[Gate-users] Fwd: voxellized phantom attenuation (no) problem:
ayanas at mail.med.upenn.edu
ayanas at mail.med.upenn.edu
Wed Mar 5 17:20:56 CET 2008
Dear Richard and fellow Gate'rs,
I confirm the "bug" that when I remove the "f=0.0" lines from the
GateMaterials.db, I get the numbers that I expect. For example for
MCAT phantom I also got ~9% as you did.
The GateMaterials.db that I have been using is the one that comes with
the GATE source code. Therefore although I had noticed "0" fractions
for some material definitions, I had never
suspected that these would introduce any instabilities in the
simulation results.
I would recommend fellow Gater's, who are using the original GateMaterials.db
file that comes with GATE source code, to check and remove any lines with f=0.0
and correct the number of entries for this material for correct results until
the problem is fixed.
Thank you very much for helping to sort out this problem.,
Best Regards,
Ahmet.
On Tue, Mar 4, 2008 at 7:39 PM, Richard Taschereau
<RTaschereau at mednet.ucla.edu> wrote:
>
> Ahmet,
>
> in your GateMaterials.db file there are several material definitions that
> contain elements with a fraction of zero, for example:
>
> RibBone: d=1.92 g/cm3 ; n=11
> +el: name=Hydrogen ; f=0.034
> +el: name=Carbon ; f=0.155
> +el: name=Nitrogen ; f=0.042
> +el: name=Oxygen ; f=0.435
> +el: name=Sodium ; f=0.001
> +el: name=Magnesium ; f=0.002
> +el: name=Phosphor ; f=0.103
> +el: name=Sulfur ; f=0.003
> +el: name=Calcium ; f=0.225
> +el: name=Scandium ; f=0.0
> +el: name=Titanium ; f=0.0
>
> Try to remove those lines (don't forget to update the number of elements),
> e.g.:
>
>
> RibBone: d=1.92 g/cm3 ; n=9
> +el: name=Hydrogen ; f=0.034
> +el: name=Carbon ; f=0.155
> +el: name=Nitrogen ; f=0.042
> +el: name=Oxygen ; f=0.435
> +el: name=Sodium ; f=0.001
> +el: name=Magnesium ; f=0.002
> +el: name=Phosphor ; f=0.103
> +el: name=Sulfur ; f=0.003
> +el: name=Calcium ; f=0.225
>
> and run your simulation again. While there is nothing wrong in doing that,
> I believe that causes a problem to Gate. If you confirm this, we'll work to
> fix that bug.
> By the way, if you want to collect info from the voxellized phantom and use
> the "comptonPhantom" field the use the attachVoxelPhantomSD command instead
> of attachPhantomSD.
>
> Richard
>
>
>
>
> On 3/4/08 12:17 PM, "Ahmet Ayan" <ahmetsedat.ayan at gmail.com> wrote:
>
>
>
> Dear Richard,
> Thank you very much for your reponse. I tried to replicate your numbers.
> Attached "spherical.mac" is what I did according to your description.
> For each run (10^4 emissions), I looked at the number of photons with
> E>0.139 as
> Singles->Draw("energy","energy>0.139")
>
> For these runs, I did a fresh gate 3.1.1 installation, I did NOT
> modify any part of GATE code.
> I used the attached GateMaterials.db. The attenuation range table
> (att.dat) is like the below example except I changed the material from
> RibBone to Lung to Water etc.
> I used the attached mcat.dat for the full MCAT phatom (uncompressed).
> The voxellized phantom was the one that I sent you earlier
> (154x102x256). I also moved the source to (1,1,1) micrometers
> position.
>
> I get the numbers below which I still do not understand much.
> The numbers that I got for Water and Lung s similar to yours. However
> MCAT and Ribbone is way off..
>
> No Phantom : 9907/1e4 ~ 99%
> Water Only : 795/1e4 ~ 8%
> Lung Only : 4895/1e4 ~ 49%
> Ribbone Only : 7180/1e4 ~ 72%
> MCAT : 7936/1e4 ~ 79%
>
> Would you please be kind to look at the macro that I am sending to see
> if I am doing something that is wrong ? This macro should run just
> fine in your gate installation.
>
> Thank you very much for your time and help,
> Best Regards,
> Ahmet.
>
>
>
> att.dat
> ---------------
> 2
> 0 0 Air false 0 0.0 0.0 0.7
> 1 20 RibBone true 0.7 0. 0. 1.
> ---------------------
>
>
>
> On Mon, Mar 3, 2008 at 8:37 PM, Richard Taschereau
> <RTaschereau at mednet.ucla.edu> wrote:
> >
> > Hi Ahmet,
> >
> > Here is what I did. I used standard Gate code (not your stepping
> action).
> > I defined a spherical shell detector, large enough to contain the phantom
> > and I "attached" a phantomSD to the voxel phantom (uncompressed). I
> > collected "singles" in a root file and I looked at the distribution of
> > scattered/unscattered photons using the field "comptonPhantom". Here's
> my
> > results with 5000 photons:
> >
> > %unscattered
> > All Bone phantom: 3.1
> > All water phantom: 7.1
> > MCAT phantom: 9.0
> > All Lung phantom: 48.3
> >
> > These results make sense to me. I did have one problem though: since
> the
> > phantom has an even number of voxels in each direction, the source at
> > (0,0,0) is at the corner of 8 voxels, and the GEANT4 navigator couldn't
> > determine in which voxels the particle was. I moved the source by 1
> micron
> > in each direction. You may want to try this approach (spherical shell
> > detector) instead of using GateSteppingAction.
> >
> > Richard
> > --
> > Richard Taschereau, Ph.D.
> > Crump Institute for Molecular Imaging
> > University of California Los Angeles
> > 700 Westwood Plaza, A222
> > Los Angeles, CA 90095-1770
> > Phone: (310) 825-0697
> > Fax: (310) 206-8975
> > email: RTaschereau at mednet.ucla.edu
> >
> >
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> > ----------------------------------------------------------
> >
>
>
>
> --
> Richard Taschereau, Ph.D.
> Crump Institute for Molecular Imaging
> University of California Los Angeles
> 700 Westwood Plaza, A222
> Los Angeles, CA 90095-1770
> Phone: (310) 825-0697
> Fax: (310) 206-8975
> email: RTaschereau at mednet.ucla.edu
>
>
>
> ----------------------------------------------------------
> IMPORTANT WARNING: This email (and any attachments) is only intended for the
> use of the person or entity to which it is addressed, and may contain
> information that is privileged and confidential. You, the recipient, are
> obligated to maintain it in a safe, secure and confidential manner.
> Unauthorized redisclosure or failure to maintain confidentiality may subject
> you to federal and state penalties. If you are not the recipient, please
> immediately notify us by return email, and delete this message from your
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> ----------------------------------------------------------
>
----- End forwarded message -----
--
Ahmet Sedat Ayan, Ph.D
Department of Radiology
University of Pennsylvania
Philadelphia, PA 19104
Voice : (++ 1 215) 349-5751 (W) (GMT-5)
----- End forwarded message -----
--
Ahmet Sedat Ayan, Ph.D
Department of Radiology
University of Pennsylvania
Philadelphia, PA 19104
Voice : (++ 1 215) 349-5751 (W) (GMT-5)
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