The slice numbering is a bit messy. First, the slice indexes are for the
world geometry, and the direction of the numbering depends on how the
geometry has been constructed. If you do 'Reinit' on an image (data manager
context menu), the world geometry will be created based on the geometry of
that image. The 'global reinit' creates a geometry (bounding box) in which
all the images of the data storage fit whose global visibility is 'on' at
that moment. This might or might not match the geometry of one of the
visible images.
What regards the direction, as I remember the axial slice numbering is
inverted (top to bottom) the others not (left to right, bottom to front).
The image navigator therefore reverts the axial number, while the status
bar shows the unaltered coordinates of the world geometry. See also
http://bugs.mitk.org/show_bug.cgi?id=17462
Moreover, other viewers could create the world geometry in a different way.
Miklos
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