[Insight-developers] strategies for orientation of mouse MRI

[Richard Beare]

Hi everyone,

I'm reorienting mouse MRI scans using the OrientImageFilter. I seem to
be able to get this working sensibly by specifying the input
orientation and desired output orientation. My output nifti images are
viewable with ImageViewer, but seem to crash fslview. I'm wondering if
I'm forgetting something that results in invalid nifti files. fslview
is able to load the original images which were converted from Bruker
format using my preliminary ITK BrukerIO module.

The nifti information from the original is

qform_code           252      1    1
  sform_code           254      1    1
  quatern_b            256      1    0.0
  quatern_c            260      1    0.0
  quatern_d            264      1    1.0
  qoffset_x            268      1    -0.0
  qoffset_y            272      1    -0.0
  qoffset_z            276      1    0.0
  srow_x               280      4    -0.03 0.0 0.0 -0.0
  srow_y               296      4    0.0 -0.017578 0.0 -0.0
  srow_z               312      4    0.0 0.0 0.03 0.0
  intent_name          328     16

After manipulation via:

  orienter->SetGivenCoordinateOrientation(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_IAL);
  orienter->SetDesiredCoordinateOrientation(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_RIA);
qform_code           252      1    1
  sform_code           254      1    1
  quatern_b            256      1    -0.5
  quatern_c            260      1    0.5
  quatern_d            264      1    0.5
  qoffset_x            268      1    11.97
  qoffset_y            272      1    -0.0
  qoffset_z            276      1    0.0
  srow_x               280      4    -0.0 -0.03 0.0 11.97
  srow_y               296      4    -0.0 0.0 -0.017578 -0.0
  srow_z               312      4    -0.03 0.0 0.0 0.0
  intent_name          328     16


Am I doing anything obviously wrong?