[vtkusers] using vtkLandmarkTransform to align two nii volumes

[The Merper]

Thank you, Mr. Gobbi!
I owe you one.
    -M

On Fri, Oct 12, 2018 at 2:11 PM David Gobbi <david.gobbi at gmail.com> wrote:

> I made a typo in the code in my last reply.  It should be:
>
> if (referenceReader->GetQFac() < 0.0) {
>     writer->SetQFac(-1.0);
> }
> On Fri, Oct 12, 2018 at 12:08 PM David Gobbi <david.gobbi at gmail.com>
> wrote:
> >
> > For writing a nifti file after registration, it's very important to
> > set the sform and qform for the writer to the sform and qform of the
> > reference image (I.e. _not_ the qform, sform of the image that was
> > resliced!)
> >
> > writer->SetSFormMatrix(referenceReader->GetSFormMatrix());
> > writer->SetQFormMatrix(referenceReader->GetQFormMatrix());
> > if (referenceReader->GetQFac() < 1) {
> >     writer->SetQFac(-1.0);
> > }
> >
> > The QFac setting ensures that the slices are written in the same order
> > as the reference image.
> >
> > It's possible to copy other parts of the header, too, but you have to
> > be careful when you do so, since some parts of the header relate to
> > the reference image, other parts of the header relate to the image
> > that was resliced, and some parts relate to neither.  Just copying the
> > qform and sform is usually sufficient.
> >
> >   David
> >
> > On Fri, Oct 12, 2018 at 11:47 AM The Merper <msmerps at gmail.com> wrote:
> > >
> > > 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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