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

[Gordon Kindlmann]

hello,

Sorry to be a total pest, but can someone help me understand the  
relationship between

1) itkImage
2) itkOrientedImage
3) The nice mathematical description that Luis previously gave:
>
>        Point = M * S * Index + Origin
>

Peter, can you help me understand what you mean by "local image  
coordinates"?  It is the same as the "Index" that appears in Luis's  
description?

Gordon

On Jan 18, 2006, at 2:13 AM, Peter Cech wrote:

> 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
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