[Gate-users] voxelized phantom setup

[Didier BENOIT]

Hi Naser,

I think you have a little error in the range file. The structure of this 
file is:
Number of the materials
min max range value Material true/false R G B alpha

For instance:
1
10 20 Body true 0.0 1.0 0.0 0.0
It means, the voxel values from 10 to 20 are Body and colored in green 
in the OpenGL visualization. After you can give an activity for Body

1
10 20 1000

You have maybe another error in the range file, could you check if 
between 1 and Air in your file it's spaces and not tabs :), because the 
error is 'could not find the definition for material '' in material file.

Kind regards,
Didier

On 10/22/2011 09:08 PM, Naser Darwish wrote:
> Dear gaters,
>
> I am having trouble setting running the XCAT with GATE. I am able to
> generate the act.bin and atn.bin for the phantom and for the source. I then
> add them up. Some things I am not sure still is how to specify the source
> with to a contrast ratio of 8 to 1 and how to specify activity (e.g.
> 15mCi/70kg).
>
> I use medcon for converting the binary files to uint16 using the following
> command:   medcon -f act.bin -c intf -i
> This generates a m000-act_1.h33 and and m000-act_1.h33.
> For GATE, I specify the attenuation range as below and the activity range
> following. I know the activity is wrong but I am just trying to see if I can
> get GATE to do the simulation without errors and I will correct the activity
> when I know how to specify it. Now I get an error also listed below. I
> appreciate your help greatly!
>
> If I use the example in GATE for voxelized source with the brain_phantom,
> the simulation runs with no errors
>
> Best regards,
> Naser
>
> 9
> 1       Air             true 0.0 0.0 1.0 0.2
> 2       Body    true 0.9 0.6 0.2 0.0
> 3       Muscle          true 1.0 0.0 1.0 0.2
> 4       Cartilage       true 0.8 0.0 0.8 0.2
> 5       Kidney  true 1.0 1.0 0.0 0.2
> 6       Liver           true 1.0 0.0 0.0 0.2
> 7       Spleen  true 0.8.0 0.8.0 0.0 0.2
> 8       SpineBone   true 0.8 0.8 0.8 0.2
> 9       RibBone         true 1.0 1.0 1.0 0.2
>
> 3
> 17   17    1000
> 163   163    0
> 204   204    0
>
> [Core-0] Initialization of geometry
> [Core-0] Initialization of physics
> [Core-0] Initialization of actors
> [Core-0]
> [Core-0]
> **********************************************************************
> [Core-0]  GATE version name: gate_v6.0_p01
> [Core-0]                     Copyright : OpenGATE Collaboration
> [Core-0]                     Reference : Phys. Med. Biol. 49 (2004)
> 4543-4561
> [Core-0]                     WWW : http://www.opengatecollaboration.org/
> [Core-0]
> **********************************************************************
> [Core-0]
> [Core-0] Starting macro GE_DLS_3D_APR2006_42rings.mac
> GeomTest: no daughter volume extending outside mother detected.
> GeomTest: no overlapping daughters detected.
> GeomTest: no daughter volume extending outside mother detected.
> GeomTest: no overlapping daughters detected.
> src/GateMaterialDatabase.cc (l.126): GateMaterialDatabase: could not find
> the definition for material '' in material files
> [G4] WARNING - Attempt to delete the physical volume store while geometry
> closed !
> [G4] WARNING - Attempt to delete the logical volume store while geometry
> closed !
> [G4] WARNING - Attempt to delete the solid store while geometry closed !
> [G4] WARNING - Attempt to delete the region store while geometry closed !
>
>
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.opengatecollaboration.org
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users


-- 
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Didier BENOIT, GATE Engineer
Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC)
IMNC -- UMR 8165 CNRS -- Université Paris 7 -- Université Paris 11
Campus d'Orsay
Bâtiment 440
91406 ORSAY Cedex

Tél : (33) 1 69 15 68 76
E-mail : benoit at imnc.in2p3.fr
http://www.imnc.in2p3.fr
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