Segmentation changes image orientation

[msofka]

1. Load Nifti (nii) image with given affine matrix as stored with the image.
2. Click Segmentation tab.
3. Add new segmentation, specify name.
4. The image changes orientation and is now upside down in the axial window.

[ypauchard]

I have seen similar behaviour with MRI images with either a coronal or sagittal native plane. My guess is that the transformation matrix in the image header is not properly used.

@araex has found the following related bug thread in MITK https://phabricator.mitk.org/T19632

In the newest MITK release MITK-2016-11 the issue is resolved, tested with MITK-Workbench on a set of MRI images.

Hence, the solution would be to use MITK-2016-11 in MITK-GEM. However, this would mean dropping the statistics plugin and help for MacOSx. Other options would be to create separate branches for Win-Linux and MacOSx, rewrite the two plugins, or wait for MITK to resolve the issue.