Hi Andreas,
Thanks for the reply. Actually, I've found a CT with a non usual
orientation where it is happening too, but, for MRIs, it is always
happening.
Best regards,
Federico
On Mon, Apr 15, 2013 at 6:35 AM, Fetzer, Andreas <
[email protected]> wrote:
> Hi Frederico,****
>
> ** **
>
> for the clarification of „Reinit“ and Global Reinit”:****
>
> ** **
>
> **- **"global reinit" makes the first/red render-window display
> transversal slices,****
>
> also if the image is not aligned along the MITK world coordinate system.
> ****
>
> I.e. the global variant calculates a smallest bounding box in world
> ****
>
> coordinates and makes this bounding box the render-window-world****
>
> ** **
>
> **- **"reinit" takes the coordinate system of the selected
> mitk::Image as the ****
>
> render-window-world****
>
> ** **
>
> There is also a bug for this since this caused some confusion among us
> either: http://bugs.mitk.org/show_bug.cgi?id=8350****
>
> In this bug the problem with the MRI is mentioned too. I assume this behavior
> only occurs with MRIs, doesn’t it?****
>
> ** **
>
> ** **
>
> Best regards****
>
> Andreas****
>
> ** **
>
> ** **
>
> ** **
>
> ** **
>
> ** **
>
> *From:* Federico Milano [mailto:[email protected]]
> *Sent:* Freitag, 12. April 2013 03:11
> *To:* [email protected]
> *Subject:* [mitk-users] Reinit****
>
> ** **
>
> 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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