[Gate-users] Problem with using Zubal phantom

[thibault.mauxion at inserm.fr]

Ok,

I'm not an intefile expert but it looks like your file is defined as a 
stack of static images. This may be ok but I find it much easier (and 
compressed!) to define your dataset as reconstructed images.
If there are no critical information to be specified for each slice, 
you can define most parameters in the "(general)" section, so you don't 
have to repeat it for every 243 slice :)

To do so :

Delete all your information, starting from GENERAL IMAGE DATA to the 
end of your file (keep the last line).

Copy/Paste the section i put bellow and just change what you need 
(image path, image size, and names even if it is not critical). My image 
was 134x501x127 and voxel size was 0.2x0.2x0.2 mm. This may help you 
identify what needs to be changed.




!GENERAL IMAGE DATA :=
!type of data := tomographic
!total number of images := 127
imagedata byte order := LITTLEENDIAN
number of energy windows := 1
flood corrected := y
decay corrected := n
!SPECT STUDY (General) :=
number of detector heads := 1
!number of images/energy window := 127
!process status := reconstructed
!matrix size [1] := 134
!matrix size [2] := 501
!number format := unsigned integer
!number of bytes per pixel := 2
scaling factor (mm/pixel) [1] := 0.2
scaling factor (mm/pixel) [2] := 0.2
!number of projections := 0
!extent of rotation := 360
!time per projection (sec) := 0
study duration (sec) := 5
!maximum pixel count := 0
patient orientation := head_in
patient rotation := supine
!SPECT STUDY (reconstructed data) :=
!number of slices :=127
number of reference frame :=127
slice thickness (pixels) := 0.2
!END OF INTERFILE :=



There are still information that are not required in the file but this 
won't hurt :)

Hope this helps

NB : I reply to the gate list, in case this works for other users in 
the future. I also skipped in your answer bellow the section that is 
repeated more than 200 times (1 for each image) and keeped the first and 
the last of the chain :)



Thibault














Dear Thibault,

This is my interfile header.

Thanks for your attention,
All my best.

!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 := 0.11.0
program date := 2011:12:27
;
!GENERAL DATA :=
original institution := NucMed
!data offset in bytes := 0
!name of data file := zubal.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 := Static
!total number of images := 243
study date := 0000:00:00
study time := 00:00:00
imagedata byte order := LITTLEENDIAN
process label := Unknown
;
number of energy windows := 1
;
energy window [1] :=
energy window lower level [1] :=
energy window upper level [1] :=
flood corrected := N
decay corrected := N
;

!STATIC STUDY (General) :=
number of images/energy window := 243
;
!Static Study (each frame) :=
!image number := 1
!matrix size [1] := 128
!matrix size [2] := 128
!number format := unsigned integer
!number of bytes per pixel := 2
scaling factor (mm/pixel) [1] := +1.000000e+000
scaling factor (mm/pixel) [2] := +1.000000e+000
image duration (sec) := 0.000000e+000
image start time := 00:00:00
label := Unknown
!maximum pixel count := +2.570000e+002
!minimum pixel count := +0.000000e+000
total counts := 0
;
!Static Study (each frame) :=
!image number := 2
!matrix size [1] := 128
!matrix size [2] := 128
!number format := unsigned integer
!number of bytes per pixel := 2
scaling factor (mm/pixel) [1] := +1.000000e+000
scaling factor (mm/pixel) [2] := +1.000000e+000
image duration (sec) := 0.000000e+000
image start time := 00:00:00
label := Unknown
!maximum pixel count := +2.570000e+002
!minimum pixel count := +0.000000e+000
total counts := 0
;

...etc

!Static Study (each frame) :=
!image number := 243
!matrix size [1] := 128
!matrix size [2] := 128
!number format := unsigned integer
!number of bytes per pixel := 2
scaling factor (mm/pixel) [1] := +1.000000e+000
scaling factor (mm/pixel) [2] := +1.000000e+000
image duration (sec) := 0.000000e+000
image start time := 00:00:00
label := Unknown
!maximum pixel count := +2.570000e+002
!minimum pixel count := +0.000000e+000
total counts := 0
!END OF INTERFILE :=


On Wed, Aug 8, 2012 at 2:42 PM, <thibault.mauxion at inserm.fr> wrote:
Hi,

Could you send us your interfile header please? Looks like you number 
of slices is set (or recognized) to 0. If you think it could be a 
XMedCon problem, you can try to manually create your header (this is how 
i did it and never got any conversion issues). You will find an example 
in the "voxelized phantom source" folder in gate example DB.

Best Regards

Thibault


INSERM UMR 1037
Centre de Recherche en Cancérologie de Toulouse
Faculté de Médecine de Toulouse-Rangueil
Biophysique - Bâtiment A3
133 route de Narbonne
31062 Toulouse
Tel:            05 62 88 90 81
Port :  06 29 53 50 77
Mail: thibault.mauxion at inserm.fr

Le 6 août 2012 à 10:06, Shahla Razaghi a écrit :


Dear Gate users,

I am trying to use zubal phantom for my CT simulation. I have converted
phantom data to interfile format by means of XMedCon. After executing 
my
macro the following error related to phantom occurs:

----------------------------------------------------------------------------
'nrecognised type name 'unsigned integer
'nrecognised type name 'unsigned integer
Header read from       'voxel_man.h33'
'Data file name         'voxel_man.i33
Nb of planes:           0
Nb of pixels per plane: 128 128
Pixel size:             1.000e+00 1.000e+00
Slice thickness:        0.000e+00
Matrix size:            1.280e+02 1.280e+02
Data type:


Error: one of the matrix dimensions is zero!
Translation speed = 0 0 32. mm/s

----------------------------------------------------------------------------
List of initialized processes:

[Core-0] Initialization of geometry
ERROR - G4Box()::G4Box(): myphantom_solid
        Dimensions too small ! - 0, 0, 0

*** G4Exception : InvalidSetup
      issued by : G4Box::G4Box()
Invalid dimensions. Too small.
*** Fatal Exception *** core dump ***

*** G4Exception: Aborting execution ***
Aborted
-----------------------------------------------------------------------------

I thought that this problem is related to conversion process, I 
repeated
the process but could not find the reason.
I do appreciate any suggestion.

Thanks.
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-- 

Shahla Razaghi
Medical Radiation Engineering
Faculty of Nuclear Engineering & Physics
AmirKabir University of Technology