Page MenuHomePhabricator

Workbench crashes when using 2D Region Growin on DWI Image (.nii) on Ubuntu 16.04
Closed, WontfixPublic

Description

Reproduce Bug:

  • Import .nii DWI Image.
  • Create new Segmentation
  • Select 2DTools / Region Growing
  • Click on the image

-> Workbench crashes

  • seems to be connected to the missing component slicer. Nifti images get a time slicer for their diffusion components.

Event Timeline

This may be somewhat similar and / or related to T19935

kislinsk edited projects, added MITK (2016-11); removed MITK.
kislinsk added a subscriber: kislinsk.

Also crashes with normal 4D images. In Multilabel segmentation 2D region crowing, too.

For 4D images the crash occurs in

mitk::RegionGrowingTool::OnMousePressed

due to

m_WorkingSlice->GetTimeGeometry()->GetGeometryForTimeStep(m_LastEventSender->GetTimeStep())

returning a nullptr, as GetTimeGeometry() only has a single timestep even for 4D images.

For me a multi component crash does not happen anymore.

The 3D+t problem should now be fixed. However, my solution is by no means an elegant one.

Currently the RegionGrowingTool gets it working/reference slices via its base class FeedbackContourTool. Previously the RegionGrowingTool assumed these slices to be 2D+t, however the FeedBackContourTool only returns a 2D slice, albeit of the correct timestep.

This was changed, the RegionGrowingTool now assumes to already have the correct timestep.

When generating the contourmodel the timestep of the working slice is internally used by the ImageToContourModelFilter. So the resulting contourmodel is written for timestep 0. This in turn results in the mapper not displaying it, as the current timestep of the contourmodel is empty.

I circumvented this problem by, for timesteps != 0, copying the contourmodel to a new one with the correct timestep before rendering and back afterwards for the segmentation generation.

This crutch should be removed when redesigning the tools.

goch moved this task from Suggested to Included on the MITK (2016-11) board.
kalali reopened this task as Open.EditedDec 7 2020, 8:41 PM
In T22412#93426, @goch wrote:

This crutch should be removed when redesigning the tools.

@floca I stumbled upon this and I was wondering if this crutch can be removed with the changes made in T27490.

floca added a subscriber: neher.
In T22412#93426, @goch wrote:

This crutch should be removed when redesigning the tools.

@floca I stumbled upon this and I was wondering if this crutch can be removed with the changes made in T27490.

May be. We would need to test it.
@neher do we have suiteable testdata?

floca moved this task from Backlog to Segmentation on the MITK (v2021.02) board.

@neher or @jaegerp can someone provide test data? Otherwise I would close this task for now, because I cannot check or reproduce the problem without data.

Also crashes with normal 4D images. In Multilabel segmentation 2D region crowing, too.

I'm not exactly sure what that means. Can we also use our default 3D data to test? Does it have to be nifty?

floca claimed this task.

Closed. @neher or who ever might stumple upon the prolem again, is welcome to open it again and provide data. :)