[Gate-users] Interfile & Xmedcon question

[Kris Thielemans]

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
>