[Insight-users] DICOM reader

[Delphine Ribes]

Hi Andreas,

Thanks for the explanation.
What I don't get is why the vector is transposed?
Is there any particular reason?

Best Regards,
Delphine

Selon Andreas Schuh <andreas.schuh.84 at googlemail.com>:

> 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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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