[Gate-users] Incorrect voxel values - Interfile import GATE
David Larsson
davlars at kth.se
Tue Dec 23 19:26:18 CET 2014
Hi Hermann,
thanks for your answer. Being quite new to GATE I though struggle to change the input file format... I assume I'm suppose to change the insertReader through
> /gate/myvoxelphantom/geometry/insertReader
but what should I choose for a metafile input?
I would though still like to find an answer to the Interfile problem, as from what I understand this is the only extension-type supported when using Voxelized Sources (which I will be doing). Is that right? Would you have any idea how to proceed in that case?
Thanks again for all the help.
Regards
David
________________________________
Från: Hermann Fuchs [hermann.fuchs at meduniwien.ac.at]
Skickat: den 23 december 2014 18:17
Till: David Larsson; gate-users at lists.opengatecollaboration.org
Ämne: Re: [Gate-users] Incorrect voxel values - Interfile import GATE
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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