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

[Simon Stute]

Hi,

Try to use the nested parameterized volume:
http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6.2:Voxelized_Source_and_Phantom#Alternative_usage_of_voxelized_geometry_.28radiation_therapy_applications.29
The regular navigator is not really validated when attached to an actor.

Regards,
Simon


On Fri, Apr 26, 2013 at 9:21 AM, Janus <nxchu at foxmail.com> wrote:

> **
> 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.
>
> Regards,
> ------------------------------
> Janus
>
>  *From:* Thibault Mauxion <thibault_mauxion at hotmail.com>
> *Date:* 2013-04-22 20:29
> *To:* Janus <nxchu at foxmail.com>
> *CC:* gate-users <gate-users at lists.opengatecollaboration.org>
> *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.
>
> Tibo
>
>  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.
>
> Regards,
> ------------------------------
> Janus
>
>
>
> 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..
> Tibo
> 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
> mActor
>
> /gate/actor/mActor/save
> ./output/PhantomDose.txt
> /gate/actor/mActor/attachTo NCAT #the name of my
> regularMatrix phantom
> /gate/actor/mActor/enableEdep false
> /gate/actor/mActor/enableUncertaintyEdep
> false
> /gate/actor/mActor/enableSquaredEdep
> false
> /gate/actor/mActor/enableDose true
> /gate/actor/mActor/enableUncertaintyDose
> 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,
>
>
> Janus
>
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