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

Thu Jan 28 11:08:37 CET 2010

Hi,

2010/1/27 Cláudia Régio Brambilla <claudinha.rb at gmail.com>

> 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
>

OK

> 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.
>

I understand now, but it is not a problem.

> Do you think it will better to change de seed from default to introduce the
> seed value?
>

You can try but there is almost no chance to get it work I think.

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

Why not but I do not guarantee that I will have time as soon as you send
your macros !
And before that I have a last question:

Does your phantom overlap with some other object ? for example the shielding
(if you are using a PET system).
Because I remember now I encountered this problem (phantom matrix was
overlapping with my shielding) and I get this type of errors.

Cheers,
Simon

>
> Thanks for help me
>
> regards
>
>
>
> -----Original Message-----
> From: gate-users-bounces at lists.opengatecollaboration.org
> [mailto:gate-users-bounces at lists.opengatecollaboration.org] On Behalf Of
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> To: gate-users at lists.opengatecollaboration.org
> 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
> > >
> > >
> > >
> > > _______________________________________________
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> >
> >
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