[Insight-users] Nifti vs Dicom orientation
Luke Bloy
luke.bloy at gmail.com
Mon Apr 6 13:33:47 EDT 2009
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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>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
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>
> ____________________
> Mathieu Coursolle, M.Ing.
> Rogue Research Inc.
> www.rogue-research.com <http://www.rogue-research.com/>
>
>
>
>
>
>
>
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