[vtkusers] using vtkLandmarkTransform to align two nii volumes

[The Merper]

Thanks very much for the speedy help, David & Jon.
Applying the inverse of the landmark transform derived from the points
solved the problem.
I still don't understand why for polydata you apply the landmark transform
and for image data you apply the inverse, but that's Ok for now.

I also want to write the transformed nii volume to file. In addition to
using SetInformationInput to set the transformed nii volume's spacing,
origin, and extent, is there any other information I should be modifying in
the transformed Nii's header?
   thank you again,
      -M


On Fri, Oct 12, 2018 at 10:31 AM David Gobbi <david.gobbi at gmail.com> wrote:

> Hi Jon,
>
> The vtkNIFTIImageReader ensures that the vtkImageData that it produces
> follows the right-hand-rule, even if the slices were ordered in
> reverse in the NIFTI file itself. As the documentation states:
>
>   ...if QFac is -1, then the first slice in the VTK image data is the
> last slice in the NIFTI file...
>
> All the details of qfac are documented in the nifti header file:
> https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h
>
> Use of the qform in VTK is optional.  Use it if you want to work in
> RAS coordinates.  But often it is both simpler and more appropriate to
> work in VTK data coordinates instead, and to me it sounds like this is
> the case for the original question.  In any case, vtkImageReslice uses
> VTK data coordinates (not VTK world coordinates, nor RAS coordinates).
>
> I know this isn't a very clear explanation, but unfortunately it's all
> I have time for (and all that my brain is capable of right now, given
> the tiny amount of sleep I've had over the past few days).
>
>  - David
>
>
> On Fri, Oct 12, 2018 at 7:05 AM Jon Haitz Legarreta Gorroño
> <jon.haitz.legarreta at gmail.com> wrote:
> >
> > Hi,
> > I'd dare to say that the short answer is yes.
> >
> > Long answer is that VTK deals with world coordinates, and according to
> > the right hand rule. NIfTI uses RAS convention. According to the
> > vtkNIFTIImageReader::GetQFormMatrix documentation, NIfTI does not
> > ensure that coordinates are stored following that convention, so you
> > should definitely use the matrix given.
> >
> > The following Slicer 3D wiki page and David Gobbi's document be
> > helpful to this end:
> > https://www.slicer.org/wiki/Coordinate_systems
> > http://calgaryimageanalysis.ca/wiki/images/5/52/Image-orientation.pdf
> >
> > May be David himself can chime in and be able to provide a better or
> > cleaner explanation.
> >
> > HTH,
> > JON HAITZ
> >
> > On Thu, Oct 11, 2018 at 11:05 AM The Merper <msmerps at gmail.com> wrote:
> > >
> > > Hi VTK experts,
> > >    I am trying to using vtkLandmarkTransform  to align two nii volumes
> and am getting puzzling results. I identify the landmarks in the two 3D
> volumes by visualizing the volumes in VTK and using the GetPickPosition
> method. The coordinates I get are in units of mm with the origin being one
> corner of 3D volume.
> > >     I then use vtkLandmarkTransform to get an affine transformation to
> align the points. The points align great, but when I apply that same
> transform to the analogous nii volume via vtkImageReslice, the results are
> wildly off (e.g., the volume is flipped upside down).
> > >    Is the qform matrix of each nii file somehow causing this? Do I
> need to first apply the qform matrix to the landmark points to get them in
> scanner coordinates before using vtkLandmarkTransform?
> > >        thank you for any advice you can provide,
> > >             -Ms. Merps
>
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