[Insight-developers] more notes on images with affine transformations in the header

[Williams, Norman K]

The SpatialOrientationAdapter is actually a pretty regrettable thing we
did back in the day.


The problem it solved: Given images in different orientations, it permutes
and swaps the voxels to get them into a common anatomical orientation
(e.g. RAI) so that INDEX-SPACE operations worked.

The problem it created: It reads the reported rotation matrix and
over-writes it with the 'nearest' orthogonal (I.e. each dir cosine in 3D
has a single 1.0 and two 0.0) direction cosines.

As far as I know this information-destroying 'squaring up' of the
direction cosines is only in the SpatialOrientationAdapter and
OrientImageFilter.

The relevant code in the NIFTI reader is in SetImageIOOrientationFromNIfTI
and SetNIfTIOrientationFromImageIO.

The problem is that the NIfTI orientation system isn't the same as ITK.
When I wrote that code, I was working from a set of test images that had
'square' direction cosines, trying to accommodate going to and from NIfTI
world.

The truth of the matter is that I barely made it through Linear Algebra
with a gentleman's 'C' so I can't begin to understand how to fix the NIfTI
code to go between ITK-world and NIfTI-world, preserving its
non-orthogonality.  If you can show me the formula to do so, I'd be glad
to implement it.

To put it more plainly, any dumb-headedness in the NIfTI ImageIO stems
directly from my dumb-headedness.

On 7/5/11 11:54 AM, "brian avants" <stnava at gmail.com> wrote:

>hi everyone (hans and kent, especially),
>
>currently, the image classes do not appear to check that the direction
>matrix is orthogonal.
>
>e.g. line 143   Modules/Core/Common/src/itkSpatialOrientationAdapter.cxx
>//TODO:  Should check that directions are orthoganal.
>  return direction;
>
>what does appear to check orthogonality is writer classes.
>
>i have only checked nifti for the moment.  test code is here:
>
>  typename ImageType::Pointer image = reader->GetOutput();
>  typename ImageType::DirectionType testdir=image->GetDirection();
>  testdir[0][0]=1;
>  testdir[0][1]=0.2;
>  testdir[1][0]=0.5;
>  testdir[1][1]=1;
>  image->SetDirection(testdir);
>  typedef itk::ImageFileWriter<ImageType> writertype;
>  typename writertype::Pointer writer = writertype::New();
>  writer->SetFileName("test.nii");
>  writer->SetInput( image );
>  writer->Update();
>
>this will write out an image with an orthogonal direction matrix
>presumably because nifti i/o forces this conversion (silently).
>
>if you switch the extension to "mhd", then the direction matrix in the
>output image is the same
>as that set in code.   you can run a registration etc using this
>non-orthogonal transform to physical space.  that is, if i use an
>image with the above direction matrix as the "fixed" image and an
>image resampled by that affine matrix (testdir), i get an identity
>transform as the solution for the mapping between them.  this is the
>use case we want to support .... and we do, to some extent, though
>the support is undocumented and inconsistent.
>
>in short, given current git itk, you can add a non-orthogonal transform
>to the
>header of an image in code.  you can then run image operations on this
>image without, it appears, any checking that the header orientation is
>orthogonal.  obviously, it requires significant code review to check
>if all filters that use direction
>matrices will be correct if the header transformation is affine.
>
>so, a minimal solution to this problem would be:
>
>-- allow nii to write non-orthogonal direction matrices via the sform
>   and setting the sform code to NIFTI_XFORM_ALIGNED_ANAT and qform code
>   to UNKOWN
>
>-- provide explicit warnings/exceptions in other i/o classes that
>cannot write affine header txs.
>
>this page has other details:
>
>http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_
>pages/qsform_brief_usage
>
>any thoughts?
>
>b.a.
>_______________________________________________
>Powered by www.kitware.com
>
>Visit other Kitware open-source projects at
>http://www.kitware.com/opensource/opensource.html
>
>Kitware offers ITK Training Courses, for more information visit:
>http://kitware.com/products/protraining.html
>
>Please keep messages on-topic and check the ITK FAQ at:
>http://www.itk.org/Wiki/ITK_FAQ
>
>Follow this link to subscribe/unsubscribe:
>http://www.itk.org/mailman/listinfo/insight-developers



________________________________
Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged.  If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited.  Please reply to the sender that you have received the message in error, then delete it.  Thank you.
________________________________