[Insight-users] Centering slices extracted from a volume

Richard Beare richard.beare at gmail.com
Tue Nov 11 19:34:54 EST 2008


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


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