[SEG] Add ITK GrowCut as segmentation tool
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	floca
	Nov 12 2021, 6:12 PM

Description

With itk 5.3 a remote packages was added: https://github.com/InsightSoftwareConsortium/ITKGrowCut

We should evaluate, if it makes sense to add the tool as soon as we have made the switch to ITK5.

Revisions and Commits

Restricted Differential Revision

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Status	Assigned	Task
Open	None	T28479 [Segmentation] Rethink / reevaluate our existing segmentation tools / algorithms
Open	None	T29191 [SEG] New segmentation tool candidates
Resolved	j762e	T28851 [SEG] Add ITK GrowCut as segmentation tool
Resolved	kislinsk	T27437 Migrate MITK to use ITK 5.x
Wontfix	None	T26413 Nifti2 support
Duplicate	None	T26456 Update ITK to v5
Resolved	floca	T28446 Migrate MatchPoint to ITK v5.1

Event Timeline

floca triaged this task as High priority.Nov 12 2021, 6:12 PM

floca created this task.

floca renamed this task from [Ssegmentation] to [Segmentation] Evaluate if we should add itkGrowCut as a tool.Nov 12 2021, 6:15 PM

floca lowered the priority of this task from High to Normal.

floca updated the task description. (Show Details)

floca added a subtask: T27437: Migrate MITK to use ITK 5.x .

floca moved this task from Backlog to Segmentation on the MITK (v2022.04) board.Nov 17 2021, 11:55 AM

@j762e This one could be important for you.

kislinsk closed subtask T27437: Migrate MITK to use ITK 5.x as Resolved.Mar 17 2022, 1:17 AM

kalali edited projects, added MITK, Next Milestone; removed MITK (v2022.04).Apr 20 2022, 5:03 PM

floca renamed this task from [Segmentation] Evaluate if we should add itkGrowCut as a tool to [SEG] Evaluate if we should add itkGrowCut as a tool.Jun 1 2022, 5:06 PM

floca added a parent task: T29191: [SEG] New segmentation tool candidates.

Pushed new branch to rMITK MITK: feature/T28851-AddITKGrowCutTool.

In newer versions of ITK the GrowCut.remote.cmake is added by default to Remote Modules (eg. https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/Remote).
Our version of ITK (https://www.mitk.org/download/thirdparty/) doesn't include that yet.
rMITKc94224c7fe81 is a "workaround" to still add the Remote Module without changing the present version of ITK on our server and might be reverted in future.

@j762e If you work in the task (which would be great ;), please claim it.

j762e claimed this task.Jun 24 2022, 3:46 PM

kalali edited projects, added MITK (v2022.10); removed Next Milestone, MITK.Jun 24 2022, 4:04 PM

kalali moved this task from Backlog to Cycle on the MITK (v2022.10) board.

Deleted branch from rMITK MITK: feature/T28851-AddITKGrowCutTool.

kalali added a revision: Restricted Differential Revision.Sep 20 2022, 2:14 PM

Some further remarks as I am leaving DKFZ:

Currently the GrowCut.remote.cmake is added in our own fork of ITK (https://github.com/MITK/ITK/commit/7014c07efd8c0585383e7ca8288d3773eb2e2dba). This might not be necessary anymore in future because the GrowCut module might be added with Version 5.3 of ITK (https://github.com/InsightSoftwareConsortium/ITK/releases/tag/v5.3rc04).
This tool was primarily tested on 3D images, although 4D images were tried. The behavior on 4D images should be further observed.
The tool just uses label on layer 0 of LabelSetImages. It might be interesting to add something like a "combobox" to support other layers as well.

I opened own tasks for these further remarks.

j762e renamed this task from [SEG] Evaluate if we should add itkGrowCut as a tool to [SEG] Add ITK Growcut as segmentation tool.Sep 21 2022, 1:33 PM

j762e renamed this task from [SEG] Add ITK Growcut as segmentation tool to [SEG] Add ITK GrowCut as segmentation tool.

j762e mentioned this in T29313: Add a Test to check if the GrowCut algorithm produces a different output.Sep 22 2022, 3:35 PM

Pushed new branch to rMITK MITK: feature/T28851-AddITKGrowCutTool.

kislinsk mentioned this in rMITK6c3702914aea: T28851-AddITKGrowCutTool (release prep).Oct 5 2022, 9:12 PM

kislinsk closed this task as Resolved.Oct 5 2022, 9:13 PM

Deleted branch from rMITK MITK: feature/T28851-AddITKGrowCutTool.