[vtkusers] using itk transform in vtk

[David Gobbi]

Hi Karl,

When I'm doing image registration or anything related to the image
coordinate system, I prefer to set FileLowerLeft=1, or to re-flip the
image if this is not possible.  The FileLowerLeft=0 setting is a
convenience so that images appear the right way up when viewed
in VTK with the default view settings.  But for some of my software
(particularly when dealing with image registration), I prefer to work
in the original coordinate system that was defined in the file.   So
I will flip the view, rather than allow the VTK reader to flip the
image.  It can be done either way (but either way, it is a headache).

  David


On Wed, Nov 17, 2010 at 10:20 PM, Karl <bulkmailaddress at gmail.com> wrote:
> Vtk folks and David,
>
> Thanks for responding.  I have yet to have success, but I believe I have
> addressed the issues you point out.
> I am using vtkGDCMImageReader with the FileLowerLeft flag set to 0.  If I
> understand correctly this importer correctly flips the Y and adjusts the
> origin.
>
> ITK transform is about the 0,0,0 physical coordinate.  When I load the image
> in itk the origin information should be used by this importer to properly
> position the image so that the 0,0,0 physical coordinate corresponds to the
> 0,0,0 vtk location.  The inverse of the itk transform can then be directly
> applied to the imported image.
>
> This still does not work however.  I need to somehow get the vtk coordinate
> system to accurately represent the physical coordinate system so that
> objects from different dicom images, with different origins and directional
> cosines, appear in proper relation to each other.
>
> Any suggestions on how to proceed?
>
> Thanks
>
> -----Original Message-----
> From: David Gobbi [mailto:david.gobbi at gmail.com]
> Sent: Tuesday, November 16, 2010 4:31 PM
> To: bulkmailaddress at gmail.com
> Cc: vtkusers at vtk.org
> Subject: Re: [vtkusers] using itk transform in vtk
>
> Hi Karl,
>
> The VTK transform operates on the physical origin, which can be at any
> desired location in the image.  The relationship between DICOM
> coordinates and VTK coordinates is explained thusly:
>
> DICOM has three fields related to the positions of the image voxels in
> physical (or patient) space:
> - ImagePositionPatient (position of upper right corner)
> - ImageOrientationPatient (row and column directions)
> - PixelSpacing (X and Y)
>
> VTK image data has two fields (no orientation):
> - Origin (position of lower right corner)
> - Spacing (X, Y, and Z)
>
> Note that the image data "Origin" is a misnomer, it is not the
> physical origin of the coordinate system.  It is just the position of
> the voxel in the lower left corner.  It is the responsibility of the
> VTK image reader that you are using to set the Origin and Spacing of
> the data correctly.  (And again, I will repeat that what VTK calls the
> image "Origin" is not the physical image origin, it is just a
> position).
>
> The fundamental difference between these two coordinate systems is not
> the location of the origin, it is a vertical flip since DICOM images
> are top-to-bottom while VTK images are bottom-to-top.  When dealing
> with DICOM, I set the VTK image "origin" to the DICOM
> ImagePositionPatient, and then apply a view transform that flips the
> image by using a rotation of 180 degrees about the X axis.
>
>  - David
>
> On Tue, Nov 16, 2010 at 2:02 PM, Karl <bulkmailaddress at gmail.com> wrote:
>> Hi,
>> I am trying to use an itk transform in vtk.  Here is a high level overview
>> of what I do:
>>
>> 1) In itk use itk::ImageRegistrationMethod with itk::AffineTransform to
> find
>> a transform.
>>
>> 2) I use itk::ResampleImageFilter to create an image transformed using the
>> itk::AffineTransform.
>>
>> 3) I use the GetLastTransformParameters() function to get the affine
>> transformation matrix to use in vtk as.
>> [param0 param1 param2 param9]
>> [param3 param4 param5 param10]
>> [param6 param7 param8 param11]
>> [0 0 0 1]
>>
>> 4) Now in vtk I try to display both the resampled image and the original
>> image with the transform applied.  They should show as exactly the same if
> I
>> can apply the transform in vtk the same as it is applied in itk.
>>
>> 5) I load both images in vtk.  The images are binary so I use marching
> cubes
>> to create meshes of them.  I display the transformed image polydata as is.
>>
>> 6) I apply a vtkTransform to the original image polydata.  I do this by
>> concatenating 3 vtkMatrix4x4. Two to adjust for different origins in itk
> and
>> vtk and one for the itk transform.
>> Translate_Back * itkTransform * Translate_itk_origin_to_vtk_origin
>>
>> Where
>> itkTransform is as shown in 3 above.
>>
>> Translate_itk_origin_to_vtk_origin is
>> [1 0 0 -originX]
>> [0 1 0 -originY]
>> [0 0 1 -originZ]
>> [0 0 0 1]
>> Where the origin is as found in the dicom header for the original image
>>
>> Translate_Back
>> [1 0 0 originX]
>> [0 1 0 originY]
>> [0 0 1 originZ]
>> [0 0 0 1]
>>
>> 7) Set vtkTransform inverse flag and transform and display the original
>> image.
>>
>> 8) The two objects show up at different places in the scene instead of at
>> the same location.
>>
>> If I understand this correctly the itk transform is to be applied about
> the
>> physical origin.  Not the location of the corner pixel or the center of
> the
>> image.
>>
>> The vtk transform uses an origin at the corner of the image.
>>
>> By translating by the origin defined in the dicom header I move the
> physical
>> origin to the corner pixel of the image.  This corrects for the
>> discrepancies between the point with itk and vtk apply their transforms.
>>
>> Also the itk transform goes from output to input, so the inverse transform
>> needs to be applied in vtk.
>>
>> Can anyone see what I am missing?
>> Thanks
>
>