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

[Gordon Kindlmann]

hello,

1) Is this a problem due to confusion between node-centered and cell- 
centered samples?  DICOM uses a cell-centered notion of image  
origin.  If the origin is the nominal location of the first sample,  
you could imagine a situation where a difference between node- 
centered and cell-centered understandings of the image position, in  
combination with a transform, could result in the origin moving.

2) As of the latest release, ITK adopted left-posterior-superior  
(LPS) as the one and only world coordinates system in which image  
orientation is defined.  My understanding was that this was motivated  
by consistency with DICOM.  What is the basis for the definition of  
image origin in ITK?

3) Working with the principle of least surprise, you probably want  
the origin recorded in NRRD or Meta output from ITK to coincide with  
the "Image Position (Patient)" tag of the first image of a series.   
Right now they are different.

Gordon

On Jan 17, 2006, at 11:58 AM, Luis Ibanez wrote:

>
> Hi Leila,
>
>
> This is somehow a matter of "definition".
>
>
>    If the "origin" is defined as the physical
>    coordinates of the first pixel in the image,
>
>
> then
>
>
>    The direction cosines should not be applied to the
>    origin, because this point is already in the physical
>    coordinates of space.  e.g. the reference frame of
>    a scanner.
>
>
>
> The direction cosines are describing the orientation
> of the axis defining the grid used for sampling the
> image. In this context, the direction cosines only
> affect the transformation between "index" and "physical
> points", and they are useful for computing the position
> of a pixel *with respect to the origin*.
>
>
>
> At this point, we may have to go back and reconsider
> if that definition of "origin" is the one that holds
> for DICOM, and whether this is the one that we want
> to keep for ITK or not.
>
>
>
>    Luis
>
>
>
> ---------------------
> Leila baghdadi wrote:
>> Hey petit frere,
>> I think you are right about the origin being a fixed point, i.e,  
>> for the
>> header information,
>> but once you apply the direction cosines to the image (i.e, right  
>> before
>> visualization), shouldn't the origin be resampled as well?
>> Leila
>> On Tue, 2006-01-17 at 13:08 -0500, Mathieu Malaterre wrote:
>>> Bill,
>>>
>>> 	We are having a discussion with Gordon about a problem regarding  
>>> the Origin of an itkImage read from a DICOM file. A while ago you  
>>> put this code into itkGDCMImageIO(*). After discussion with Luis  
>>> we came to the conclusion that the Origin is a fixed point. If  
>>> you want to compute a point then yes you need to use the  
>>> direction cosine and refer to the origin. But the origin should  
>>> not change, right ?
>>>
>>> Comments welcome,
>>> Mathieu
>>>
>>>
>>> (*)
>>>   // DICOM specifies its origin in LPS coordinate, regardless of how
>>>   // the data is acquired. itk's origin must be in the same
>>>   // coordinate system as the data. This code transforms the DICOM
>>>   // origin into the itk origin. The itk origin is computed by
>>>   // multiplying the inverse(transpose) of the direction cosine  
>>> times
>>>   // the dicom origin.
>>>   vnl_vector<double> itkOrigin(3), dicomOrigin(3);
>>>   vnl_matrix<double> dicomDirection(3,3);
>>>   dicomOrigin[0] = header.GetXOrigin();
>>>   dicomOrigin[1] = header.GetYOrigin();
>>>   dicomOrigin[2] = header.GetZOrigin();
>>>   for (unsigned int ii = 0; ii < 3; ii++)
>>>     {
>>>     dicomDirection[0][ii] = rowDirection[ii];
>>>     dicomDirection[1][ii] = columnDirection[ii];
>>>     dicomDirection[2][ii] = sliceDirection[ii];
>>>     }
>>>   itkOrigin = dicomDirection * dicomOrigin;
>>>   m_Origin[0] = itkOrigin[0];
>>>   m_Origin[1] = itkOrigin[1];
>>>   m_Origin[2] = itkOrigin[2];
>>> _______________________________________________
>>> Insight-developers mailing list
>>> Insight-developers at itk.org
>>> http://www.itk.org/mailman/listinfo/insight-developers
>
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