[Insight-users] Nifti vs Dicom orientation

[Antoine DUCHAMPS]

Hi Luis,

I've read the original DICOM with ITK and I've obtained exactly the same
direction cosines:

 0.9997  0.0000  0.0252
 0.0002  1.0000 -0.0072
-0.0252  0.0072  0.9997

So, should I assume a LAS orientation in nii image? (even when the
standard is RAS)

Antoine.



Le lundi 06 avril 2009 à 11:47 -0400, Luis Ibanez a écrit :
> Hi Antoine,
> 
> Could you please read the original DICOM series with ITK and
> report the Direction that you get from the ITK image in that case ?
> 
> 
> 
> In this way we will be able to figure out if the problem is in
> 
> 
> A) the conversion from DICOM to Nifti as processed by "dcm2nii"
> 
>                  or
> 
> B) the process of reading the nifti file with itkNiftiImageIo.
> 
> 
> Please post to the list the Direction cosines that you obtain
> when your read the original DICOM series with ITK.
> 
> 
>     Thanks
> 
> 
>           Luis
> 
> 
> -----------------
> On Mon, Apr 6, 2009 at 10:46 AM, Antoine DUCHAMPS
> <antoine.duchamps at gmail.com> wrote:
> > Hi all,
> >
> > I have a DWI sequence (brain) acquired with a Siemens scanner in Dicom
> > format. After converting it to NIfTI with dcm2nii
> > (http://www.sph.sc.edu/comd/rorden/mricron/dcm2nii.html) I tried to read
> > it an recover the orientation by using ITK (I've copied the code below).
> > The matrix I obtain is the following:
> >
> >  0.9997  0.0000  0.0252
> >  0.0002 -1.0000 -0.0072
> > -0.0252 -0.0072  0.9997
> >
> > However, the transforation matrix in the Dicom header is
> >
> >  0.9997  0.0000  0.0252
> >  0.0002  1.0000 -0.0072
> > -0.0252  0.0072  0.9997
> >
> > If the Dicom image orientation is LPS, this means that the image
> > orientation in NIfTI is LAS (And not RAS as I believed). Could anybody
> > clarify this please? Are there several possible orientations in NIfTI?
> > If so, how can I know the specific image orientation?
> >
> > Antoine.
> >
> >
> > #include "itkImageFileReader.h"
> > #include "itkOrientedImage.h"
> >
> > const unsigned int Dimension = 4;
> > typedef short PixelType;
> > typedef itk::OrientedImage<PixelType, Dimension> ImageType;
> > typedef ImageType::Pointer ImagePointerType;
> > typedef itk::ImageFileReader< ImageType > ReaderType;
> >
> >
> > int main(int argc, char* argv[])
> > {
> >
> >  ImageType::Pointer image = ImageType::New();
> >
> >  ReaderType::Pointer reader = ReaderType::New();
> >  reader->SetFileName(argv[1]);
> >  reader->Update();
> >
> >  image = reader -> GetOutput();
> >  std::cout << image->GetDirection() << std::endl; std::cout.flush();
> >
> > }
> >
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