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Multilabel Segmentation file cannot be converted to multilabel segmentation in MITK
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Dear MITK-Team,

I am working with 4D raw images and corresponding segmentations (again nifti). I use MITK-v2018.04.2-32-g17d6368 (installer for which the "matrix inversion problem" is fixed) on ubuntu.

For most patients I can proceed as follows:

  1. load image and segmentation into MITK
  2. right click on segmentation file in the file manager-> "convert to segmentation" -> multilabel segmentation is created and displayed with all labels in the multilabel segmentation window.

However for some patients the second step fails. After right clicking and "convert to segmentation" the segmentation is not shown in the multilabel segmentation window (and not in the "single" segmentation tool window) . All labels are displayed with distinguished colors, but it seem that MITK combines all of them into one big label (surrounded by a red line). I cannot choose a specific label. If I decided to add something to the segmentations anyways, I will automatically add an area having the some color as the first label (in my case yellow). But I cannot change any other label.

For me it seems like all labels are internally merged into one big segmentation (since I cannot choose a specific label plus all three labels are surrounded by a red line). On the other hand, all three labels are displayed in different colors which implies that the information of which pixel belongs to which class is not lost.

Example data can be found at:

  • patient 0084 works as expected
  • patient 0058 does not work as expected

Thanks for your support.

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kislinsk added a subscriber: kislinsk.

HI Peter, MITK (2018-04-4) the the current milestone. I nearly missed this task as you put it in the already archived milestone MITK (2018-04). The safest way to raise awareness is to just set the task priority to Needs Triage and stick with the MITK tag. ❤

It turned out that if I load the file holding the segmentation alone and the right click -> convert to segmentation, everything works as expected. Only if I load the raw image plus the corresponding segmentation simultaneously (which is my usual workflow), the bug above arises.


kislinsk triaged this task as Normal priority.Jun 24 2019, 1:43 PM
kalali renamed this task from Multilabel Segmentation fil ecannot be converted to multilabel segmentation in MITK to Multilabel Segmentation file cannot be converted to multilabel segmentation in MITK.Oct 1 2020, 2:11 PM

@full Is this still an issue (with the current release)?