[Gate-users] Gate Materials Database

[Hannes Hofmann]

Thanks for that hint. It is also true for materials Body and LungMoby.

Please correct these typos in future versions.

Regards,
Hannes

On 04/07 07:30, kathy at physics.usyd.edu.au wrote:
> 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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