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[Segmentation] How to handle 3D and 4D Segmentations on 4D images
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Description

It is now possible to create a static (3D) or dynamic (4D) mask on a 4D image.
The segmentation tools / algorithms have different ways to create a segmentation, e.g.

some tools always take the first time steps (like Threshold for 3D seg on 4D image, while 4D image on 4D images is OK)
others end always with 3D segs (e.g. Otsu when making a 4D seg on a 4D image)
others don't allow to confirm (Threshold in multilabel images for 3D on 4D)

Some masks are created on all time steps but are only valid for the first time step.

Also:

Discussion:

  • Should the expected behavior be that only the current timestep is taken into consideration during 3D region growing? Or is the goal to have a real 4D region growing?
  • Consequently, should the outcome be a
    1. 3D image of the current timestep?
    2. 4D image with one timestep containing a Segmentation
    3. 4D Image with region growing over location and time?

We should discuss this here and create a consistent user experience.

Event Timeline

kalali triaged this task as Normal priority.Mon, Jun 29, 1:36 PM
kalali created this task.
floca added a comment.Mon, Jun 29, 1:48 PM

I would propose the following policy:

  1. All tools per default work only on the respective time step of the reference data and the segmentation, that are indicated by the currently selected time point (SliceNavigator). So this is general and independent from the fact if it is a 3D or a 4D segmentation. This is the same behavior like the interactive tools and does not break user expectations.
  2. It is up to the specific tool (must be discussed there) if for 4D reference images others then the current time step of the reference data step should be used. Per se, I would say no.
  3. It is up to the specific (3D) tool to allow the altering of more then the current segmentation time step (if the segmentation is 4D). If one wants such a feature I would add e.g. a check box to the tool like "confirm for all time steps".