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DICOM Seg IO skips empty slices when storing DICOM seg
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Description

Status: Currently our DCM seg writer skips empty slices (thats the default of dcmqi). This results in the fact, that segs stored and loaded into MITK cannot be directly used for e.g. statistics or modifying the segmentation, because we assume/test in most code parts that mask and image have the same geometry, which will mostly not be the case (or in other words MITK currently does not support yet segmentations that are only a cropped grid of the image, so smaller extend but same geometry).

I think we should at least change to not skip the empty slices on save for now. To produce segs that MITK fully supports currently. If we support cropped segmentations somewhen in the future, we could switch it on again.

This seems also to mitigate the problem noted in T26949.

Revisions and Commits

rMITK MITK
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Event Timeline

floca triaged this task as Normal priority.Wed, May 13, 10:34 PM
floca created this task.
kislinsk moved this task from Backlog to DICOM SEG on the MITK (2020) board.Wed, May 20, 10:35 AM

Discussion result: For now (MITK 2020) we well deactivate the skipping of empty slices. But such a support would make sense longterm, but it is also a bigger issue. I have opened a dedicated Task T27439: [Segmentation] Support of Mask/Segmentations that are cropped / do not cover the whole image grid for that.

floca added a revision: Restricted Differential Revision.Sun, May 24, 3:53 PM
floca claimed this task.Sun, May 24, 3:54 PM