[Insight-users] Nifti vs Dicom orientation

[Luis Ibanez]

Hi Antoine,

Thanks for looking at the original image orientation.

It seems that the problem lies in the interpretation
of orientation in the Nii file...
or... it may be a bug in dcm2nii...


I would suggest to post the question about the assumed
orientation of the Nifti file format to the Nifti forum:

     http://nifti.nimh.nih.gov/board/list.php?f=1

Of course, we will be interested in learning about their
reply.

It may mean that we need to modify the NiftiImageIO
class in ITK...


---

On the other hand, please note that in practice you don't
need to use "dcm2nii" since you can achieve exactly the
same goal by runing the example:


     Insight/Examples/IO
        DicomSeriesReadImageWrite2.cxx

(reading DICOM and saving it as a nifti file).

Which should give you a consistent set of orientations.


     Thanks


        Luis


------------------------
Antoine DUCHAMPS wrote:
> 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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> 
> 
>