the solution.</span><br>
<span style="white-space:nowrap;">Best regards,Pawe? Kowalski,National Centre for Nuclear Research</span></blockquote></blockquote></div></div>_______________________________________________<br>Gate-users mailing list<br><a ymailto="mailto:Gate-users@lists.opengatecollaboration.org" href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a><br><a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><br><br></div> </div> </div> </div></div></body></html>