[Gate-users] Interfile format for STIR

Kris Thielemans kris.thielemans at csc.mrc.ac.uk
Sun Apr 27 18:22:16 CEST 2008

> I realized that the email address I found on the web site  
> http://stir.sourceforge.net/  
> (stir-users at lists.sourceforge.net) is not the correct one. 

that address is correct, why did you think it isn't? (I used lists.sf.net
because sourceforge has registered both sf.net and sourceforge.net).

> I will be more specific about what I am trying to do for 
> attenuation correction. We have data of a voxellized phantom 
> simulated with an interfile of a CT scan using GATE and we 
> want to reconstruct the data.  What I thought that I need to 
> do for attenuation correction as a part of precorrection 
> using "correct_projdata" is to use the interfile of a CT scan 
> used for the simulation as input of "attenuation image 
> filename". 

sounds good

> So I simply copied the example of an interfile 
> header file you sent to me and changed the file name for 
> "name of data file" and matrix sizes and scaling factors to 
> be correct for the interfile of a CT scan. 

sounds almost good.

> Then I ran 
> "manip_image" to see whether that simple changes work.

excellent idea.

>   It 
> did not work and I have gotten the following message
> WARNING: Interfile Warning: only 'type of data := PET' supported.

you can ignore this warning

> WARNING: read_data: error after reading from stream.

this can happen for 3 reasons: either you have the dimensions wrong, or you
have the data type wrong, or you have the offset wrong (but you set it to 0,
so that can't be your problem). you can easily check this comparing the size
of your (binary) files with x-size*y-size*z-size*num_bytes_per_pixel. The
header that you used was set for floats. Maybe you're using short ints or

Note that if manip_image can't read a file, no routine in STIR can, as all
IO goes via the same function (ok, aside from the convert routines of


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