[Gate-users] Gate Materials Database

[kathy at physics.usyd.edu.au]

Hi Daniel,

there is an error in the materials.db file for adipose - you will notice
that there is a ',' instead of ';' for the Vandium element. I also found
this with the db file, so it is not just yours. I have another definition
of Adipose that you may want to try, as I also had some trouble running a
simulation using this. Try:

Adipose: d=0.95 g/cm3 ; n=7
+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

I hope this helps,

Kathy


Quoting Daniel Woodsworth <danieljw at phas.ubc.ca>:

> Hi,
>
> I have been trying to create a voxelized phantom based on the Zubal MRI
> head phantom. I have been getting errors relating to the readTable
> command:
>
> the command
>
> /gate/zubal_brain/interfileReader/rangeTranslator/readTable
> atten_map.dat
>
> yields:
>
> !!! GateMDBFile:
>         The definition of the element/material 'Adipose' is incorrect:
>         Could not find any prefix for the abundance field.
>         You should check this definition in the database file.
>         Computation aborted!!!
>
>
> *** G4Exception: Aborting execution ***
> Abort
>
> I checked the Adipose definition and it is fine. To investigate this, I
> changed anywhere I had entered Adipose in the atten_map.dat file to
> Water,
> and re-ran the simulation. This gave:
>
> GateVGeometryVoxelReader::GateVGeometryVoxelReader: m_voxelTranslator 0
> GateVGeometryVoxelReaderMessenger::SetNewValue: newValue
> (translatorType)
> : range
>
> !!! GateMDBFile::LookForElementIndbStream:
>         I could not find any section [Materials] in the material
> database
> file.
>         You should check the database file.
>         Computation aborted!!!
>
>
> *** G4Exception: Aborting execution ***
> Abort
>
>
> However I have looked in the materials.db file and it is fine. I have
> tried the command with the materials.db file in the simulation working
> directory, with the same error.
>
> Finally, when I use the range_vox.dat file (which comes with the
> hoffmann
> example in the GATE distribution) instead of atten_map.dat, the
> simulation
> runs fine.
>
> This makes me think that it is something to do with the formatting of
> the
> atten_map.dat file (although why that would manifest itself as a
> materials.db file problem is beyond me). However, both file formats are
> identical. I have pasted them below. I also attached my GateMaterials.db
> file.
>
> If anyone has any insights I would be really appreciative.
>
> Thanks,
>
> Daniel Woodsworth
>
>
> #range_vox.dat file
>    6
>    0   12  Plastic
>   13   25  Glass
>   26   50  Plastic
>   51   75  Glass
>   76  100  Water
>  101  250  Air
>
>
> #atten_map.dat file
> 47
> 0	0	Air
> 1	1	Water
> 2	2	Water
> 3	3	Water
> 4	4	Skull
> 5	5	SpineBone
> 9	9	Muscle
> 15	15	Water
> 16	16	Water
> 22	22	Adipose
> 23	23	Blood
> 26	26	Water
> 29	29	Bone
> 30	30	Cartilage
> 63	63	Brain
> 70	70	Bone
> 71	71	Bone
> 72	72	Water
> 74	75	Water
> 76	76	Bone
> 77	77	Brain
> 78	78	Water
> 81	81	Bone
> 82	82	Cartilage
> 83	83	Brain
> 84	84	Water
> 85	96	Brain
> 97	97	Water
> 98	98	Adipose
> 99	99	Bone
> 100	100	Bone
> 101	101	Brain
> 102	102	Skull
> 103	103	Brain
> 104	104	Air
> 105	105	Brain
> 106	106	Water
> 107	109	Brain
> 110	110	Water
> 111	115	Brain
> 116	116	Water
> 117	118	Brain
> 119	119	Water
> 120	120	Brain
> 121	121	Water
> 122	124	Brain
> 125	125	Bone
>
>
>




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