<div dir="ltr"><div>Hi,<br><br>Try to use the nested parameterized volume: <a href="http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6.2:Voxelized_Source_and_Phantom#Alternative_usage_of_voxelized_geometry_.28radiation_therapy_applications.29">http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6.2:Voxelized_Source_and_Phantom#Alternative_usage_of_voxelized_geometry_.28radiation_therapy_applications.29</a><br>
</div>The regular navigator is not really validated when attached to an actor.<br><br>Regards,<br>Simon<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Apr 26, 2013 at 9:21 AM, Janus <span dir="ltr"><<a href="mailto:nxchu@foxmail.com" target="_blank">nxchu@foxmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><u></u>
<div style="MARGIN:10px">
<div>Hi, Tibo:</div>
<div> </div>
<div>Thanks for your kind suggestion. I have run the simulation
with 64912000 events (static point source with limited angles covering the
whole phantom), but it does not go well. I think the number of
events should be enough for the phantom (72*88*63 matrix) accumulating
dose. In fact, if I do not use the command
"/gate/NCAT/setSkipEqualMaterials 0", most elements of the matrix is not
"1", although some matrix elements are "NaN". I'm not sure if the problem
comes from how i import phantom matrix. Currently i use the commands
"/gate/UWCEM/imagReader/tabulatedTranslator/readTable" &
"readFile" from ASCII file but not the commonly used command
"interfileReader". </div>
<div> </div>
<div>Any comments or suggestions would be greatly appreciated. </div>
<div> </div>
<div>Regards,</div>
<hr style="WIDTH:210px;min-height:1px" color="#b5c4df" align="left" size="1">
<div><span>Janus</span></div>
<div> </div>
<div style="BORDER-BOTTOM:medium none;BORDER-LEFT:medium none;PADDING-BOTTOM:0cm;PADDING-LEFT:0cm;PADDING-RIGHT:0cm;BORDER-TOP:#b5c4df 1pt solid;BORDER-RIGHT:medium none;PADDING-TOP:3pt">
<div style="padding-right:8px;padding-left:8px;padding-top:8px;font-size:12px;background:#efefef;padding-bottom:8px">
<div><b>From:</b> <a href="mailto:thibault_mauxion@hotmail.com" target="_blank">Thibault
Mauxion</a></div>
<div><b>Date:</b> <a href="tel:2013-04-22%C2%A020" value="+12013042220" target="_blank">2013-04-22 20</a>:29</div>
<div><b>To:</b> <a href="mailto:nxchu@foxmail.com" target="_blank">Janus</a></div>
<div><b>CC:</b> <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users</a></div>
<div><b>Subject:</b> Re: Gate-users Digest, Vol 83, Issue
16</div></div></div><div><div class="h5">
<div>
<div>Looks good to
me, it just means that your fractional standard deviations at the voxel level
are equal to 1. You need to run more particles to have these numbers going
down.
<div><br></div>
<div>Tibo </div>
<div><br>
<div>
<div>Le 22 avr. 2013 à 14:07, Janus a écrit :</div><br>
<blockquote type="cite"><span style="TEXT-TRANSFORM:none;TEXT-INDENT:0px;BORDER-COLLAPSE:separate;FONT:medium Helvetica;WHITE-SPACE:normal;LETTER-SPACING:normal;WORD-SPACING:0px">
<div style="line-height:1.5;font-size:10.5pt;font-family:宋体;margin:10px">
<div>Hi, Thibault:</div>
<div> </div>
<div>Thanks for your kind reply. I have used the command:
/gate/NCAT/setSkipEqualMaterials 0 as you suggested, but I got "1 1 1 1 1
1 1 1 1 ... " in file PhantomDose-Dose-Uncertainty.txt. It seems worse than
NaN issue. I do not know what is wrong. Do you have any
other suggestion? Thanks in advance. </div>
<div> </div>
<div>Looking forward to hearing from you.</div>
<div> </div>
<div>Regards,</div>
<hr style="WIDTH:210px;min-height:1px" color="#b5c4df" align="left" size="1">
<div><span>Janus</span></div>
<div> </div>
<div style="BORDER-BOTTOM:medium none;BORDER-LEFT:medium none;PADDING-BOTTOM:0cm;PADDING-LEFT:0cm;PADDING-RIGHT:0cm;BORDER-TOP:rgb(181,196,223) 1pt solid;BORDER-RIGHT:medium none;PADDING-TOP:3pt"> </div>
<div>
<div> </div>
<div>Message: 2</div>
<div>Date: Fri, 19 Apr 2013 09:58:21 +0200</div>
<div>From: Thibault Mauxion <<a href="mailto:thibault_mauxion@hotmail.com" target="_blank">thibault_mauxion@hotmail.com</a>></div>
<div>To: Janus <<a href="mailto:nxchu@foxmail.com" target="_blank">nxchu@foxmail.com</a>>, gate-users</div>
<div><<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>></div>
<div>Subject: Re: [Gate-users] NaN errors on some pixels of regularMatrix</div>
<div>phantom in CTScanner system</div>
<div>Message-ID: <<a href="mailto:DUB113-W841894178357953C80E70DE2C80@phx.gbl" target="_blank">DUB113-W841894178357953C80E70DE2C80@phx.gbl</a>></div>
<div>Content-Type: text/plain; charset="iso-8859-1"</div>
<div> </div>
<div>Hi, I'm far from an expert but try to add the command :</div>
<div>/gate/nameofyourregularMatrixvolume/setSkipEqualMaterials 0</div>
<div>at the end of the geometry macro, after you define your volume. </div>
<div>Hope this will help..</div>
<div>Tibo </div>
<div>Date: Fri, 19 Apr 2013 09:23:55 +0800</div>
<div>From: <a href="mailto:nxchu@foxmail.com" target="_blank">nxchu@foxmail.com</a></div>
<div>To: <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a></div>
<div>Subject: [Gate-users] NaN errors on some pixels of regularMatrix phantom in
CTScanner system</div>
<div> </div>
<div>Dear Gate users, </div>
<div> </div>
<div>I attached an DoseActor to the regularMatrix phantom on a CTScanner system. </div>
<div>The following macros show how I collect dose:</div>
<div>/gate/actor/addActor DoseActor </div>
<div>mActor</div>
<div> </div>
<div>/gate/actor/mActor/save </div>
<div>./output/PhantomDose.txt</div>
<div>/gate/actor/mActor/attachTo NCAT #the name of my </div>
<div>regularMatrix phantom</div>
<div>/gate/actor/mActor/enableEdep false</div>
<div>/gate/actor/mActor/enableUncertaintyEdep </div>
<div>false</div>
<div>/gate/actor/mActor/enableSquaredEdep </div>
<div>false</div>
<div>/gate/actor/mActor/enableDose true</div>
<div>/gate/actor/mActor/enableUncertaintyDose </div>
<div>true</div>
<div>/gate/actor/mActor/normaliseDose false</div>
<div>/gate/actor/mActor/setResolution 72 88 63 #the pixel size is the </div>
<div>same with the size of regularMatrix</div>
<div> </div>
<div>After the simulation (more than 10^7 events), I got the output file </div>
<div>"PhantomDose-Dose-Uncertainty.txt" that I expected. However, I found some </div>
<div>NaN value in the file. It looks like: </div>
<div> </div>
<div>0.335632 nan 0.283809 0.277518 0.311712 0.232881 nan nan nan </div>
<div>0.14158 nan nan nan 0.11352 0.118089 nan nan nan nan 0.117827 nan nan 0.111348 </div>
<div>nan nan 0.114444 nan 0.120727 0.112061 nan nan nan nan nan nan nan nan 0.114227 </div>
<div>nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan 0.112236 nan nan </div>
<div>0.116712 nan nan nan nan nan nan 0.0982464 nan 0.695156 0.736034 0.694313 </div>
<div>0.501348 0.876738 0.593643 0.684897 </div>
<div>0.387904 0.308451 0.292645 0.307023 0.274505 0.196699 nan 0.125794 </div>
<div>0.119966 0.122969 nan 0.0921764 nan nan 0.116727 nan nan nan nan 0.121635 nan </div>
<div>nan 0.089028 nan nan nan 0.115871 0.110041 0.120644 nan nan nan nan nan nan </div>
<div>0.113381 nan nan nan 0.115092 0.109492 nan nan nan nan nan nan nan 0.122921 nan </div>
<div>nan nan nan nan nan nan nan 0.110586 nan nan 0.103074 nan nan nan nan 1 0.712306 </div>
<div>0.555066 0.52936 0.792737 0.498393 0.627436 </div>
<div> </div>
<div>Please can any expert tell me why I got these errors? </div>
<div> </div>
<div> </div>
<div>Any suggestions or comments will be sincerely appreciated.</div>
<div> </div>
<div>Best regards,</div>
<div> </div>
<div> </div>
<div>Janus</div>
<div> </div>
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