Hi. I was wondering if somebody could kindly provide us with a general
explanation of what "ReInit" is doing behind the scenes.
This question arises since we are trying to use the ExtractSliceFilter, but
we are witnessing some puzzling results.
For example, we load a 3D volume (MRI/CT). The anatomical views are correct
in the mitkWorkbench. We execute ExtractSliceFilter (in a plugin). The
first problem is that the plane we are building to get a Geometry2D is
initialized with the "Frontal" orientation, but it is producing an "Axial"
slice. After experimenting for a while (maybe this is really basic), we
have noticed a second issue: that if you get the vtk image from the mitk
image and then reconvert it to a mitk image but without adding it the
geometry of the original mitk image, it appears a rotation in the generated
mitk image, and the anatomical views are wrong, but the PlaneGeometry is
correct. Paradoxically, if we do a reinit on the original mitk image, the
same happens in the mitkWorkbench, the image is rotated in one of the axis
and the views don't correspond to the anatomy anymore, but, in this case,
the PlaneGeometry is still incorrect, that is, it does not extract the
correct slice when used with the filter.
In conclusion, PlaneGeometry (and its use in ExtractSliceFilter) is
consistent with the vtk image, that is, the "frontal" plane is correctly
located if we convert the image to vtk and back to mitk without adding the
original geometry, but the problem is that, that image, is not oriented in
an anatomical correct way, so the views presented in mitkWorkbech are
incorrect.
I find this kind of hard to express verbally, so please ask my for any
additional data you may need.
Thanks in advance,
Federico
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