[Gate-users] Interfile & Xmedcon question

[Stephen Yip]

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
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140311/9b03f9ce/attachment.html>