[Insight-developers] Centering slices extracted from a volume

[Richard Beare]

Hi,

I'm running into issues preparing histology and MR images for registration.

I'm extracting slices from the MRI using the ExtractImageFilter and
attempting to reset the origin using ChangeInformationImageFilter

If I start with a 2D image (such as the histology scans) then the
centering works correctly, as judged using fslview - i.e cursors in
the middle reports a coordinate of (0,0).

However, when starting with the 3D data, nothing seems to work unless
I pretend that the output image is 3D with only one slice. There seems
to be an interaction between the extraction and the orientation
information that produces incorrect results. - for example the
DIrection information appears to become invalid:

  Spacing: [0.0299728, 0.03]
  Origin: [5.61499, 10.3093]
  Direction:
-1 0
0 0