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Maniphest T28991

[Segmentation] 3D tools overwrite / remove previous mask if reconfirmed
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Description

The 3D Tools (e.g. Threshold, FastMarching 3D, Region Growing 3D) compute a preview for the current settings. The preview can be confirmed and written into the slice (slices for 4D segmentations).
This will overwrite any existing segmentation mask - also if this mask was e.g. created by the simple Add-tool or even the same tool (e.g. using Threshold twice).

So in contrast to the 2D tools it is not possible to add up / combine different segmented patches one after another, like it can be easily done with the 2D tools.

This is especially problematic for static 4D segmentations: here you can not use the 3D tools (e.g. Threshold) to segment a slice and add another segmentation on the next timestep - it will overwrite the segmentation from the previous timestep.

To reproduce:

  • load a 3D image, open the segmentation plugin, create a new segmentation (labelsetimage)
  • use the Threshold-tool to create a segmentation mask
  • confirm the preview and see how the segmentation is written into the slice
  • use e.g. the UL Threshold to create another segmentation mask
  • confirm the preview and see how the new segmentation is written into the slice and the previous mask is completely removed
  • load a 4D image, open the multilabel-segmentation plugin, create a new STATIC segmentation (labelsetimage)
  • create a new label on the first layer
  • create another label on the first layer (distinct color)
  • use the 2D Add-tool to create a segmentation mask for the second label
  • use the 3D Threshold-tool to create a segmentation mask for the first label
  • see how the new segmentation is written into the slice and the previous mask is completely removed
  • change the timestep
    • see how the threshold segmentation mask does not fit the underlying image anymore that well
  • use the 3D Threshold-tool to create a segmentation mask for the first label on the new timestep
  • see how the new segmentation is written into the slice and the previous mask is completely removed
  • change back to the previous timestep
    • see how the threshold segmentation mask does not fit the underlying image anymore that well

There is a checkbox "Create as new segmentation" but this will only allow to create a new segmentation node and prevent overwriting - but it does not change the behavior when it comes to "combining masks one after another".

Revisions and Commits

Restricted Differential Revision
rMITK MITK
Restricted Differential RevisionrMITKf97486ba8334 Removed m_SpacingNodes out of dataStorage upon closing of IGT…
Restricted Differential RevisionrMITKc192e5c8a143 Show interpolator only if valid data was selected
Restricted Differential RevisionrMITKa761c112ae54 Simplify volume rendering
Restricted Differential RevisionrMITK3830dafcd734 Merge remote-tracking branch 'Alfred-Franz/T27260…
Restricted Differential RevisionrMITK1e08152896c2 Make background of help search results browser white
Restricted Differential RevisionrMITK827c3bebc9dc Improve label set color table with distinctive colors
Restricted Differential RevisionrMITK27b96239f36c Fixed T29062
Restricted Differential RevisionrMITK6dcbff22f6b8 Merge branch 'release/T29075-v2022.04' of https://phabricator.mitk.
Restricted Differential RevisionrMITK6332e7e4a4b1 Add default labelset preset setting to segmentation preferences
Restricted Differential RevisionrMITK2ef49f51d547 Completely remove Fast Marching and Watershed tools
AuditedRestricted Differential RevisionrMITK99c7cd50740b Add Segmentation.labelSetPreset command-line argument
Restricted Differential RevisionrMITKae5d84e547d6 Migrate segmentation preferences to .ui file
Restricted Differential RevisionrMITK048ae9d92f3e Show hint if the label set preset is overriden by command-line argument
Restricted Differential RevisionrMITKb73c37478dbe Improved generic naming and coloring of newly created labels
Restricted Differential RevisionrMITKce753d0b4e25 Improve language in message box when removing selected labels
Restricted Differential RevisionrMITK9cfad23a894c Add non const option for mitk::AutoSegmentationTool::GetImageByTimeStep
Restricted Differential RevisionrMITKb3cc84fe26ce Added label awareness to AutoSegmentationWithPreviewTool
Restricted Differential RevisionrMITKd7e8f65fe420 Makes picking tool label aware and improves it.
Restricted Differential RevisionrMITK2db1230de67b Make AutoMLSegmentationWithPreviewTools label and active label aware.
Restricted Differential RevisionrMITK00d30235b556 Added documentation and precondition checks
Restricted Differential RevisionrMITK4e6176508567 Fixed gcc compile errors
Restricted Differential RevisionrMITKc042953a0088 Fixed bug in PointSet::RemovePointAtEnd.
Restricted Differential RevisionrMITKe7d9e43da490 Deactivated the possibility to pick background.
Restricted Differential RevisionrMITK636fe05faa33 Fixed review comments
Restricted Differential RevisionrMITKf2fc9d8a3b81 Fixed the probelem/bug if active label was changed between
Restricted Differential RevisionrMITKf44db9ed8748 Make AutoSegmentationTool label aware
Restricted Differential RevisionrMITK04ef3f0c5cde Fixed review remarks
Restricted Differential RevisionrMITKee32bb9512c6 Added ResetReviewContent

Related Objects

Event Timeline

kalali triaged this task as Normal priority.EditedFeb 23 2022, 3:44 PM
kalali created this task.

This is a know issue and was already discussed here: T28131#223660

kalali mentioned this in T28131: [MultiLabel Segmentation] 3D Threshold tool does not work with multiple labels / layers.Feb 24 2022, 10:01 AM
kalali added a comment.Mar 15 2022, 11:27 AM

I just realized that this should be mentioned in the checklists!

kalali mentioned this in T29087: [Segmentation] Some AutoTools confirm objects to the first Label instead of selected and/or completely override existing segmentations.Apr 3 2022, 9:11 PM
floca claimed this task.Apr 4 2022, 12:14 PM
floca added a revision: Restricted Differential Revision.Apr 5 2022, 5:47 PM
floca added a revision: Restricted Differential Revision.Apr 5 2022, 6:07 PM
floca added a revision: Restricted Differential Revision.Apr 6 2022, 6:51 PM
kalali added a comment.Apr 9 2022, 10:56 AM

I realized that this is a slightly different topic and is not completely solved with D622:

  • creating a new e.g. Threshold-Segmentation on an already existing label will overwrite the same label
    • this is maybe desired but I would like to discuss the use case where a user wants to create different patches for the same mask by a segmentation tool multiple times
      • e.g. by using the threshold with a very low and a very high threshold and combining / adding both masks / patches
      • e.g. by creating different patches on different time steps for the same label (i.e. as written in the task description)
floca added a comment.Apr 11 2022, 1:55 PM
In T28991#236323, @kalali wrote:

I realized that this is a slightly different topic and is not completely solved with D622:

  • creating a new e.g. Threshold-Segmentation on an already existing label will overwrite the same label
    • this is maybe desired but I would like to discuss the use case where a user wants to create different patches for the same mask by a segmentation tool multiple times
      • e.g. by using the threshold with a very low and a very high threshold and combining / adding both masks / patches
      • e.g. by creating different patches on different time steps for the same label (i.e. as written in the task description)

This is also covered by the transfer function. But I havent activated this feature. I deemed it to much intervention in the release phase. That feature should be generaly added for all auto tools after the upcoming release.

kalali added a comment.EditedApr 12 2022, 3:09 PM

Ok, then we keep it for now with the Next Milestone tag. However, do you still claim this task? Do you want the D622 to be linked with this task?

floca removed floca as the assignee of this task.Apr 13 2022, 1:10 PM
floca added a project: Request for Discussion.

Task text needs clarification before some one works on it.

The feature to add preview content to a label instead of replacing it is understood. But the task text also criticises things, where I am not sure if it is realy a bug but just intended behavior.
e.g.

  • change the timestep
    • see how the threshold segmentation mask does not fit the underlying image anymore that well

As a static seg is used. I would expect this behavior. Even for a dynamic seg, if not "process all time steps" are activated.

kislinsk mentioned this in T29075: 2022 Week 17 (Very Late April).Apr 25 2022, 12:43 PM
floca added a commit: rMITK04ef3f0c5cde: Fixed review remarks.Apr 25 2022, 3:24 PM
floca added a commit: rMITKee32bb9512c6: Added ResetReviewContent.
floca added a commit: rMITKf44db9ed8748: Make AutoSegmentationTool label aware.
floca added a commit: rMITKf2fc9d8a3b81: Fixed the probelem/bug if active label was changed between.
floca added a commit: rMITK636fe05faa33: Fixed review comments.
floca added a commit: rMITKe7d9e43da490: Deactivated the possibility to pick background..
floca added a commit: rMITKc042953a0088: Fixed bug in PointSet::RemovePointAtEnd..
floca added a commit: rMITK4e6176508567: Fixed gcc compile errors.
floca added a commit: rMITK00d30235b556: Added documentation and precondition checks.
floca added a commit: rMITK2db1230de67b: Make AutoMLSegmentationWithPreviewTools label and active label aware..
floca added a commit: rMITKd7e8f65fe420: Makes picking tool label aware and improves it..
floca added a commit: rMITKb3cc84fe26ce: Added label awareness to AutoSegmentationWithPreviewTool.
floca added a commit: rMITK9cfad23a894c: Add non const option for mitk::AutoSegmentationTool::GetImageByTimeStep.
kislinsk added a commit: rMITKce753d0b4e25: Improve language in message box when removing selected labels.Apr 25 2022, 3:25 PM
kislinsk added a commit: rMITKb73c37478dbe: Improved generic naming and coloring of newly created labels.
kislinsk added a commit: rMITK048ae9d92f3e: Show hint if the label set preset is overriden by command-line argument.
kislinsk added a commit: rMITKae5d84e547d6: Migrate segmentation preferences to .ui file.
kislinsk added a commit: rMITK99c7cd50740b: Add Segmentation.labelSetPreset command-line argument.
kislinsk added a commit: rMITK6332e7e4a4b1: Add default labelset preset setting to segmentation preferences.
kislinsk added a commit: rMITK2ef49f51d547: Completely remove Fast Marching and Watershed tools.
floca added a commit: rMITK6dcbff22f6b8: Merge branch 'release/T29075-v2022.04' of https://phabricator.mitk..Apr 25 2022, 3:25 PM
floca added a commit: rMITK27b96239f36c: Fixed T29062.
kislinsk added a commit: rMITK827c3bebc9dc: Improve label set color table with distinctive colors.Apr 25 2022, 3:25 PM
kislinsk added a commit: rMITK1e08152896c2: Make background of help search results browser white.
kislinsk added a commit: rMITK3830dafcd734: Merge remote-tracking branch 'Alfred-Franz/T27260….
kislinsk added a commit: rMITKa761c112ae54: Simplify volume rendering.
kalali added a commit: rMITKc192e5c8a143: Show interpolator only if valid data was selected.Apr 25 2022, 3:25 PM
kannberg added a commit: rMITKf97486ba8334: Removed m_SpacingNodes out of dataStorage upon closing of IGT….Apr 25 2022, 3:25 PM
kalali added a comment.Apr 28 2022, 4:00 PM
In T28991#236421, @floca wrote:

[...] But the task text also criticises things, where I am not sure if it is realy a bug but just intended behavior.
e.g.

  • change the timestep
    • see how the threshold segmentation mask does not fit the underlying image anymore that well

As a static seg is used. I would expect this behavior. Even for a dynamic seg, if not "process all time steps" are activated.

This was not meant as a criticism but just to bring this behavior to the attention of the user. Because it is important to realize what's happening, to understand that a new mask was created and the old one was overwritten.

floca added a comment.Apr 30 2022, 8:11 PM
In T28991#237063, @kalali wrote:

This was not meant as a criticism but just to bring this behavior to the attention of the user. Because it is important to realize what's happening, to understand that a new mask was created and the old one was overwritten.

Thank you for the clarification. 🙏

floca claimed this task.May 13 2022, 2:13 PM
floca edited projects, added MITK (v2022.10); removed Request for Discussion, Next Milestone, MITK.
floca moved this task from Backlog to Cycle on the MITK (v2022.10) board.May 16 2022, 12:30 PM
floca closed this task as Resolved.May 18 2022, 3:37 PM

Solved in context of i.a. T28982. Now this is handled correctly and user can also configure the behavior.

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