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

[David Gobbi]

Hi Matthew,

I've written a patch that includes your fix:
https://gitlab.kitware.com/vtk/vtk/merge_requests/181

Hopefully we'll get this merged soon.

 - David



On Wed, May 6, 2015 at 2:10 PM, David Gobbi <david.gobbi at gmail.com> wrote:

> 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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