[Gate-users] how to generate an 3D image that can be used for the voxellized sources by GATE

[Kris Thielemans]

Hi Guifen

please please please stop sending email to me directly. I have other
things to do as well, so by sending to a list, you increase your changes
of getting an answer. 

it seems GATE doesn't understand the .hv files, but you knew that
already. Try the .ahv (after suitable editing as indicated in the file)
or other variations of the interfile header.

Kris

 On Thu, 2007-05-24 at 16:54 +0800, Guifen Lin wrote:
> Hi,Kris
> Hi,
> I run gate according to your suggests.
> But I face the new problem.When I run gate,the screen shows:
> physicsList->setCut() start.
> WARNING !
>  SetCutValueForOthers became obsolete.
>  It is harmless to remove this invokation without any side effects.
>  This dummy method implementation will be removed soon.
> Warning: the selected insertion name ('adder') was already in use.
> Name 'adder2' will be used instead.
> Nof Higher level 2
>  Range Translator
>         Range   0 : imageValue in [    5.000e+01 , 5.000e+01 ]  --->
> activity (Bq) 2.000e+01
>         Range   1 : imageValue in [    1.500e+02 , 1.500e+02 ]  --->
> activity (Bq) 2.000e+02
> GateSourceVoxelImageReader::ReadFile : fileName: image.hv
>  Header read from       'image.hv'
>  Data file name         'image.v'
>  Nb of planes:           0
>  Nb of pixels per plane: 128 128
>  Pixel size:             2.000e+00 2.000e+00
>  Slice thickness:        0.000e+00
>  Matrix size:            2.560e+02 2.560e+02
>  Data type:              UNSIGNED INTEGER
> 
> Error: one of the matrix dimensions is zero!
>  Ignoring confine condition
> Source ---------------> voxel_brain
>   ID                  : 0
>   type                : backtoback
>   startTime (s)       : 0.000e+00
>   time (s)            : 0.000e+00
>   forcedUnstable      : 1
>   forcedLifetime (s)  : 9.502e+03
>   verboseLevel        : 0
> -----------------------
>   Voxel reader ---------->   number of voxels       : 0
>   total activity (Bq)    : 0.000e+00
>   position  (mm)         : 0.000e+00 0.000e+00 0.000e+00
>   voxel size  (mm)    : 1.000e+00 1.000e+00 1.000e+00
>     GPS info ---------------->
>     particle                 : gamma
>     SourcePosType            : Point
>     Shape                    : NULL
>     Positron Range           : NULL
>     halfx,halfy,halfz  (mm)  : 0.000e+00 0.000e+00 0.000e+00
>     Radius             (mm)  : 0.000e+00
>     Radius0            (mm)  : 0.000e+00
>     CentreCoords       (mm)  : 0.000e+00 0.000e+00 0.000e+00
>     Direction         : (1.000e+00,0.000e+00,0.000e+00)
>     Confine                  : 0
>     VolName                  : NULL
>     EnergyDisType            : Mono
>     MonoEnergy         (MeV) : 5.110e-01
>     MinTheta, MaxTheta (deg) : 0.000e+00 1.800e+02
>     MinPhi, MaxPhi     (deg) : 0.000e+00 3.600e+02
>     --------------------------
> I give you the files "generate_image1.par" "activityRange.dat" and
> gate script "Voxel_source.mac".Could you help me to find the error?
> Thanks you very much!
> guifen
> 
> 
> Kris Thielemans <kris.thielemans at csc.mrc.ac.uk> 写道：
>         Hi
>         
>         you can ask generate_image directly to use unsigned integers
>         by adding a
>         few lines to the par file. something like
>         
>         output file format:=Interfile
>         Interfile Output File Format Parameters:=
>         ; optional to specify non-native byte-order
>         ; byte order := littleendian
>         ; type specification as in Interfile
>         number format:=unsigned integer
>         number of bytes per pixel:=2
>         ; optional to fix the scale factor used when writing the data
>         ; otherwise the maximum range of the output data will be used
>         ; if it's an integer type
>         ;scale_to_write_data:=1
>         End Interfile Output File Format Parameters:=
>         
> 
> 
> 
> 
> ______________________________________________________________________
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> plain text document attachment (activityRange.dat), "351235018-
> activityRange.dat"
>   2
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>