[Gate-users] Re2: Gate-users Digest, Vol 83, Issue 16

Janus nxchu at foxmail.com
Fri Apr 26 09:21:31 CEST 2013

Hi, Tibo:

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". 

Any comments or suggestions would be greatly appreciated. 



From: Thibault Mauxion
Date: 2013-04-22 20:29
To: Janus
CC: gate-users
Subject: Re: Gate-users Digest, Vol 83, Issue 16
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. 


Le 22 avr. 2013 à 14:07, Janus a écrit :

Hi, Thibault:

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.  

Looking forward to hearing from you.



Message: 2
Date: Fri, 19 Apr 2013 09:58:21 +0200
From: Thibault Mauxion <thibault_mauxion at hotmail.com>
To: Janus <nxchu at foxmail.com>, gate-users
<gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] NaN errors on some pixels of regularMatrix
phantom in CTScanner system
Message-ID: <DUB113-W841894178357953C80E70DE2C80 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"

Hi, I'm far from an expert but try to add the command :
/gate/nameofyourregularMatrixvolume/setSkipEqualMaterials 0
at the end of the geometry macro, after you define your volume. 
Hope this will help..
Date: Fri, 19 Apr 2013 09:23:55 +0800
From: nxchu at foxmail.com
To: gate-users at lists.opengatecollaboration.org
Subject: [Gate-users] NaN errors on some pixels of regularMatrix phantom in CTScanner system

Dear Gate users, 

I attached an DoseActor to the regularMatrix phantom on a CTScanner system. 
The following macros show how I collect dose:
/gate/actor/addActor DoseActor 

/gate/actor/mActor/attachTo NCAT #the name of my 
regularMatrix phantom
/gate/actor/mActor/enableEdep false
/gate/actor/mActor/enableDose true
/gate/actor/mActor/normaliseDose false
/gate/actor/mActor/setResolution 72 88 63 #the pixel size is the 
same with the size of regularMatrix

After the simulation (more than 10^7 events), I got the output file 
"PhantomDose-Dose-Uncertainty.txt" that I expected. However, I found some 
NaN value in the file. It looks like: 

0.335632 nan 0.283809 0.277518 0.311712 0.232881 nan nan nan 
0.14158 nan nan nan 0.11352 0.118089 nan nan nan nan 0.117827 nan nan 0.111348 
nan nan 0.114444 nan 0.120727 0.112061 nan nan nan nan nan nan nan nan 0.114227 
nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan 0.112236 nan nan 
0.116712 nan nan nan nan nan nan 0.0982464 nan 0.695156 0.736034 0.694313 
0.501348 0.876738 0.593643 0.684897 
0.387904 0.308451 0.292645 0.307023 0.274505 0.196699 nan 0.125794 
0.119966 0.122969 nan 0.0921764 nan nan 0.116727 nan nan nan nan 0.121635 nan 
nan 0.089028 nan nan nan 0.115871 0.110041 0.120644 nan nan nan nan nan nan 
0.113381 nan nan nan 0.115092 0.109492 nan nan nan nan nan nan nan 0.122921 nan 
nan nan nan nan nan nan nan 0.110586 nan nan 0.103074 nan nan nan nan 1 0.712306 
0.555066 0.52936 0.792737 0.498393 0.627436 

Please can any expert tell me why I got these errors? 

Any suggestions or comments will be sincerely appreciated.

Best regards,


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