[Insight-users] Nifti vs Dicom orientation

Mon Apr 6 14:06:25 EDT 2009

Hi,

the bug I reported would probably affect a tool that uses ITK to  
convert Nifti files to DICOM format but not vice versa, as just the  
write operation of the itk::GDCMImageIO class is affected. Moreover  
wouldn't it affect the orientation in the manner reported by Antoine.  
What's wrong with itk::GDCMImageIO::Write() in my opinion is that it  
writes the inverse/transposed orientation. See my comments on the bug  
report for an example.

--
regards
Andreas

Am 06.04.2009 um 18:38 schrieb Mathieu Malaterre <mathieu.malaterre at gmail.com 
 >:

> 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
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