[Insight-users] Nifti vs Dicom orientation

[Mathieu Coursolle]

Hi,

I am having a similar issue, which may be related.

I have a NIfTI file, which I load using itkNIfTIImageIO.

By stepping into ITK, I can see that the s-form (sto_xyz) is:

[1, 0, 0, -90]
[0, 1, 0, -126]
[0, 0, 1, -72]
[0, 0, 0, 1]

However, when it read the origin and orientation of the resulting  
itkImage,
I get:

[-1, 0, 0, 90]
[0, -1, 0, 126]
[0, 0, 1, -72]
[0, 0, 0, 1]

This data is in the MNI-152 space. I know that the index (0, 0, 0)  
should be
(-90, -126, -72) mm in LPI  coordinate system (NIfTI's default I  
believe).

Since I want my data in the RAI coordinate system, I then use the  
itkOrientImageFilter.
Assuming it converts the image from LPI to RAI, I would expect the  
ouput to be:
[-1, 0, 0, 90]
[0, -1, 0, 90]
[0, 0, 1, -72]
[0, 0, 0, 1]

But I get:
[1, 0, 0, -90]
[0, 1, 0, -90]
[0, 0, 1, -72]
[0, 0, 0, 1]

By the way, my image dimensions are 181 x 217 x 181.

I know that index (0, 0, 0) is (90,  90, -72) mm in RAI.

I am right that the matrix I get from ITK is not what is expected ?

It looks to me that the itkNIfTIImageIO is doing some transform to
the orientation matrix.

What would be that transformation's purpose ?

Thanks a lot!

Mathieu

____________________
Mathieu Coursolle, M.Ing.		
Rogue Research Inc.
www.rogue-research.com


On 6-Apr-09, at 10:46 AM, Antoine DUCHAMPS 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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