[gate-users] RE: STIR reconstruction software (GATE simualtions)

Vandana Kohli kohli.vandana at gmail.com
Mon Sep 12 21:22:39 CEST 2005

Dear Kris and Claude,
Thanks for your reply. As of now I am simulating CTI/Siemens scanner so I 
should be okay with using STIR reconstruction software.

 On 9/12/05, Kris Thielemans <kris.thielemans at csc.mrc.ac.uk> wrote: 
> Hi Claude
> >
> > > An alternative way would be to let GATE write Interfile
> > headers that
> > > STIR can understand. This shouldn't be incredibly difficult, but I
> > > don't know of anybody who has plans in that direction.
> >
> > For now, the sinogram outputs (raw or ecat7) are only defined
> > for ECAT systems as the LOR-to-SinogramBIN conversion follows
> > the ECAT specifications. It means, in particular, that the
> > sinogram radial sampling is not uniform (arc effect) and
> > requires reconstruction routines that handle this specific
> > feature. If we can keep these ECAT specifications, it is
> > quite straightforward to convert an ECAT7 sinogram to an
> > Interfile sinogram (remove the binary headers and directory
> > matrices and write a separate ascii header file, plus byte
> > swapping for the raw data if needed).
> >
> You can keep ECAT conventions without changes.
> As an example, STIR contains a utility ifheaders_for_ecat7 which given an
> ECAT7 file, it cooks up an Interfile header that points towards the binary
> data in the ECAT7 file. Of course, this routine can only give correct
> scanner dimensions if the system_type is known.
> So, maybe a very ugly work-around would be to let GATE write an ECAT7 file
> (with some junk system_type), run ifheaders_for_ecat7 on the data, and 
> then
> correct the scanner dimensions etc by hand.
> An alternative would be to write some extra code for GATE that essentially
> writes only the binary data of the sinogram (just as it would have done 
> for
> ECAT7), but writes in addition a fairly simple text file (with the 
> Interfile
> header).
> Unfortunately, I'm not volunteering.
> [In fact, all the stuff that we say is still correct for GE scanners (to 
> the
> best of my knowledge, although this is limited...). The main difference
> between GE VOLPET and ECAT files is the order of the data and the 
> different
> axial compression scheme. In essence, VOLPET uses span=3 for segment 0, 
> and
> no axial compression (span=1) for all ring differences>1.]
> > An alternative, valid for all PET systems, would be to have
> > an "exact" rebining from the LOR to the sinogram (or
> > projection ) space
> <snip>
> >
> > Kris, do you think that such an output would be useful for
> > STIR ?
> Not necessary, no. In any case, you wouldn't want that for iterative
> reconstructions I think.
> Kris
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