[Gate-users] Interfile & Xmedcon question
Stephen Yip
stephen.fyip1 at gmail.com
Tue Mar 11 22:50:28 CET 2014
I did ask GATE to read the header file in the macro.
/gate/geometry/setMaterialDatabase
/home/gate/Progs/Gate/gate_v6.2/GateMaterials.db
/gate/world/daughters/name phantom
/gate/world/daughters/insert regularMatrix
/gate/phantom/geometry/insertReader interfile
/gate/phantom/interfileReader/insertTranslator range
/gate/phantom/interfileReader/rangeTranslator/readTable
/home/gate/example_PET/Gemini/test.dat
/gate/phantom/interfileReader/rangeTranslator/describe 1
/gate/phantom/interfileReader/readFile
/home/gate/example_PET/Gemini/m000-atn_1.h33
/gate/phantom/placement/setTranslation 0. 0. 0. mm
/gate/phantom/placement/setRotationAxis 1 0 0
/gate/phantom/placement/setRotationAngle 0 deg
/gate/phantom/attachVoxelPhantomSD
The errors just look very strange
', assuming default BIGENDIAN'LITTLEENDIAN
'nrecognised type name 'unsigned integer
Header read from '/home/gate/example_PET/Gemini/m000-atn_1.h33'
'Data file name 'm000-atn_1.i33
Nb of planes: 120
Nb of pixels per plane: 256 256
Pixel size: 1.000e+00 1.000e+00
Slice thickness: 2.000e+00
Matrix size: 2.560e+02 2.560e+02
Data type:
Data byte order: BIGENDIAN
'!ror: Could not open header file 'm000-atn_1.i33
-------- EEEE ------- G4Exception-START -------- EEEE -------
*** G4Exception : GeomSolids0002
issued by : G4Box::G4Box()
Dimensions too small for Solid: phantom_solid!
hX, hY, hZ = 0, 0, 0
*** Fatal Exception *** core dump ***
-------- EEEE -------- G4Exception-END --------- EEEE -------
On Tue, Mar 11, 2014 at 10:44 PM, Kris Thielemans <
kris.f.thielemans at gmail.com> wrote:
> I suspect you need to pass the name of the header file to GATE, not the
> binary file.
>
> Kris
> > -----Original Message-----
> > From: gate-users-bounces at lists.opengatecollaboration.org
> [mailto:gate-users-
> > bounces at lists.opengatecollaboration.org] On Behalf Of Stephen Yip
> > Sent: 11 March 2014 22:25
> > To: Chaitanya Kolluru
> > Cc: gate-users at lists.opengatecollaboration.org
> > Subject: Re: [Gate-users] Interfile & Xmedcon question
> >
> > Hi Chaitanya,
> >
> > I did what you suggested. But I am getting the following error (where
> m000-
> > atn_1.i33 is my file name in unsigned integer 2 byte format). Do you know
> what
> > went wrong? Thanks!
> >
> > '!ror: Could not open header file 'm000-atn_1.i33
> >
> > -------- EEEE ------- G4Exception-START -------- EEEE -------
> > *** G4Exception : GeomSolids0002
> > issued by : G4Box::G4Box()
> > Dimensions too small for Solid: phantom_solid!
> > hX, hY, hZ = 0, 0, 0
> > *** Fatal Exception *** core dump ***
> > -------- EEEE -------- G4Exception-END --------- EEEE -------
> >
> >
> > Here is my header file:
> >
> > !INTERFILE :=
> > !imaging modality := nucmed
> > !originating system := greetings
> > !version of keys := 3.3
> > date of keys := 1996:09:24
> > conversion program := (X)MedCon
> > program author := Erik Nolf
> > program version := 0.7.4
> > program date := 2002:02:18
> > ;
> > !GENERAL DATA :=
> > !data offset in bytes := 0
> > !name of data file := m000-atn_1.i33
> > patient name := hf
> > !patient ID := 271097
> > patient dob := 0000:00:00
> > patient sex := Unknown
> > !study ID := brain
> > exam type := pet study
> > data compression := none
> > data encode := none
> > ;
> > !GENERAL IMAGE DATA :=
> > !type of data := Tomographic
> > !total number of images := 120
> > study date := 1997:11:28
> > study time := 00:00:00
> > imagedata byte order := LITTLEENDIAN
> > ;
> > 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 := 120
> > !process status := Reconstructed
> > !matrix size [1] := 256
> > !matrix size [2] := 256
> > !number format := unsigned integer
> > !number of bytes per pixel := 2
> > scaling factor (mm/pixel) [1] := +1.000000e+00
> > scaling factor (mm/pixel) [2] := +1.000000e+00
> > !number of projections := 120
> > !extent of rotation :=
> > !time per projection (sec) := 0
> > study duration (sec) := 0
> > !maximum pixel count := +1.704600e+04
> > patient orientation := head_in
> > patient rotation := supine
> > ;
> > !SPECT STUDY (reconstructed data) :=
> > method of reconstruction := Unknown
> > !number of slices := 120
> > number of reference frame := 0
> > slice orientation := Transverse
> > slice thickness (pixels) := +2.00000e+00
> > centre-centre slice separation (pixels) := +2.00000e+00
> > filter name := Unknown
> > filter parameters := Cutoff
> > method of attenuation correction := measured
> > scatter corrected := N
> > oblique reconstruction := N
> > !END OF INTERFILE :=
> >
> >
> >
> > On Tue, Mar 11, 2014 at 8:50 PM, Chaitanya Kolluru
> > <kolluru.chaitanya at gmail.com> wrote:
> >
> >
> > Hi Stephen,
> >
> > You could first compare your header file with the example header
> file
> > in Gate (it's in
> > examples/example_Phantom_Source/Voxelized_phantom_source folder). It's
> > called brain_phantom.h33
> >
> > There are four places in the header file where you give the number
> of
> > images value (140 in your case). They are:
> > Total number of images
> > number of images/energy window
> > number of projections
> > number of slices
> >
> > If it still doesn't work, try using this example header file
> itself.
> Make
> > changes for a few fields like name of data file, scaling factor in x and
> y, matrix
> > size, slice thickness (this is actually in mm, not pixels as mentioned).
> >
> > Finally make sure your image file (i33) is in unsigned integer 2
> byte
> > format. Gate can read only that.
> >
> > Thanks,
> > Chaitanya.
> >
> >
> > On Tuesday, March 11, 2014, Stephen Yip <stephen.fyip1 at gmail.com>
> > wrote:
> >
> >
> > Hello,
> >
> > For my binary XCAT phantom, I used Xmedcon to create a
> > header (h33) and image (i33) files.
> >
> > medcon -f xcat.bin -c inf -i
> >
> > When it asked number of image? I typed 140 (number of
> slices
> > I have).
> >
> > Then for column and row, I entered 256, since my image is
> 256
> > by 256 by 140.
> >
> > However, when I tried to insert the phantom into a PET
> > scanner, Gate always complains that one of the matrix dimensions is zero.
> >
> > I wonder if anybody knows what I did wrong.
> >
> > Thanks,
> > Stephen
> >
>
>
>
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