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Maniphest T26949

DICOM SEG - 3D segmentations with only one slice cannot be reloaded as DICOM SEG
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Description

How to reproduce:

  1. Take a 3D image
  2. Generate a segmentation that is only on one slice of the image (if it spanns multiple slices, everything works fine)
  3. Store as DICOM SEG
  4. Load the DICOM SEG -> Error/exception.

Reason: DCMQI deduces an invalid origin of the segmentation image and throws an exception. Why? If it is a bug in DCMQI or a usage proplem on our side, is not clear yet?

Did not have the time to investigate further but wanted to report as known issue.

Related Objects

Event Timeline

floca created this task.Dec 20 2019, 9:34 PM
kislinsk triaged this task as Normal priority.Dec 23 2019, 2:54 PM
floca edited projects, added MITK (v2021.02), Missing Info, DICOM; removed MITK.May 13 2020, 10:24 PM

The reason is still unkown. But if you store the segs without skipping the empty slices, then mitk is able to load also segs with one slice.

floca mentioned this in T27416: DICOM Seg IO skips empty slices when storing DICOM seg.May 13 2020, 10:34 PM
kislinsk moved this task from Backlog to DICOM SEG on the MITK (v2021.02) board.May 20 2020, 10:34 AM
floca edited projects, added MITK; removed MITK (v2021.02).May 24 2020, 7:10 PM

As we have with T27416 a mitigation strategy for the next reales cycle, I retag it as MITK general. It should be checked somewhen, but given the current needs/information, I don't think it is necessary for the next cycle.
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floca mentioned this in rMITKa3af7d685863: Fixed T27416.May 24 2020, 8:02 PM
floca mentioned this in rMITKcfe5ef0b4943: Fixed T27416.
kislinsk closed this task as Wontfix.Mar 10 2021, 9:02 AM
kislinsk added a project: Auto-closed.
kislinsk added a subscriber: kislinsk.

Hi there! 🙂

This task was auto-closed according to our Task Lifecycle Management.
Please follow this link for more information and don't forget that you are encouraged to reasonable re-open tasks to revive them. 🚑

Best wishes,
The MITK devs

floca reopened this task as Open.Mar 10 2021, 9:42 AM
floca removed a project: Auto-closed.
kislinsk closed this task as Wontfix.Oct 14 2021, 11:39 AM

Hi there! 🙂

This task was auto-closed according to our Task Lifecycle Management.
Please follow this link for more information and don't forget that you are encouraged to reasonable re-open tasks to revive them. 🚑

Best wishes,
The MITK devs

floca reopened this task as Open.Dec 3 2021, 11:27 AM
kislinsk closed this task as Wontfix.Sep 9 2022, 10:24 AM
kislinsk added a project: Auto-closed.

Hi there! 🙂

This task was auto-closed according to our Task Lifecycle Management.
Please follow this link for more information and don't forget that you are encouraged to reasonable re-open tasks to revive them. 🚑

Best wishes,
The MITK devs

MITK · MIC · IMSY · DKFZ