[Insight-users] Nifti vs Dicom orientation

[Mathieu Malaterre]

On Mon, Apr 6, 2009 at 6:33 PM, Mathieu Coursolle
<mcoursolle at rogue-research.com> wrote:
> Hi,
> Thanks for your clarifications.
> However, I must admit that I am still a bit confused.
> Since NIfTI and ITK have different Left/Right and Anterior/Posterior
> directions,
> I admit that the direction matrix needs to be modified.
> Since my image dimension is 181 x 217 x 181, a flip in X means that to
> change
> the direction, the new origin is -90 + (181 - 1) = 90.
> A flip in Y however means that the new origin should be -126 + (217 - 1) =
> 90.
> Should I then expect instead a GetDirection() and GetOrigin() result  of:
> [-1, 0, 0, 90]
> [0, -1, 0, 90]
> [0, 0, 1, -72]
> [0, 0, 0, 1]
> Just inverting the sign of the origin would then mean that the world
> coordinates
> are centered on (0, 0, 0)mm, which is not the always the case.
> Am I right ?
> Thanks!
> Mathieu
> On 6-Apr-09, at 12:13 PM, Luke Bloy wrote:
>
> Hi all,
>
> So this is my understanding of how orientations and ITK work.
>
> the GetDirection and GetOrigin methods in itk::Image return the directional
> cosines in an LPS world frame. Thus an identity matrix returned by
> GetDirection() would mean the image is stored in LPS.
>
> The QForm and SForm matrices in the nifti file format  are in the RAS world
> coordinate frame. See
> http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html
>
> So Mathieu, what you are reporting is the expected behavior.
> qform (shown by fslhd etc) of
> [1, 0, 0, -90]
> [0, 1, 0, -126]
> [0, 0, 1, -72]
> [0, 0, 0, 1]
> should yield a GetDirection() and GetOrigin of
> -1  0  0   90
> 0  -1  0   126
> 0   0  1  -72
> 0   0  0   1
>
>
> Antoine,
> Your situation is more confusing, I'm not familiar with dcm2nii, but it
> isn't unheard of to have dicom converters change the orientation of the
> output image, to bring it into some consistent frame (LAS is a favorite of
> labs that have lots of old code expecting analyze files). From what you
> posted it seems that dcm2nii converted your image from an LPS arranged dicom
> to an LAS arranged Nifti file. I would investigate the nifti file's qform
> and sform matrics using either nifti_tool, fslhd or pynifti to confirm this.
>
> Hope this helps,
> Luke
>
> Mathieu Coursolle wrote:
>
> 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();
>
> }

I haven't had yet the time to investigate, but could this be due to bug #7748:

http://www.itk.org/Bug/view.php?id=7748&nbn=5



-- 
Mathieu