[Insight-users] Re: [Insight-developers] itkOrientedImage type definition

[Simon Warfield]

It would be great if the documentation of the direction cosines 
mentioned this convention has been adopted.

Gordon Kindlmann wrote:

> hello,
>
> Okay, this sounds fine to me.  So you're saying that when an ITK  
> image is using direction cosines, the semantics of the direction  
> cosines dictate that the coefficients of those vectors can be  
> guaranteed to be measured relative to DICOM's standard LPS (towards  
> left, towards posterior, towards superior) patient-centered  
> coordinate system?  I just didn't know that LPS had been settled  
> upon, as opposed to, say RAS (and I do not mean orientation codes by  
> these letter combinations...).
>
> Gordon
>
> On Aug 23, 2005, at 10:52 AM, Kent Williams wrote:
>
>> Gordon (and others): I am working on the nifti ImageIO right now.  
>> There's a version right now, that will be included in the next  
>> checkpoint release, that just supports reading NIFTI files and  
>> doesn't consider orientation at all.
>>
>> After the checkpoint release, I'll be checking in a version that A)  
>> both reads and writes and B) handles embedded orientation information.
>>
>> The 'gold standard' of orientation in ITK is (and will be) the  DICOM 
>> direction cosines.  In other words, the direction cosines in  
>> itk::ImageBase will be either A) the image file format's native  
>> orientation information converted to Dicom Direction Cosines or B)  
>> 'Identity' direction cosines, with no indication of anatomical  
>> orientation.
>>
>> An open issue would be how to determine if the Direction Cosines  
>> just happen to correspond to Identity, or if no orientation  
>> information is given.  In Dicom terms, identity would correspond to  
>> Transverse scan, with dimensions (fastest moving to slowest)   
>> Patient right to left, anterior to posterior, inferior to superior.
>>
>> Presumably, once the orientation issues get settled in Insight, any  
>> remaining ambiguity can be addressed by the client application --  
>> one presumes any specific applications could make some simplifying  
>> assumptions about the input data.
>>
>>
>>
>> Gordon Kindlmann wrote:
>>
>>
>>>
>>> If the orientation information came from Analyze or NIFTI, is it   
>>> converted to LPS?
>>>
>>> Gordon
>>>
>>> On Aug 18, 2005, at 4:08 PM, Lorensen, William E (Research) wrote:
>>>
>>>
>>>> I believe that the direction cosines in ITK are always in LPS. I   
>>>> just copy in the dicom direction cosines.
>>>>
>>>> Bill
>>>>
>>>> -----Original Message-----
>>>> From: insight-developers-bounces+lorensen=crd.ge.com at itk.org
>>>> [mailto:insight-developers-bounces+lorensen=crd.ge.com at itk.org] On  
>>>> Behalf
>>>> Of Simon Warfield
>>>> Sent: Thursday, August 18, 2005 3:01 PM
>>>> To: insight-users at itk.org; insight-developers at itk.org
>>>> Subject: [Insight-developers] itkOrientedImage type definition
>>>>
>>>>
>>>>
>>>> I am looking at the documentation that describes directions here:
>>>> http://www.itk.org/Doxygen/html/classitk_1_1Image.html#w14
>>>>
>>>> This indicates that there is the possibility to represent a  matrix of
>>>> direction cosines.
>>>> Direction cosines represent the angle between two sets of basis   
>>>> vectors.
>>>> http://mathworld.wolfram.com/DirectionCosine.html
>>>>
>>>> In order to understand what the orientation of an  itkOrientedImage 
>>>> is,
>>>> there must be some way to specify or to record what those basis   
>>>> vectors are.
>>>> For example, the definition of DICOM direction cosines warrants that
>>>> what is being provided is the angle between the patients anatomy  
>>>> in  what
>>>> is referred to as the Left-Posterior-Superior orientation and  the  
>>>> image
>>>> columns and rows.
>>>>
>>>>   With respect to what are the ITK direction cosines computed ?   
>>>> If it
>>>> is not specified then the orientation of an image containing such
>>>> direction cosines is still unknown, which would defeat the  purpose of
>>>> providing an orientation.
>>>>
>>>> -- 
>>>> Simon
>>>>
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>>>
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>>
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>
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