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Maniphest T29437

[SEG] Add TotalSegmentator
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Description

Add TotalSegmentator as a tool like we did for nnUnet.

https://github.com/wasserth/TotalSegmentator

UI might even be simpler, as we have less settings options with TotalSegmentator.
For now I would start with integrating the inferencing. Retraining might be added later.

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StatusAssignedTask
ResolvedkislinskT29191 [SEG] New segmentation tool candidates
ResolvedflocaT29437 [SEG] Add TotalSegmentator
Resolveda178nT29457 Introduce basic TotalSegmentator tool in Workbench
Resolveda178nT29458 Include Advanced settings support for TotalSegmentator tool in MITK
WontfixflocaT29465 How to display available statistics of segmentation
ResolvedkislinskT29459 Docker support for TotalSegmentator
ResolvedNoneT29461 TotalSegmentator output label names conundrum
Resolveda178nT29462 TotalSegmentator (Python) issues
Resolveda178nT29463 Doxygen documentation for TotalSegmentator
Resolveda178nT29464 Test plan for TotalSegmentator
Resolveda178nT29468 Let MITK handle TotalSegmentator setup
ResolvedkislinskT29485 TotalSegmentator User Testing
ResolvedkislinskT29487 Tool Icon for TotalSegmentator
Resolveda178nT29497 Full support for all subtasks
ResolvedkislinskT29510 Migrate installer from Qt GUI level to MITK level
Resolveda178nT29538 Test with latest Totalsegmentator v1.5.5
Resolveda178nT29558 TotalSegmentator: Modify as per new Segmentation changes
Resolveda178nT29560 TotalSegmentator Label naming scheme
Resolveda178nT29566 TotalSegmentator GUI bug: Install button not Activated correctly
Resolveda178nT29567 TotalSeg: inferencing issue on MacOS
Resolveda178nT29569 [Checklist] Update TotalSegmentator & nnUNet checklist
ResolvedkislinskT29596 Move out FAST checkbox from Advanced
Resolveda178nT29597 TotalSeg didn't remember python environment
Resolveda178nT30215 [SEG] Support TotalSegmentatorV2
ResolvedNoneT30256 TotalSeg: Add check for Python version
Resolveda178nT30300 Remember "Fast" checkbox setting
ResolvedkislinskT30301 Move Totalsegmentator installation into Preferences
Resolveda178nT30353 [TotalSeg] Add confirmation dialog before exiting the tool
Wontfixa178nT30447 [TotalSeg] Levelwindow effect
Resolveda178nT30457 Add TotalSegmentator MR image (v 2.2) support in MITK

Event Timeline

floca renamed this task from [SEG] Add Totel to [SEG] Add TotalSegmentator.Dec 14 2022, 8:25 AM
floca created this task.
floca moved this task from Backlog to MITK Meeting on the Request for Discussion board.
floca moved this task from Backlog to Segmentation on the MITK (v2023.04) board.
kislinsk triaged this task as High priority.Jan 11 2023, 11:49 AM

As it is a really nice user-friendly feature, we have a high interest in getting TotalSegmenter integrated soon into MITK.

kislinsk moved this task from MITK Meeting to Backlog on the Request for Discussion board.Jan 25 2023, 11:48 AM
kislinsk removed a project: Request for Discussion.
a178n claimed this task.Jan 25 2023, 1:55 PM
floca moved this task from Segmentation to Cycle on the MITK (v2023.04) board.Feb 8 2023, 10:46 AM
a178n closed subtask T29461: TotalSegmentator output label names conundrum as Resolved.Mar 22 2023, 3:10 PM
a178n closed subtask T29538: Test with latest Totalsegmentator v1.5.5 as Resolved.Apr 25 2023, 2:19 PM
a178n closed subtask T29457: Introduce basic TotalSegmentator tool in Workbench as Resolved.May 3 2023, 11:06 AM
a178n closed subtask T29463: Doxygen documentation for TotalSegmentator as Resolved.
a178n closed subtask T29464: Test plan for TotalSegmentator as Resolved.
a178n closed subtask T29468: Let MITK handle TotalSegmentator setup as Resolved.
a178n closed subtask T29497: Full support for all subtasks as Resolved.May 3 2023, 11:09 AM
a178n closed subtask T29458: Include Advanced settings support for TotalSegmentator tool in MITK as Resolved.May 3 2023, 11:21 AM
a178n added a subtask: T29558: TotalSegmentator: Modify as per new Segmentation changes.May 3 2023, 4:52 PM
a178n closed subtask T29558: TotalSegmentator: Modify as per new Segmentation changes as Resolved.May 4 2023, 8:12 AM
a178n closed subtask T29566: TotalSegmentator GUI bug: Install button not Activated correctly as Resolved.May 15 2023, 7:11 PM
kislinsk edited projects, added MITK (v2023.12); removed MITK (v2023.04).May 17 2023, 2:55 PM
kislinsk moved this task from Backlog to Segmentation on the MITK (v2023.12) board.May 17 2023, 3:08 PM
a178n closed subtask T29567: TotalSeg: inferencing issue on MacOS as Resolved.May 23 2023, 4:42 PM
a178n edited projects, added MITK; removed MITK (v2023.12).Jul 13 2023, 10:35 AM
a178n closed subtask T29569: [Checklist] Update TotalSegmentator & nnUNet checklist as Resolved.Jul 25 2023, 11:46 AM
a178n removed a178n as the assignee of this task.Aug 9 2023, 5:22 PM
a178n closed subtask T29560: TotalSegmentator Label naming scheme as Resolved.Aug 11 2023, 2:55 PM
a178n closed subtask T30215: [SEG] Support TotalSegmentatorV2 as Resolved.Dec 19 2023, 10:36 AM
a178n closed subtask T30256: TotalSeg: Add check for Python version as Resolved.Dec 19 2023, 11:38 AM
a178n closed subtask T29462: TotalSegmentator (Python) issues as Resolved.Dec 19 2023, 11:40 AM
a178n closed subtask T30300: Remember "Fast" checkbox setting as Resolved.Apr 8 2024, 10:17 AM
a178n closed subtask T30353: [TotalSeg] Add confirmation dialog before exiting the tool as Resolved.May 2 2024, 8:22 AM
floca closed this task as Resolved.May 4 2024, 11:57 AM
floca claimed this task.

The open sub tasks are still valid. But as TotalSegmentator itself is added, I would close this very task.

a178n closed subtask T30447: [TotalSeg] Levelwindow effect as Wontfix.May 15 2024, 11:18 AM
a178n closed subtask T30457: Add TotalSegmentator MR image (v 2.2) support in MITK as Resolved.Jun 11 2024, 9:31 AM
kislinsk closed subtask T30301: Move Totalsegmentator installation into Preferences as Resolved.Sep 16 2024, 1:49 PM
kislinsk closed subtask T29597: TotalSeg didn't remember python environment as Resolved.
kislinsk closed subtask T29596: Move out FAST checkbox from Advanced as Resolved.
kislinsk closed subtask T29510: Migrate installer from Qt GUI level to MITK level as Resolved.
kislinsk closed subtask T29487: Tool Icon for TotalSegmentator as Resolved.
kislinsk closed subtask T29485: TotalSegmentator User Testing as Resolved.
kislinsk closed subtask T29459: Docker support for TotalSegmentator as Resolved.
MITK · MIC · IMSY · DKFZ