[Gate-users] Interfile format for STIR

[Thielemans, Kris]

Dear Hyejoo 

> I have posted a question to the STIR user list and someone suggested to post it to 
> the GATE user list. 
 
that's weird. I haven't seen anything and can't immediatelly find anything in the mailing lists archive

> I am trying to use STIR to reconstruct simulated data using GATE, and I have a 
> question about the input intefile format for STIR.

> STIR seems to require its own interfile format as input.  The intefile format 
> seems to be different from the Intefile 3.3 standard.  

yes, unfortunately STIR doesn't read strict 3.3 images. However, it does read 3.3 "proposed" format where you can set the number of dimensions to 3 and add matrix size[3] keywords etc. In addition, it uses a keyword to specify the scale of the image in case you need it.

The following is (probably) a minimal version

!INTERFILE  :=
name of data file := test_image_5.v
imagedata byte order := LITTLEENDIAN
!number format := float
!number of bytes per pixel := 4
number of dimensions := 3
matrix axis label [1] := x
!matrix size [1] := 97
scaling factor (mm/pixel) [1] := 3.1088
matrix axis label [2] := y
!matrix size [2] := 97
scaling factor (mm/pixel) [2] := 3.1088
matrix axis label [3] := z
!matrix size [3] := 31
image scaling factor[1] := 1 ; scale factor
quantification units := 1 ; alternative (was used by LLN software and is supported by medcon)
data offset in bytes[1] := 0
!END OF INTERFILE :=


> I would to know how to convert the Interfile 3.3 standard header and 
> image files generated with medcon to the input format for the STIR 
> executables.

some simple text editing would do the trick.

>  I tried to look at the web site http://www.HammersmithImanet.com/~kris <http://www.hammersmithimanet.com/~kris>  
> but I got a "not found" message on the web, I just found several email in the 
> stir-user archive saying that the web site does not.  

indeed. The info is on http://stir.sf.net in the section "Other info".

> I am wondering whether there is any existing STIR executable converting the 
> interfile 3.3 standard to .hv or I have to convert myself.  

STIR doesn't help you at present, but it is something one could do with a little scripting. Editing by hand is easiest of course.

 

Hope this helps. 

Kris

 

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