[Insight-users] DICOM reader

[Delphine Ribes]

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