I’m working on adding support for orientation in VTK image data and what depends on it (filters, mappers, IO… more details here ). I was working on the MetaIO (.mha, .mhd) reader and tested using a sample dataset with the following header: ObjectType = Image NDims = 3 BinaryData = True BinaryDataBy…

Hi @agirault - yes, this has come up a couple of times. I believe the post from Andras sums up the current understanding. [image] Import mhd data Support Slicer uses ITK image reader to load metaimage files. This reader intentionally ignores AnatomicalOrientation (I’ve r…

Right on, thank you Steve. [image] pieper: This reader intentionally ignores AnatomicalOrientation (I’ve raised this question before to ITK developers and Kitware and they confirmed that this is not a bug and they will not change the behavior) Well… we probably won’t have that in VTK, and I’…

I agree, I don’t like having this standard field for “informational purposes” only (that readers should ignore), especially because similar field in nrrd is actually used by the readers. However, I understand the reluctance in investing more time into improving the file format, as there are already…

[image] Import mhd data Does the TransformationMatrix specify rotation between (i,j,k) and the RAS coordinate? Yes. @lassoan in the other thread linked above, you mention that the TransforMatrix (is that different from the Orientation field?) is a rotation from ijk to RAS. However, when sav…

After discussion with @thewtex and @aylward , we agreed that the current integration of MetaIO inside ITK is incorrect, namely: The reader ignores the anatomical orientation and assumes the data is always in LPS. It should instead adjust the orientation matrix described in the file to go from IJK t…

FYI: an attempt at updating the MetaIO reader and writer in VTK can be found here: https://gitlab.kitware.com/vtk/vtk/merge_requests/5656

For the sake of cross-referencing/documenting, the change was NOT implemented as suggested in the last two comments, following a discussion that occurred in the ITK issue tracker: https://github.com/InsightSoftwareConsortium/ITK/issues/1017

BUG when reading mha file with AnatomicalOrientation

Development

pieper (Steve Pieper (Isomics, Inc.)) June 5, 2019, 6:05pm 2

Hi @agirault - yes, this has come up a couple of times. I believe the post from Andras sums up the current understanding.

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BUG when reading mha file with AnatomicalOrientation

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