<div dir="ltr"><div><div><div>Hi, </div>It seems correct to me... If I did not miss something, it is the same as what's done in Gate (file GateImageWithStatistic.cc, line 346). </div>Are you sure the images are correctly read in Matlab? Maybe it's a precision issue? I put our conversation back to the mailing list in case someone spots something... </div>Simon <div><div> </div></div></div><div class="gmail_extra"> <div class="gmail_quote">On Tue, Feb 3, 2015 at 11:55 AM, Florian Bretin <<a href="mailto:fbretin84@googlemail.com" target="_blank">fbretin84@googlemail.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 Simon, Thanks for your answer! The paper did clear up a few things indeed. In theory, according to the equation (2), I should be able to reproduce the uncertainty per voxel from one simulation provided by GATE, if I have the dose and the dose squared from the simulation. However, if I try to calculate the uncertainty, I run into complex numbers, because the term under the square root is turning negative (squared dose coming from GATE is smaller than the mean dose squared). I am using Matlab to do so: uncertainty=sqrt((1/(N-1)).*((dose_squared./N)-((dose./N).*(dose/N)))); with N being the number of primary events, dose_squared the squared dose map from GATE and dose being the dose map from GATE. Or should I just use equation (4) with the uncertainties from the single acquisitions and set the weighting to 1? If that is the case, why don’t they say it like that in the GATE manual. If you have any idea where I am making a mistake or whether I should just use equation (4), it would be great if you could let me know. Thanks & kind regards,Florian <div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0cm 0cm 0cm">From: <a href="mailto:simon.rit@gmail.com" target="_blank">simon.rit@gmail.com</a> [mailto:<a href="mailto:simon.rit@gmail.com" target="_blank">simon.rit@gmail.com</a>] On Behalf Of Simon Rit Sent: 03 February 2015 08:26 To: <a href="mailto:florian.bretin@ulg.ac.be" target="_blank">florian.bretin@ulg.ac.be</a> Subject: Re: [Gate-users] Calculating standard error of the mean from multiple files</div><div><div class="h5"> <div><div>Hi, No, N is the number of primary particles. The way you compute the standard deviation is given in <a href="http://www.sciencedirect.com/science/article/pii/S0360301606005311" target="_blank">Chetty's paper</a>, I think it's clearer than in the Gate doc. From equation 2 in the paper, you see that you need the sum of the average squared dose per event and the average dose per event. I'm not sure but I think that the number of hit is not used for this computation, I actually don't know why it's part of the DoseActor. The LastHitEventImage is used to know when to square values but it's a different image and you don't need it anymore after performing several simulations. In case you're profficient in bash and you want to have a look, we do have a public merge script that does it correctly for the dose: <a href="https://git.creatis.insa-lyon.fr/git/?p=clitk.git;a=blob;f=cluster_tools/gate_power_merge.sh" target="_blank">https://git.creatis.insa-lyon.fr/git/?p=clitk.git;a=blob;f=cluster_tools/gate_power_merge.sh</a> The interesting function for you is merge_dispatcher_uncertainty which uses command line tools from <a href="http://vv.creatis.insa-lyon.fr" target="_blank">vv</a>.</div>Simon</div><div> <div>On Fri, Jan 30, 2015 at 11:38 AM, <<a href="mailto:florian.bretin@ulg.ac.be" target="_blank">florian.bretin@ulg.ac.be</a>> wrote:Dear GATE experts, I am simulating dose maps from multiple CT acquisitions and I am trying to calculate the final standard error of the mean of the summed dose maps. The GATE manual states regarding this the following: "The dose/edep squared is used to calculate the uncertainty when the output from several files are added. The uncertainty is the relative statistical uncertainty. "SquaredDose" flag allows to store the sum of squared dose (or energy). It is very useful when using GATE on several workstations with numerous jobs. To compute the final uncertainty, you only have to sum the dose map and the squared dose map to estimate the final uncertainty according to the uncertainty equations." The equations for the calculation of the uncertainty are given on page 98 of the GATE manual (GATE_v6.2_Complete_Users_Guide.pdf). Am I correct to assume that N equals the number of hits (I did set the flag to collect number of hits!)? My sample variance is already negative, since the squared dose values are far lower than values stored in the dosemap (all values very small, since only a fraction of real photons are simulated!). This leads to complex numbers when I try to calculate the standard mean of the error! It would be much appreciated if somebody could point me in the right direction or share his experience! Cheers, Florian _______________________________________________ Gate-users mailing list <a href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank">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></div> </div></div></div></div> <hr style="border:none;color:#909090;background-color:#b0b0b0;min-height:1px;width:99%"> <table style="border-collapse:collapse;border:none"> <tbody><tr> <td style="border:none;padding:0px 15px 0px 8px"> <a href="http://www.avast.com/" target="_blank"> <img src="http://static.avast.com/emails/avast-mail-stamp.png" border="0"> </a> </td> <td> This email is free from viruses and malware because <a href="http://www.avast.com/" target="_blank">avast! Antivirus</a> protection is active. </td> </tr> </tbody></table> </div></blockquote></div> </div>