[vtk-developers] Bug in vtkNIFTIImageReader's handling of left-handed images?

[David Gobbi]

Hi Matthew,

I have confirmed that when qfac=-1, the z-offset in the qform and sform
differ when they should be exactly the same.  It is a very good thing that
you found this problem.  I'll get to work on verifying your fix.

 - David


On Wed, May 6, 2015 at 9:25 AM, mbrown <mbrown2 at ualberta.ca> wrote:

> Is the following behaviour a bug in vtkNIFTImageReader ?
>
> If you load SPM8's EPI.nii MNI template file using vtkNIFTIImageReader, it
> produces different q-form and s-form matrices. Note that the EPI.nii file
> obeys radiological convention (i.e. left-right flipped, qfac=-1 and
> left-handed s-form matrix), and vtkNIFTIImageReader flips the slice order
> and changes the q-form and s-form matrices as described in
> vtkNIFTIImageReader.cxx. To reproduce, in Python 2.7.3, running on Ubuntu
> 12.04, using vtk 6.2.0, do this:
>
> import vtk
> file_path = '<path/to/SPM8>/templates/EPI.nii'
> r = vtk.vtkNIFTIImageReader()
> r.SetFileName(file_path)
> r.Update()
> print(r.GetNIFTIHeader()) # original header values
> print(r.GetQFormMatrix()) # q-form matrix, with modifications by
> vtkNIFTIImageReader
> print(r.GetSFormMatrix()) # s-form matrix, with modifications by
> vtkNIFTIImageReader
>
> The last three lines produce ...
>
> original NIFTI header values (unnecessary fields not shown):
> Dim: 3 91 109 91 1 1 1 1
> PixDim: -1 2 2 2 0 0 0 0
> QFormCode: 4
> SFormCode: 4
> QuaternB: 0
> QuaternC: 1
> QuaternD: 0
> QoffsetX: 90
> QoffsetY: -126
> QoffsetZ: -72
> SRowX: -2 0 0  90
> SRowY:  0 2 0 -126
> SRowZ:  0 0 2 -72
>
> q-form matrix
> -1  0  0   90
>  0 -1  0 -126
>  0  0 -1  108
>  0  0  0  1
>
> s-form matrix
> -1  0  0   90
>  0 -1  0 -126
>  0  0 -1 -252
>  0  0  0  1
>
> I.e. the z-offset number in the fourth column is different between the
> q-form and s-form matrices. I tracked down the cause. In
> vtkNIFTIImageReader.cxx (accessed from
> https://github.com/Kitware/VTK/blob/master/IO/Image/vtkNIFTIImageReader.cxx
> on 2015-05-06):
>
> lines 974-976, where it adjusts the q-form matrix when qfac<0:
>       mmat[3] -= rmat[0][2]*hdr2->pixdim[3]*(hdr2->dim[3] - 1);
>       mmat[7] -= rmat[1][2]*hdr2->pixdim[3]*(hdr2->dim[3] - 1);
>       mmat[11] -= rmat[2][2]*hdr2->pixdim[3]*(hdr2->dim[3] - 1);
>
> versus lines 1031-1033, where it adjusts the s-form matrix when qfac<0:
>       mmat[3] -= hdr2->srow_x[2]*(hdr2->dim[3] - 1);
>       mmat[7] -= hdr2->srow_y[2]*(hdr2->dim[3] - 1);
>       mmat[11] -= hdr2->srow_z[2]*(hdr2->dim[3] - 1);
>
> Importantly, the rmat matrix (computed on line 926) used in lines 974-976
> is
> positive definite whereas the matrix defined by srow_x,y,z and used in
> lines
> 1031-1033 has negative determinant, in the case of SPM8's EPI.nii file.
> This
> means that rmat[2,2]=-1 and line 976 adds 180 to mmat[11] taking it from
> -72
> to 108 in the case of EPI.nii. In contrast, srow_z[2]=2, and line 1033
> subtracts 180 from mmat[11] taking it from -72 to -252.
>
> Is this difference in behaviour intentional? If so, why?
>
> Other tests suggest that the q-form code is correct and the s-form code is
> incorrect. A possible fix would be to replace lines 1031-1033 with:
>       mmat[3] += hdr2->srow_x[2]*(hdr2->dim[3] - 1);
>       mmat[7] += hdr2->srow_y[2]*(hdr2->dim[3] - 1);
>       mmat[11] += hdr2->srow_z[2]*(hdr2->dim[3] - 1);
>
> What do you think? Thanks.
> Matt
>
> ----------
> Matthew Brown, PhD
> Department of Psychiatry, University of Alberta
> Edmonton, Canada
>
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