[Insight-users] Nifti vs Dicom orientation
Mathieu Coursolle
mcoursolle at rogue-research.com
Mon Apr 6 14:37:05 EDT 2009
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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>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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>>>>
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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
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