[Gate-users] Voxelized Phantom Defined in Gate v.6.2

[thibaultmauxion]

Hi Ney, 

looks like you figured out  pretty much everything :) I think you are right and that is definitely a little/big endian problem. I haven't been using Gate for a couple of month but I remember having a similar problem. I think one of the two types is not well supported, no matter what you set in the input file. 

This is not the nicest solution to provide but I think I just changed my phantom to little endian to make it work (what you can easily do with imageJ for example). Did you give it a try?  

Best Regards 

Thibault 




Post-doctoral fellow
Division of Medical Imaging Physics 
Johns Hopkins Medical Institutions
JHOC 4260, 601 N. Caroline street, Baltimore, MD, 21287
Tel: +1 410 502 3772
Fax: +1 410 614 1060
http://www.hopkinsradiology.org/dmip/




On Sep 26, 2013, at 3:24 PM, Auranuch Lorsakul <auranuch.lorsakul at gmail.com> wrote:

> Hi Gate Users,
> 
> With Gate v.6.2, I have a voxelized XCAT phantom uint 16 for a CT simulation, but I got an error message shown below.
> 
> "GateGeometryVoxelInterfileReader::ReadFile: WARNING: voxel not added (material translation not found); value 43520."
> 
> This phantom works fine with Gate 6.1 on the PET simulation.
> 
> However, I could reproduce a problem by simply generating a two-value phantom and a table. I found out that it is because there is a index value in the phantom is not defined in the table.
> 
> Regarding the error message shown above, I don't have the index value = 43520 in the phantom anymore (all index values in the phantom are less than 1000). I think it might be something wrong with the data type or data byte order. As the header file and the output log shown below, the data byte order is "Bigendian."
> 
> I am wondering how to define the phantom correctly in Gate 6.2. Is there anything changed/upgraded for defining the phantom?
> 
> 
> !INTERFILE :=
> 
> !name of data file := IMG_LESION_1.dat
> 
> !matrix size [1] := 512
> !matrix size [2] := 242
> !number format := unsigned integer
> scaling factor (mm/pixel) [1] := 1.030
> scaling factor (mm/pixel) [2] := 1.030
> !number of slices := 231
> slice thickness (pixels) := +0.687
> ce thickness (pixels) := +0.687
> 
> 
> OUTPUT LOG:
> ---------------------------
> Header read from       'Xcat_header.h33'
> Data file name         'IMG_LESION_1.dat'
> Nb of planes:           231
> Nb of pixels per plane: 512 242
> Pixel size:             1.03 1.03
> Slice thickness:        0.687
> Matrix size:            527.36 249.26
> Data type:              UNSIGNED INTEGER
> Data byte order:	 BIGENDIAN
> 
> Thanks,
> Ney
> 
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