[Insight-users] Nifti vs Dicom orientation

[Bill Lorensen]

I believe, that the OrientImageFilter defines its orientations the
reverse of dicom/itk. In other words, to achieve RAI in ITK's world,
you should specify LPS to OrientImageFilter. But, LPS is ITK's
coordinate system. So you should not need to use OrientImageFilter.

Confused... I am,. See my recent e-mail regarding this.

Bill

On Mon, Apr 6, 2009 at 2:37 PM, Mathieu Coursolle
<mcoursolle at rogue-research.com> wrote:
> Hi,
> Thanks again.
> Maybe I did not understand the way ITK stores its direction and origin
> then...
> My NIfTI file doesn't have a qform, but it has a sform that defines the
> transform to MNI-152 space.
> Limited to the data size, this space is bound to :
> Left is -90 mm
> Right is +90 mm
> Posterior is -126 mm
> Anterior is 90 mm
> Inferior is -72 mm
> Superior is +108 mm
> What I am looking for is a 4 x 4 matrix I could use to multiply an index in
> RAI
> to get the location in MNI-152 space.
> I though that the origin was the location of the first voxel in space (in
> this case MNI-152).
> In this case, 126 is out of my space.
> I would expect an origin of (90, 90, -72), since this is the most Right,
> Anterior, Inferior point of
> the data.
> I typically read the file using itkNIfTIImageIO, then convert it to RAI
> using itkOrientImageFilter.
> I expect an origin of (90, 90, 72) mm at the ouput of itkOrientImageFilter,
> but I instead get (-90, -90, -72).
> What could I do to get the expected result ? I guess I am missing a
> transformation somehow...
> Thanks,
> MAthieu
>
>
>
>
>
>
> On 6-Apr-09, at 1:33 PM, Luke Bloy wrote:
>
> Hi Mathieu,
>
> So nothing happens to the data buffer, meaning that its ordering isn't
> rearranged. the only thing that is changed is the way we relate the i,j,k
> coordinates to 'world coordinates'.
>
> the 'origin' in both nifti and itk refers to the world coordinates of the
> first voxel in the data buffer (0,0,0).
> so with a qform =
> [1, 0, 0, -90]
> [0, 1, 0, -126]
> [0, 0, 1, -72]
> [0, 0, 0, 1]
>
> you get an origin of (-90 mm, -126 mm, -72 mm), since nifti qforms use RAS
> as the world frame this means that the (0,0,0) ijk voxel is located 90mm to
> the left, 126 posterior and 72 mm inferior, to whatever is at 0mm,0mm,0mm
> (in MRI this usually the scanner isocenter).  So in itk's LPS world frame
> the origin should be set to (90,126,-72).
>
> This is unrelated to the itkOrientImageFilter, which does do actually
> flipping and transposing of the data buffer.
>
> -Luke
>
>
> Mathieu Coursolle 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
> <http://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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>
> ____________________ Mathieu Coursolle, M.Ing.
>
> Rogue Research Inc.        www.rogue-research.com
> <http://www.rogue-research.com/>
>
>
>
>
>
>
>
>
>
> ____________________
> Mathieu Coursolle, M.Ing.
> Rogue Research Inc.
> www.rogue-research.com
>
>
>
>
>
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
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>
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