[Gate-users] Incorrect voxel values - Interfile import GATE

[Hermann Fuchs]

Hi David,

have you tried the metafile (.mhd, .hdr) file format? It usually works better.

Seasons greetings,
Hermann

Am 23. Dezember 2014 17:59:13 MEZ, schrieb David Larsson <davlars at kth.se>:
>Dear GATE-users,
>
>I am trying to implement a voxelized phantom into my GATE-simulations
>for the first time, but seem to encounter problems in the
>Interfile-read of my script.
>
>Using a simple imageconverter ((x)medcon) I've created a test-interfile
>(.h33 + .i33) with a 10x10x10 matrix with voxel values ranging from 0
>to 10. The conversion seems to work fine, and when I open to generated
>interfile-set in a random image viewer (ImageJ/MATLAB) I can see that
>the voxel values are preserved (ranging from 0 - 10).
>
>However, when I run my script I notice that the loader does not import
>the voxels as ranging from 0-10, instead I can see (through the error
>messages) that all voxels are given one value (in this specific case
>9280). The original values and the corresponding input structure is
>therefore lost.
>
>I've tried to compare my generated code to the (working) example with
>the hof_brain but cannot seem to understand the problem. I've provided
>the essential parts of the mac-files and the interfile-header of my
>testfile below. Can anyone identify what the problem might be?
>
>----------------------------main.mac----------------------------------------
>
># WORLD
>/gate/world/geometry/setXLength       400. cm
>/gate/world/geometry/setYLength       400. cm
>/gate/world/geometry/setZLength       400. cm
>
># VOXEL PHANTOM
>
>/gate/world/daughters/name                                             
>         teststack
>/gate/world/daughters/insert                                           
>          fictitiousVoxelMap
>/gate/teststack/geometry/insertReader                                  
>   interfile
>/gate/teststack/interfileReader/insertTranslator                      
>range
>/gate/teststack/interfileReader/rangeTranslator/readTable    
>attenuation_range.dat
>/gate/teststack/interfileReader/rangeTranslator/describe        1
>/gate/teststack/interfileReader/readFile                               
>     testintf.h33
>/gate/teststack/placement/setTranslation                               
>  0. 0. 0. mm
>/gate/teststack/placement/setRotationAxis                              
> 1 0 0
>/gate/teststack/placement/setRotationAngle                            
>0 deg
>/gate/teststack/attachVoxelPhantomSD
>
>-------------------attenuation_range.dat--------------------------
>
>5
>0 1     Air        false    0.0    0.0    0.0    0.0
>1 2     Water        true    1.0    0.0    0.0    0.0
>2 3     Water        true    1.0    0.0    0.0    0.0
>4 9280     Water        true    1.0    0.0    0.0    0.2
>9280 9280     Air    true    1.0    0.0    0.0    0.2     #This changed
>for visualisation of incorrect values
>
>------------------------- testintf.h33--------------------------
>
>!INTERFILE :=
>!imaging modality := nucmed
>!originating system := (X)MedCon
>!version of keys := 3.3
>date of keys := 1996:09:24
>conversion program := (X)MedCon
>program author := Erik Nolf
>program version := 0.13.0
>program date := 2013:06:23
>;
>!GENERAL DATA :=
>original institution := NucMed
>!data offset in bytes := 0
>!name of data file := m000-testnew.i33
>patient name := Unknown
>!patient ID := Unknown
>patient dob := 0000:00:00
>patient sex := Unknown
>!study ID := Unknown
>exam type := Unknown
>data compression := none
>data encode := none
>organ := Unknown
>isotope := Unknown
>dose := 0
>NUD/Patient Weight [kg] := 0.00
>NUD/imaging modality := NM
>NUD/activity := 0
>NUD/activity start time := 00:00:00
>NUD/isotope half life [hours] := 0.000000
>;
>!GENERAL IMAGE DATA :=
>!type of data := Tomographic
>!total number of images := 10
>study date := 0000:00:00
>study time := 00:00:00
>imagedata byte order := LITTLEENDIAN
>process label :=
>;
>number of energy windows := 1
>;
>energy window [1] :=
>energy window lower level [1] :=
>energy window upper level [1] :=
>flood corrected := N
>decay corrected := N
>;
>!SPECT STUDY (general) :=
>number of detector heads := 1
>;
>!number of images/energy window := 10
>!process status := Reconstructed
>!matrix size [1] := 10
>!matrix size [2] := 10
>!number format := long float
>!number of bytes per pixel := 8
>scaling factor (mm/pixel) [1] := +10.000000e+00
>scaling factor (mm/pixel) [2] := +10.000000e+00
>!number of projections := 10
>!extent of rotation :=
>!time per projection (sec) := 0
>study duration (sec) := 0
>!maximum pixel count := +1.000000e+01
>patient orientation := Unknown
>patient rotation := Unknown
>;
>!SPECT STUDY (reconstructed data) :=
>method of reconstruction := Unknown
>!number of slices := 10
>number of reference frame := 0
>slice orientation := unknown
>slice thickness (pixels) := +10.000000e+00
>centre-centre slice separation (pixels) := +1.000000e+00
>filter name := Unknown
>filter parameters := Cutoff
>method of attenuation correction := measured
>scatter corrected := N
>oblique reconstruction := N
>!END OF INTERFILE :=
>
>----------------------------------------------------------------------------
>
>Best regards,
>
>David
>
>
>------------------------------------------------------------------------
>
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