[Gate-users] Problem with voxelised phantom and tabulatedtranslator in GATE v6.0

Thu Apr 8 13:34:43 CEST 2010

Thank you very much Simon.

It would be very helpful if someone from the developing team tested the placement of the phantoms using the tabulatedTranslator.

I compared the GateRegularParameterization.cc scripts of Gate 5 and Gate 6. I spotted some differences but I am not sure if they actually have a significant impact on the translator.

-----------------------------------------------------------------
Marios Myronakis

PhD Student
Joint Department of Physics
Institute of Cancer Research and 
Royal Marsden Foundation Trust
Fulham Road
London SW3 6JJ
UK

Tel.: +44 (0) 207 808 2500
Fax.: +44 (0) 207 808 2522
E-mail: Marios.Myronakis at icr.ac.uk
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>>> Simon Stute <gate.stute at gmail.com> 04/08/10 12:04 PM >>>
Hi Marios,

On Thu, Apr 8, 2010 at 12:51 PM, Marios Myronakis <
Marios.Myronakis at icr.ac.uk> wrote:

> Dear Simon,
>
> thanks for the suggestion.
>
> I have to mention though that the exact same phantom is working perfectly
> using the regularMatrix in Gate 5 without any code modification.
>
>
OK

> I would like to ask what phantom was used to test the regularMatrix using
> the tabulatedTranslator in Gate v6. In this way I might be able to find why
> the regularMatrix doesn't work properly with my phantom.
>
>
Unfortunatly we did not test translation on voxelized phantom since our
tests were performed using PET or SPECT detectors as ring and so the
phantoms were simply positionned in the center of the FOV without using any
translation.
I was not part of the developers who implemented the geometry part of the
code so I have no hint at all.
Maybe Sebastien has a suggestion ?

> I am using Gate for dose simulations and I want to avoid the
> compressedMatrix. Therefore I would be grateful if any of the developers
> provided the above information.
>
>
Yes I agree with you, regular is much faster than compressed matrix.

Cheers,
Simon

Thanks for your time,
> Marios
>
> -----------------------------------------------------------------
> Marios Myronakis
>
> PhD Student
> Joint Department of Physics
> Institute of Cancer Research and
> Royal Marsden Foundation Trust
> Fulham Road
> London SW3 6JJ
> UK
>
> Tel.: +44 (0) 207 808 2500
> Fax.: +44 (0) 207 808 2522
> E-mail: Marios.Myronakis at icr.ac.uk
> -----------------------------------------------------------------
> >>> Simon Stute <gate.stute at gmail.com> 04/08/10 10:53 AM >>>
> Hi Ali,
>
> I though I answered to you... Maybe I have a hint.
> Concerning the Regular algorithm, there is a special feature used in the
> particule transportation, that consists in skipping voxel boundaries when
> neighboors voxels have the same material. It limits the number of steps and
> speeds up the transportation.
> And maybe you get some 0 in your dose collection because of that.
>
> You can try (in gate_v5) to modify the file
> source/voxel/src/GateRegularParameterization.cc, at line 172:
>
>     SetSkipEqualMaterials(1);
>
> Just set the value to 0, and voxel boundaries will be forced to produce a
> step.
>
> It is just a suggestion ! I hope it could solve the problem, but maybe it
> is
> something much more subtle and so difficult to find.
> Because the Regular navigation is totally managed by G4 (building of the
> parameterization), that was not the case for Parameterized and Compressed,
> so maybe it could explain also the problem of placement described by
> Marios.
>
> Hope this helps,
> Simon
>
> On Wed, Apr 7, 2010 at 11:47 PM, AliAsghar Parach <aaparach at gmail.com
> >wrote:
>
> > Dear Simon and marios
> > I asked the same question a few month ago but I couldn't get my answer
> too.
> > you can see it in gate users mails. it's subject was:
> > voxelphantom_GATE5_error
> > if you used compressed and regular without dose actor and use previous
> dose
> > collection method you can see what I said about their differences.
> > if you solved your problem please aware me.
> > regards
> > On Wed, Apr 7, 2010 at 9:14 PM, Marios Myronakis <
> > Marios.Myronakis at icr.ac.uk> wrote:
> >
> >> Dear Simon,
> >>
> >> Thank you for your reply.
> >>
> >> Indeed I tested it and I got hits (that make sense) only when the
> >> compressedMatrix is used. In other words it seems like it is not a
> >> visualisation problem. I attach the results from the dose actor for each
> >> method.
> >>
> >> I also tested it in the patched version (V6.0_p01) and I get the same
> >> results.
> >>
> >> I also tested it using the virtual GATE machine and I still get the
> same.
> >>
> >> I am really puzzled as I cannot find where am I making any mistake.
> >>
> >> Thank you for your help.
> >>
> >> Marios
> >>
> >> -----------------------------------------------------------------
> >> Marios Myronakis
> >>
> >> PhD Student
> >> Joint Department of Physics
> >> Institute of Cancer Research and
> >> Royal Marsden Foundation Trust
> >> Fulham Road
> >> London SW3 6JJ
> >> UK
> >>
> >> Tel.: +44 (0) 207 808 2500
> >> Fax.: +44 (0) 207 808 2522
> >> E-mail: Marios.Myronakis at icr.ac.uk
> >> -----------------------------------------------------------------
> >> >>> Simon Stute <gate.stute at gmail.com> 04/07/10 5:30 PM >>>
> >>  Hi Marios,
> >>
> >> Do the results of your simulation agree with the visualization, or is it
> >> just a visualization problem ?
> >> Did you test this ? It would be very important to know that to try to
> >> understand the problem.
> >>
> >> Cheers,
> >> Simon
> >>
> >> On Wed, Apr 7, 2010 at 5:04 PM, Marios Myronakis <
> >> Marios.Myronakis at icr.ac.uk
> >> > wrote:
> >>
> >> > Hello,
> >> >
> >> > since I didn't get any reply to my previous post (Fri Mar 5 15:16:10
> CET
> >> > 2010
> >> >
> >>
> http://lists.opengatecollaboration.org/mailman/private/gate-users/2010-March/003974.html
> >> )
> >> > I would like to rephrase my question.
> >> >
> >> > I am using a tabulated translator to insert a voxelised phantom. When
> I
> >> use
> >> > the compressedMatrix the phantom is properly displayed and placed.
> When
> >> I
> >> > use the regularMatrix, the phantom is placed at the axes origin. In
> both
> >> > cases when I type the command /gate/phantom/describe the phantom is
> >> shown at
> >> > its defined position.
> >> >
> >> > I attach the mac file and two images where the above described problem
> >> is
> >> > depicted.
> >> >
> >> > Thanks for your time,
> >> > Marios
> >> >
> >> > -----------------------------------------------------------------
> >> > Marios Myronakis
> >> >
> >> > PhD Student
> >> > Joint Department of Physics
> >> > Institute of Cancer Research and
> >> > Royal Marsden Foundation Trust
> >> > Fulham Road
> >> > London SW3 6JJ
> >> > UK
> >> >
> >> > Tel.: +44 (0) 207 808 2500
> >> > Fax.: +44 (0) 207 808 2522
> >> > E-mail: Marios.Myronakis at icr.ac.uk
> >> > -----------------------------------------------------------------
> >> >
> >> > The Institute of Cancer Research: Royal Cancer Hospital, a charitable
> >> > Company Limited by Guarantee, Registered in England under Company No.
> >> 534147
> >> > with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
> >> >
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> >>
> >> The Institute of Cancer Research: Royal Cancer Hospital, a charitable
> >> Company Limited by Guarantee, Registered in England under Company No.
> 534147
> >> with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
> >>
> >> This e-mail message is confidential and for use by the addressee only.
>  If
> >> the message is received by anyone other than the addressee, please
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> >
> >
> >
> > --
> > Ali Asghar Parach,Ph.D. student in Medical Physics,Tarbiat Modares
> > University,Tehran,Iran
> >
>
>
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable
> Company Limited by Guarantee, Registered in England under Company No. 534147
> with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
>
> This e-mail message is confidential and for use by the addressee only.  If
> the message is received by anyone other than the addressee, please return
> the message to the sender by replying to it and then delete the message from
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>

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.