[Insight-developers] [GDCM] ITK Origin and coordinate system

[Peter Cech]

On Tue, Jan 17, 2006 at 23:14:13 -0500, Bill Lorensen wrote:
> In your experiment you must use an itkOrientedImage, not an itkImage. Is 
> that what you used?

Exactly. My data volumes are not axis-aligned and itkOrientedImage gives
much better spatial relation between anatomical structures (in global
coordinates).

itkImage assumes not only volume to be axis-aligned, but local frame
actually matches global ITK frame. Recent decision to fix global ITK
frame as LPS breaks this assumption.

We clearly need different treatment of origin in itkImage and
itkOrientedImage. What about having two representations of origin: in
global ITK coordinates and in local image coordinates? Local origin
would be permuted and axis-flipped to match itkImage orientation (for
axis-aligned images, it's the same as applying direction cosines to
origin, for the rest permutation+flipping would retain behavior from
before direction cosines were introduced).

How do you like the idea?

Regards,
Peter

> 
> Bill
> 
> At 08:13 PM 1/17/2006, Peter Cech wrote:
> >On Tue, Jan 17, 2006 at 18:06:02 -0500, Bill Lorensen wrote:
> >> In an experiment I did a few months back, I had 6 MR scans done of the 
> >same
> >> object in each of the 6 orthogonal directions. I read them in using the
> >> current GDCMImageIO  (which transforms the origin using the direction
> >> cosines). All of the volumes roughly lined up without any additional
> >> transformations.
> >>
> >> If I did not apply the direction cosines, the datasets were all shifted.
> >
> >I got several MRI scans of head, the same scanning sequence, but taken
> >at various times over last half-year. My experience is exactly opposite
> >to yours. With directional cosines applied to origin, there alignment
> >was very poor (cca. 10cm shift, both in I-S and A-P direction). Today I
> >tried without directional cosines applied to origin and they aligned
> >much better, maximum shift was around 5cm and only in S-I direction.
> >
> >> Go figure,
> >
> >Yes, go figure...
> >
> >Regards,
> >Peter
> >_______________________________________________
> >Insight-developers mailing list
> >Insight-developers at itk.org
> >http://www.itk.org/mailman/listinfo/insight-developers