- load the image: . The image will be displayed correctly (but reinit is necessary)
- right click on image -> reinit
Log output with debug version:
!5.547! WARNING: EnsurePerpendicularNormal(): Plane geometry was _/askew/_, so here it gets rectified by substituting the 3rd column of the indexToWorldMatrix with an appropriate normal vector: [ 0.921861 -0.918454 -0.746066 ], original vector zed was: [ -0.943643 -3.64367e-09 -1.16599 ]. MitkWorkbench: ../../../../MITK/Modules/Core/src/DataManagement/mitkSlicedGeometry3D.cpp:273: virtual void mitk::SlicedGeometry3D::InitializePlanes(const mitk::BaseGeometry*, mitk::PlaneGeometry::PlaneOrientation, bool, bool, bool): Assertion `(standardPlaneNormal - (top ? 1.0 : -1.0) * worldPlaneNormal).GetSquaredNorm() < 0.000001' failed.
@full @schererj @kislinsk : how did you convert these files exactly? If I load the DICOM with a current MITK Workbench -> no problem, re-init fine. Save as nifti, quit, restart, load nifti, re-init -> no problem as well.
So we should investigate two things: 1. what is different in your conversion process? 2. are "your" nifti files somehow invalid and should be rejected on load or should we able to handle them as well.
I converted them with a simple two-liner: mitk::IOUtil::Load<mitk::Image>(); mitk::IOUtil::Save();
Peter and I checked some output NIFTI images and they are valid 3d+t images. Reinit did also work. So for now I suspect that there is another processing step involved? The images above do not match my output files regarding name and file extension I think.
I have the issue again with other data data from a cooperation partner. Also Slicer has issues with the original DICOM data set:
Geometric issues were found with 1 of the series. Please use caution. reg inside examine Loading with imageIOName: GDCM Window/level found in DICOM tags (center=212.0, width=487.0) has been applied to volume 25: CINE_segmented_SAX_InlineVF Irregular volume geometry detected, but maximum error is within tolerance (maximum error of 4.00539e-05 mm, tolerance threshold is 0.001 mm). Loading with imageIOName: GDCM Window/level found in DICOM tags (center=212.0, width=487.0) has been applied to volume 25: CINE_segmented_SAX_InlineVF_1 Irregular volume geometry detected, but maximum error is within tolerance (maximum error of 4.00539e-05 mm, tolerance threshold is 0.001 mm).
Looks like the Slicer warning is important, but still it succeeds in loading the data. The numerical error is rather low. Found this discussion which also links to the python code Slicer is using and which emits the warning. Could be of some use for further investigations. https://discourse.slicer.org/t/dicom-scalar-volume-load-irregular-geometry-warning-overly-stringent/3761/14