[Gate-users] Gate-users Digest, Vol 44, Issue 15

Wed Jan 27 17:17:30 CET 2010

Hi Simon and gate users,

I put the voxelized activity map a half from the whole dimensions in cm (my
phantom has 40 cm and I put the source in -20 -20 -20)
and on the 3 axes in a negative direction.
My headers are the same too
I mean my phantom is not completely rounded by air on interfile image. Next
to the arms is cut. I mean next the arms is the final of the image in x
axes. Do you think is it the problem? But I used the same phantom before in
all simulations and this problem didn't appear.
Do you think it will better to change de seed from default to introduce the
seed value?

If I didn't solve the problem Could I send you my scripts for you check? if
you Could?

Thanks for help me

regards

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Subject: Gate-users Digest, Vol 44, Issue 15

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Today's Topics:

   1. Re: NCAT Source-phantom (Simon Stute)

----------------------------------------------------------------------

Message: 1
Date: Mon, 25 Jan 2010 11:18:47 +0100
From: Simon Stute <gate.stute at gmail.com>
Subject: Re: [Gate-users] NCAT Source-phantom
To: Cl?udia R?gio Brambilla <claudinha.rb at gmail.com>
Cc: gate-users at lists.opengatecollaboration.org
Message-ID:
	<38e368331001250218m8544b8cy9010d405ce984ee at mail.gmail.com>
Content-Type: text/plain; charset=windows-1252

Hi,

2010/1/22 Cl?udia R?gio Brambilla <claudinha.rb at gmail.com>

>  Hello,
>
>
>
> Ok.
>
>  My phantom and source are the same size for sure because is the same
> interfile and I put the source a half from the phantom in a negative
> direction axis, I just define different data on range tables for att or
act
> table that call for the same image.
>

OK, did you put the voxelized activity map a half from the whole dimensions
(the total length of your phantom in size unit, not in voxel), and on the 3
axes ?
An concerning your headers of the interfile images, are they the same too ?

> My phantom body finishes in the end of the image. Do you think it is
> possible to be the problem? I think not because is the same phantom from I
> used in Gate4 and it didn?t have problems before.
>

I don't really understand. What do you mean exactly saying that your phantom
finishes at the end of the image ??

Again when you used Gate4 you used another navigator, and the problem that
you have in only due to the regularNavigator. This navigator is more severe
than the other on its boundaries.

> If I try to use compressed function Do you think it can resolve?
>

Yes, it would work, but not really resolve the problem ! And your simulation
will run slower.

Cheers,
Simon

>
> thanks
>
>
>
> *From:* Simon Stute [mailto:gate.stute at gmail.com]
> *Sent:* sexta-feira, 22 de janeiro de 2010 13:23
>
> *To:* Cl?udia R?gio Brambilla
> *Cc:* Ida H?ggstr?m; gate-users at lists.opengatecollaboration.org
> *Subject:* Re: [Gate-users] NCAT Source-phantom
>
>
>
> Hi again,
>
> 2010/1/22 Cl?udia R?gio Brambilla <claudinha.rb at gmail.com>
>
> Hello,
>
>
>
> I was using gate4 when I did that script with parametrizedBoxMatrix. When
> gate was released for gate5 I just take the same script change the
commands
> for regular Matrix and ran.
>
>
> OK I understand, I forgot that there was no regularMatrix in Gate4.
>
>
>  The problem starts to appeared after that. In gate4 I?ve never seen this
> error message with my simulation.
>
>
> It is normal since this error message is on related to the
RegularNavigator
> based on the PhantomParameterization in G4 (only used for this navigator).
>
>
>  We are trying to run in another computer to check if there is a problem
> with our installation. Our G4 version is 4.9.2.p01 with gate5.
>
>
> It is OK, because in the 9.1 version there was a bug in the G4 code in the
> GetReplicatNo function in the PhantomParameterization class. But it was
> corrected for the 9.2 version.
>
>
>  I think the last one was G4.9.2 and gate 4, I?m not have sure I can check
> and reply for you again.
>
>
>
>
> It is not important anymore, because you used the parameterizedBox only
> with Gate4.
>
>
> So to sum up, your problem may come from a wrong definition of your
> voxelized volumes (attenuation and/or sources) that did not cause trouble
> using the parameterizedBoxMatrix but not with the regularMatrix. Do your
> source is has exactly the same dimensions as your phantom ? If you have a
> voxelized phantom, your source has to be equal or smaller than this
phantom
> (analytical or not). Because if it is bigger, some particle may born
between
> the end boundaries of your phantom box and the distance tolerance in G4
> (some nanometer I think). I think in this case you will get this error.
> Otherwise, I don't know what is the cause of your problem ! I use regular
> and fictitious navigators every time and I only met this error when
> developing the regularNavigator in GATE.
>
> Regards,
> Simon
>
>  Regards
>
>
>
> Cl?udia
>
>
>
> *From:* Simon Stute [mailto:gate.stute at gmail.com]
> *Sent:* sexta-feira, 22 de janeiro de 2010 09:49
> *To:* Cl?udia R?gio Brambilla
> *Cc:* Ida H?ggstr?m; gate-users at lists.opengatecollaboration.org
>
>
> *Subject:* Re: [Gate-users] NCAT Source-phantom
>
>
>
> Hi,
>
> I did not understand that this is a systematic error ! in this case it is
> not a rounding error, something goes wrong in your simulation definition I
> think.
> But it is strange that your macro ran fine in Gate4 and not anymore in
> Gate5...
>
> 2 questions:
>
>  - If you really change nothing in your macro (I mean really nothing) and
> you launch it using Gate4, does it work ?
>  - which G4 versions are you currently using with Gate4 and Gate5, the
same
> or different ? and which ?
>
> Cheers,
> Simon
>
> On Thu, Jan 21, 2010 at 8:49 PM, Cl?udia R?gio Brambilla <
> claudinha.rb at gmail.com> wrote:
>
> Hello,
>
>
>
> Thanks for clarify my question, I didn?t know about this problem in G4.
I?m
> using a random seed (auto) and all runs have been  with the same problem.
> What Do you suggest for this problem? Is Just to run many times after bug
> until work? Or Is the best way to change the regular matrix for compress
or
> another compatible command?
>
>
>
> Thanks all  for all suggestions
>
>
>
> Best regards
>
>
>
> Cl?udia
>
>
>
> *From:* Simon Stute [mailto:gate.stute at gmail.com]
> *Sent:* quinta-feira, 21 de janeiro de 2010 12:31
> *To:* Ida H?ggstr?m
> *Cc:* Cl?udia R?gio Brambilla; gate-users at lists.opengatecollaboration.org
> *Subject:* Re: [Gate-users] NCAT Source-phantom
>
>
>
> Hi all,
>
> This bug comes from the G4PhantomParameterization class of G4 that is used
> when using the G4RegularNavigator (it is the case only when you use the
> regularMatrix object in GATE, it is not possible for other types of
> volumes).
> And unfortunatly it is probably a rounding bug when some particle are
> generated or interact exactly on the phantom border within the distance
> tolerance of G4.
> This bug has been already tracked but no satisfying solution was found !
> And there is nothing related to the version of Gate in this problem.
>
> Just launch again your simulation with another random seed...
>
> Cheers,
> Simon
>
> 2010/1/21 Ida H?ggstr?m <ida.haggstrom at radfys.umu.se>
>
> Dear Cl?udia,
>
> I've seen that error message myself and have not figured out exactly why
it
> appears. I got it when I used a voxelized phantom based on
> "parameterizedBoxMatrix" in Gate 5 (never used Gate 4). When I switched to
> "compressedMatrix" instead, everything else exactly the same, the error
> disappeared. You can give it a go! =) You can also try "regularMatrix".
>
> /Ida
>
>
> 2010/1/20 Cl?udia R?gio Brambilla <claudinha.rb at gmail.com>
>
> > Hello Gate Users,
> >
> >
> >
> > I was running a simulation with NCAT phantom and this error starts to
> > appear
> > using GATE 5. I usually used the same code in GATE 4 that any errors
> > appeared before.
> >
> > Does anybody know about the error bellow?
> >
> >
> >
> >
> >
> > ERROR - G4PhantomParameterisation::GetReplicaNo()
> >
> >        localPoint - (-1.743113937,-1.77535309,-1.503948302) - is outside
> > container solid: NCAT_S
> >
> >
> >
> > *** G4Exception : InvalidSetup
> >
> >      issued by : G4PhantomParameterisation::GetReplicaNo()
> >
> > Point outside voxels!
> >
> > *** Fatal Error In Argument *** core dump ***
> >
> >
> >
> > *** G4Exception: Aborting execution ***
> >
> > Aborted
> >
> >
> >
> >
> >
> > __________________________________
> >
> >
> >
> > Cl?udia R?gio Brambilla
> >
> >
> >
> > F?sica M?dica
> >
> > Supervisora de Radioprote??o - CNEN FM-0089
> >
> >
> >
> > Mestranda em Cl?nica M?dica - FAMED/PUCRS
> >
> > Grupo de Pesquisa em Imagens M?dicas - NIMed - PUCRS
> >
> > TECNOPUC 96A
> >
> >
> >
> > Contato:
> >
> >
> >
> > +55 51 84251368
> >
> > +55 51 3320 3682 ramal 7813
> >
> >
> >
> > _______________________________________________
> > Gate-users mailing list
> > Gate-users at lists.opengatecollaboration.org
> > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> >
> _______________________________________________
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>
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>

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