[Insight-users] DICOM reader

[Andreas Schuh]

Hi Delphine,

the image direction matrix of an itk::Image is just the transpose  
(inversion) of the DICOM direction. The conversion from one into  
another is done by the writers/readers (for instance,  
itk::ImageFileReader, itk::ImageFileWriter).

--
regards
Andreas

On Apr 21, 2009, at 3:01 PM, Delphine Ribes <delphine.ribes at epfl.ch>  
wrote:

> Hi Mathieu,
>
> Thanks a lot for your answer and the explanations for the first part  
> (1 to 160
> and 160 to 1).
>
> Concerning the Image Direction, in the DICOM header there is:
> (0020,0037) DS |0\1\0\0\0\-1|    #   12, Image Orientation (Patient)
>
> I directly read it and put it into a
> ImageType::DirectionType ImDiritk;
> After cross product :
> ImDiritk[0][0]  0
> ImDiritk[0][1]  1
> ImDiritk[0][2]  0
>
> ImDiritk[1][0]  0
> ImDiritk[1][1]  0
> ImDiritk[1][2]  -1
>
> ImDiritk[2][0]  -1
> ImDiritk[2][1]  0
> ImDiritk[2][2]  0
>
> For itk Dicom Read :
> ImDiritk[0][0]  0
> ImDiritk[0][1]  0
> ImDiritk[0][2]  -1
>
> ImDiritk[1][0]  1
> ImDiritk[1][1]  0
> ImDiritk[1][2]  0
>
> ImDiritk[2][0]  0
> ImDiritk[2][1]  -1
> ImDiritk[2][2]  0
>
>
> and once I wrote it using itk writer:
>
> Me DICOM reader (header .mhd): The Tag : TransformMatrix is = to 0 0  
> -1 1 0 0 0
> -1 0
> itk DICOM reader (header .mhd): TransformMatrix = 0 1 0 0 0 -1 -1 0 0
>
> Apparently there is a conversion. Could you explain me?
>
> Thanks a lot,
> Delphine
>
> Selon Mathieu Malaterre <mathieu.malaterre at gmail.com>:
>
>> Salut Delphine,
>>
>> On Tue, Apr 21, 2009 at 10:52 AM, Delphine Ribes <delphine.ribes at epfl.ch 
>> >
>> wrote:
>>> Dear itk users,
>>>
>>> I've implemented a DICOM reader and I wanted to compare it with  
>>> itk DICOM
>>> reader.
>>> The output of the DICOM reader I've implemented is an itk Image.
>>>
>>> I have some MPRAGE saggital data. First I've realized that I was not
>> reading my
>>> data the same direction as itk.
>>> Me from 1 to 160
>>> itk from 160 to 1
>>> Is it a convention?
>>
>> What is '1' ? what is '160' ? My cristal ball is telling me you are
>> refering to Instance Number, right ? Since this is a DICOM Type 3,
>> this cannot be used to order the individual DICOM slice. Instead the
>> only other information you can use reliably in cross-sectional
>> aquisition (CT, MR...) is the pair Image Orientation (Patient) (IOP)
>> and Image Positon (Patient) (IPP). Then the ordering is defined along
>> this normal, with a positive spacing.
>>
>> It is described as 'jolinda' algorithm in gdcm. I could find this  
>> old ref:
>> http://www.itk.org/pipermail/insight-users/2003-September/004762.html
>>
>>> In addition, when I write for example a .mhd file, and I read  
>>> directly the
>>> header.
>>> The Tag : TransformMatrix is = to 0 0 -1 1 0 0 0 -1 0
>>> or it should be = to TransformMatrix = 0 1 0 0 0 -1 -1 0 0 as for  
>>> the itk
>> DICOM
>>> reader.
>>>
>>> In "My" DICOM reader, I get the direction from the DICOM header  
>>> tag :
>>> 0x0020,0x0037
>>> For direction 0 and 1 and then I do a cross product to get  
>>> direction 2.
>>> I suppose there is something I miss understood concerning the image
>> direction in
>>> itk.
>>> I should obtain the same as the itk dicom reader as output !
>>
>> I believe we are doing the same. could there be an issue in inverting
>> columns and rows ?
>>
>> HTH
>> --
>> Mathieu
>>
>
>
> Delphine Ribes
> Advanced Clinical Imaging Technology, Siemens Medical Solutions-CIBM
> Laboratory of functional and metabolic imaging,
> École Polytechnique Fédérale de Lausanne,
> Bâtiment CH, Station 6
> CH-1015 Lausanne
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