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Fri, Jun 4

floca added a parent task for T28524: Refactor LabelSetImage and associated classes.: T28275: [Segmentation] AdaptiveRegionGrowingTool must be refactored / 4D Segmentation returns error message when point is not on the correct timestep.
Fri, Jun 4, 7:09 PM · MITK (v2021.10)
floca added a subtask for T28499: Refactor/rewrite RegionGrowing3D tool: T28524: Refactor LabelSetImage and associated classes..
Fri, Jun 4, 7:09 PM · Request for Discussion, MITK (v2021.10)
floca added a parent task for T28524: Refactor LabelSetImage and associated classes.: T28499: Refactor/rewrite RegionGrowing3D tool.
Fri, Jun 4, 7:09 PM · MITK (v2021.10)
floca added a parent task for T28523: Evaluate MITK segmentation survey: T28499: Refactor/rewrite RegionGrowing3D tool.
Fri, Jun 4, 7:08 PM · MITK (v2021.10)
floca added a parent task for T27437: Migrate MITK to use ITK 5.x : T28499: Refactor/rewrite RegionGrowing3D tool.
Fri, Jun 4, 7:08 PM · MITK (v2021.10)
floca added subtasks for T28499: Refactor/rewrite RegionGrowing3D tool: T27437: Migrate MITK to use ITK 5.x , T28523: Evaluate MITK segmentation survey.
Fri, Jun 4, 7:08 PM · Request for Discussion, MITK (v2021.10)
floca triaged T28525: Design refactoring of LabelSetImage and associated classes as Unbreak Now! priority.
Fri, Jun 4, 7:06 PM · MITK (v2021.10)
floca triaged T28524: Refactor LabelSetImage and associated classes. as Unbreak Now! priority.
Fri, Jun 4, 7:04 PM · MITK (v2021.10)
floca moved T28464: [Segmentation] New Add/Remove tool from Backlog to MITK Meeting on the Request for Discussion board.
Fri, Jun 4, 6:53 PM · Request for Discussion, MITK (v2021.10)
floca moved T28464: [Segmentation] New Add/Remove tool from Backlog to Segmentation on the MITK (v2021.10) board.
Fri, Jun 4, 6:53 PM · Request for Discussion, MITK (v2021.10)
floca raised the priority of T28142: [Segmentation] Remove plugin redundancy with MultiLabelSegmentation from Normal to Unbreak Now!.
Fri, Jun 4, 6:51 PM · MITK (v2021.10)
floca added a subtask for T28479: [Segmentation] Rethink / reevaluate our existing segmentation tools / algorithms: T28142: [Segmentation] Remove plugin redundancy with MultiLabelSegmentation.
Fri, Jun 4, 6:50 PM · MITK (v2021.10)
floca added a parent task for T28142: [Segmentation] Remove plugin redundancy with MultiLabelSegmentation: T28479: [Segmentation] Rethink / reevaluate our existing segmentation tools / algorithms.
Fri, Jun 4, 6:50 PM · MITK (v2021.10)
floca updated the task description for T28479: [Segmentation] Rethink / reevaluate our existing segmentation tools / algorithms.
Fri, Jun 4, 6:50 PM · MITK (v2021.10)
floca added a project to T28145: SetRegionTool does not work as expected (flood fill like) with concentric structures.: Missing Info.
Fri, Jun 4, 6:42 PM · Missing Info, MITK (v2021.10)
floca added a project to T28247: [Segmentation] Watershed tool freezes when slider and threshold are set to a low value: Missing Info.
Fri, Jun 4, 6:42 PM · Missing Info, MITK (v2021.10), Request for Discussion
floca added a subtask for T28320: [Segmentation] Region growing does not work if seed point is already inside a segmentation: T28523: Evaluate MITK segmentation survey.
Fri, Jun 4, 6:41 PM · Missing Info, MITK (v2021.10), Request for Discussion
floca added a parent task for T28523: Evaluate MITK segmentation survey: T28320: [Segmentation] Region growing does not work if seed point is already inside a segmentation.
Fri, Jun 4, 6:41 PM · MITK (v2021.10)
floca added a project to T28320: [Segmentation] Region growing does not work if seed point is already inside a segmentation: Missing Info.

This issue should be postponed until T28523: Evaluate MITK segmentation survey (to now the new priority) and T27437: Migrate MITK to use ITK 5.x (check for performance improvments due to refactored ITK) is done.

Fri, Jun 4, 6:41 PM · Missing Info, MITK (v2021.10), Request for Discussion
floca added a subtask for T28145: SetRegionTool does not work as expected (flood fill like) with concentric structures.: T28523: Evaluate MITK segmentation survey.
Fri, Jun 4, 5:42 PM · Missing Info, MITK (v2021.10)
floca added a parent task for T28523: Evaluate MITK segmentation survey: T28145: SetRegionTool does not work as expected (flood fill like) with concentric structures..
Fri, Jun 4, 5:42 PM · MITK (v2021.10)
floca added a comment to T28145: SetRegionTool does not work as expected (flood fill like) with concentric structures..

This issue should be postponed until T28523: Evaluate MITK segmentation survey (to now the new priority) is done.

Fri, Jun 4, 5:42 PM · Missing Info, MITK (v2021.10)
floca added subtasks for T28247: [Segmentation] Watershed tool freezes when slider and threshold are set to a low value: T28523: Evaluate MITK segmentation survey, T27437: Migrate MITK to use ITK 5.x .
Fri, Jun 4, 5:41 PM · Missing Info, MITK (v2021.10), Request for Discussion
floca added a parent task for T28523: Evaluate MITK segmentation survey: T28247: [Segmentation] Watershed tool freezes when slider and threshold are set to a low value.
Fri, Jun 4, 5:41 PM · MITK (v2021.10)
floca added a parent task for T27437: Migrate MITK to use ITK 5.x : T28247: [Segmentation] Watershed tool freezes when slider and threshold are set to a low value.
Fri, Jun 4, 5:41 PM · MITK (v2021.10)
floca added a comment to T28247: [Segmentation] Watershed tool freezes when slider and threshold are set to a low value.

This issue should be postponed until T28523: Evaluate MITK segmentation survey (to now the new priority) and T27437: Migrate MITK to use ITK 5.x (check for performance improvments due to refactored ITK) is done.

Fri, Jun 4, 5:41 PM · Missing Info, MITK (v2021.10), Request for Discussion
floca added a project to T28244: [Segmentation] Fast Marching Tool not really responsive for large images: Missing Info.

This issue should be postponed until T28523: Evaluate MITK segmentation survey (to now the new priority) and T27437: Migrate MITK to use ITK 5.x (check for performance improvments due to refactored ITK) is done.

Fri, Jun 4, 5:40 PM · Missing Info, MITK (v2021.10)
floca added a subtask for T28244: [Segmentation] Fast Marching Tool not really responsive for large images: T27437: Migrate MITK to use ITK 5.x .
Fri, Jun 4, 5:39 PM · Missing Info, MITK (v2021.10)
floca added a parent task for T27437: Migrate MITK to use ITK 5.x : T28244: [Segmentation] Fast Marching Tool not really responsive for large images.
Fri, Jun 4, 5:39 PM · MITK (v2021.10)
floca added a subtask for T28244: [Segmentation] Fast Marching Tool not really responsive for large images: T28523: Evaluate MITK segmentation survey.
Fri, Jun 4, 5:38 PM · Missing Info, MITK (v2021.10)
floca added a parent task for T28523: Evaluate MITK segmentation survey: T28244: [Segmentation] Fast Marching Tool not really responsive for large images.
Fri, Jun 4, 5:38 PM · MITK (v2021.10)
floca added a comment to T28479: [Segmentation] Rethink / reevaluate our existing segmentation tools / algorithms.

Also see our internal discussion about who to address several more fundamental design issues: https://hub.dkfz.de/f/5459842

Fri, Jun 4, 5:37 PM · MITK (v2021.10)
floca added a parent task for T28523: Evaluate MITK segmentation survey: T28479: [Segmentation] Rethink / reevaluate our existing segmentation tools / algorithms.
Fri, Jun 4, 5:34 PM · MITK (v2021.10)
floca added a subtask for T28479: [Segmentation] Rethink / reevaluate our existing segmentation tools / algorithms: T28523: Evaluate MITK segmentation survey.
Fri, Jun 4, 5:34 PM · MITK (v2021.10)
floca added a project to T28490: Segmentation plugin: "new" segmentation should not run reinit!: Cleared.
Fri, Jun 4, 5:33 PM · Cleared, MITK (v2021.10)
floca added a subtask for T27613: Improve reinit behavior: T28490: Segmentation plugin: "new" segmentation should not run reinit!.
Fri, Jun 4, 5:32 PM · MITK
floca added a parent task for T28490: Segmentation plugin: "new" segmentation should not run reinit!: T27613: Improve reinit behavior.
Fri, Jun 4, 5:32 PM · Cleared, MITK (v2021.10)
floca moved T28523: Evaluate MITK segmentation survey from Backlog to Cycle on the MITK (v2021.10) board.
Fri, Jun 4, 5:26 PM · MITK (v2021.10)
floca triaged T28523: Evaluate MITK segmentation survey as Unbreak Now! priority.
Fri, Jun 4, 5:26 PM · MITK (v2021.10)
kleina updated subscribers of T28520: XNAT on e230-xnat.
Fri, Jun 4, 12:21 PM · Restricted Project
kleina updated the task description for T28520: XNAT on e230-xnat.
Fri, Jun 4, 12:21 PM · Restricted Project
isensee updated the task description for T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations.
Fri, Jun 4, 12:19 PM · MITK (v2021.10)
isensee added a comment to T28491: Slice interpolation 'confirm for all slices' not working for large images.

As it is an inexpensive operation my first guess would be an issue related to the amount of used memory. For example, the image above eats 3,5 GB, Activating the interpolation already triples it. Confirming adds at least another 3,5 GB. That could also explain why it is so slow (swapping). But at this point it is just a first assumption. On a 16 GB Windows machine I was able to complete the interpolation without crash but it took a while.

Fri, Jun 4, 12:17 PM · MITK (v2021.10)
isensee created T28522: Segmentations are drawn differently depending on whether the segmentation tool is open or not.
Fri, Jun 4, 12:15 PM · MITK
isensee created T28521: multilabel segmentation add switch to disable contour.
Fri, Jun 4, 12:12 PM · MITK
kleina triaged T28520: XNAT on e230-xnat as Normal priority.
Fri, Jun 4, 12:06 PM · Restricted Project
kislinsk added a comment to T26427: Support software rendering.

Without looking into it yet, I think the Nvidia solution for accelerated remote desktop is currently by far the most promising as it tackles the actual issue.

Fri, Jun 4, 9:52 AM · MITK
kislinsk merged T28514: [Multilabel Segmentation] Changing visibility of labels on higher layers does not trigger update into T28383: [Multilabel Segmentation] In case of two layers, a change of visibility is not updated automatically.
Fri, Jun 4, 9:48 AM · Next Milestone, MITK
kislinsk merged task T28514: [Multilabel Segmentation] Changing visibility of labels on higher layers does not trigger update into T28383: [Multilabel Segmentation] In case of two layers, a change of visibility is not updated automatically.
Fri, Jun 4, 9:48 AM · MITK
laticiagibson updated laticiagibson.
Fri, Jun 4, 8:26 AM

Thu, Jun 3

bangaloreescort updated bangaloreescort.
Thu, Jun 3, 11:29 PM
bangaloreescort updated bangaloreescort.
Thu, Jun 3, 11:28 PM
tpenzkofer added a comment to T26427: Support software rendering.

Running MITK within a Windows Server 2012 R2 Session (VMWare virtualized) and using the fdossena's opengl mesa libraries the current state is (no crash, though):

Thu, Jun 3, 9:56 AM · MITK
nolden updated subscribers of T26427: Support software rendering.

This seems to be still an issue. Maybe there is new information out there or it could be re-tested with newer Windows versions / drivers?

Thu, Jun 3, 9:42 AM · MITK
marysmith26 updated marysmith26.
Thu, Jun 3, 8:42 AM

Wed, Jun 2

s434n added a comment to T28514: [Multilabel Segmentation] Changing visibility of labels on higher layers does not trigger update.

It seems to be the same bug, I just failed to find the existing task. Since I found it in the last Release version, the bugfix was just not included yet, but the problem is still solved. I guess this task can be closed then

Wed, Jun 2, 3:58 PM · MITK
s434n claimed T28481: [Checklist] [Test data] Define publicly available user test data.
Wed, Jun 2, 3:43 PM · MITK (v2021.10)
scholzpa added a member for CAMI: a795a.
Wed, Jun 2, 2:56 PM
floca moved T27684: [Segmentation] Improve Region Growing 2D algorithm and interaction from Segmentation to Cycle on the MITK (v2021.10) board.
Wed, Jun 2, 1:43 PM · MITK (v2021.10)
kalali removed a project from T27506: Extend checklists for segmentation view: Restricted Project.
Wed, Jun 2, 1:38 PM · MITK (v2021.10), Cleared
thomass added a comment to T28514: [Multilabel Segmentation] Changing visibility of labels on higher layers does not trigger update.

I am indeed still reading since I still have tasks to do (I will not leave beforehand just as promised :-)). I think you are referring to T28383 / D477 ... maybe it didn’t fully do the trick.

Wed, Jun 2, 1:07 PM · MITK
kislinsk added a comment to T28491: Slice interpolation 'confirm for all slices' not working for large images.

A few things that impact the handling of huge images:

Wed, Jun 2, 12:48 PM · MITK (v2021.10)
kislinsk closed T28144: CorrectorTool does not properly handle unlocked lables of LabelSet Images as Resolved.

The tool was already removed from the last release because people tend to use the Add/Subtract tool for the same tasks anyway and we could reduce code/complexity.

Wed, Jun 2, 11:52 AM · Request for Discussion, MITK (v2021.10)
kislinsk moved T28159: Officially support MITK using system Qt from MITK Meeting to Backlog on the Request for Discussion board.
Wed, Jun 2, 11:42 AM · CI, Kaapana (internal), Request for Discussion, MITK
kleina added a comment to T28455: RT struct 3D visibility is not working correctly.

Discussed it in the MITK meeting:

Wed, Jun 2, 11:39 AM · MITK (v2021.10)
kleina moved T28455: RT struct 3D visibility is not working correctly from Backlog to MITK Meeting on the Request for Discussion board.
Wed, Jun 2, 11:14 AM · MITK (v2021.10)
kislinsk moved T28491: Slice interpolation 'confirm for all slices' not working for large images from Backlog to Cycle on the MITK (v2021.10) board.
Wed, Jun 2, 10:51 AM · MITK (v2021.10)
kislinsk claimed T28491: Slice interpolation 'confirm for all slices' not working for large images.
Wed, Jun 2, 10:51 AM · MITK (v2021.10)
kislinsk added a comment to T28491: Slice interpolation 'confirm for all slices' not working for large images.

And we seem to have a huge leak here. Even after deleting all the nodes again, half of my RAM is still in use.

Wed, Jun 2, 10:40 AM · MITK (v2021.10)
kislinsk added a comment to T28491: Slice interpolation 'confirm for all slices' not working for large images.

As it is an inexpensive operation my first guess would be an issue related to the amount of used memory. For example, the image above eats 3,5 GB, Activating the interpolation already triples it. Confirming adds at least another 3,5 GB. That could also explain why it is so slow (swapping). But at this point it is just a first assumption. On a 16 GB Windows machine I was able to complete the interpolation without crash but it took a while.

Wed, Jun 2, 10:37 AM · MITK (v2021.10)
isensee updated subscribers of T28491: Slice interpolation 'confirm for all slices' not working for large images.

@kislinsk I know you have plenty of things to do, but this bug (along with T28516) is a blocker at the moment. I would like to recommend MITK as an annotation tool for our collaborators but cannot do that as along as the slice interpolation does not work (fast enough, T28516) for large images :-)

Wed, Jun 2, 9:24 AM · MITK (v2021.10)
isensee created T28516: 2D slice interpolation should use multiprocessing.
Wed, Jun 2, 9:22 AM · MITK (v2021.10)
kislinsk updated subscribers of T28514: [Multilabel Segmentation] Changing visibility of labels on higher layers does not trigger update.

Maybe @thomass is still reading. :) I think she reported the same thing some weeks ago but I cannot find it. It's just a missing RequestRenderWindowUpdate().

Wed, Jun 2, 9:03 AM · MITK

Tue, Jun 1

isensee added a comment to T28422: Multilabel color map does not produce unique colors.

@kislinsk sorry for the late reply. I am not using the convert to segmentation functionality because it draws contours by default and that is annoying because it obstructs too much from the image. Multilabel color map does exactly the right thing, is easy to use and does not require and additional mouse clicks. It is just more convenient :-)

Tue, Jun 1, 5:02 PM · MITK (v2021.10)
s434n triaged T28515: [Statistics] Difference in behavior between the two data selection methods as Low priority.
Tue, Jun 1, 2:48 PM · MITK
s434n triaged T28514: [Multilabel Segmentation] Changing visibility of labels on higher layers does not trigger update as Normal priority.
Tue, Jun 1, 2:37 PM · MITK
s434n closed T28472: [Geldosimetry] Add editing options to calibration table as Resolved.
Tue, Jun 1, 2:20 PM · Restricted Project, Restricted Project
s669m closed T28387: Testing Gvisor with Kube8s as Resolved.

closing gVisor experiments since Kata is our first choice and Kata is able to run in our bare-metal machine, hence temporarily closing gVisor testing.

Tue, Jun 1, 10:35 AM · Restricted Project
s669m closed T28350: Trial Run with Isolated Sandbox Container gVisor, a subtask of T28175: TFDA MVP v1, as Resolved.
Tue, Jun 1, 10:34 AM · Restricted Project
s669m closed T28350: Trial Run with Isolated Sandbox Container gVisor as Resolved.

Closing the issue since gVisor has lots of limitations with microk8s and our current Kaapana architecture.

Tue, Jun 1, 10:34 AM · Restricted Project

Mon, May 31

paul jaeger <p.jaeger@dkfz.de> committed rMDTPUBLICf678bc5e91c3: update retina unet citation (authored by paul jaeger <p.jaeger@dkfz.de>).
update retina unet citation
Mon, May 31, 7:04 PM

Sat, May 29

elijahbenjamin057 updated elijahbenjamin057.
Sat, May 29, 8:18 AM

Fri, May 28

kislinsk moved T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations from Backlog to Segmentation on the MITK (v2021.10) board.
Fri, May 28, 11:10 AM · MITK (v2021.10)
kislinsk triaged T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations as High priority.
Fri, May 28, 11:10 AM · MITK (v2021.10)

Thu, May 27

p212r committed rKAAPANA1efc5bdf277b: Merge branch 'feature/T28512-zip-upload-non-dicom' into develop (authored by p212r).
Merge branch 'feature/T28512-zip-upload-non-dicom' into develop
Thu, May 27, 2:37 PM
p212r committed rKAAPANA39614cdac125: Add --no-halt option to dcmsend command (authored by p212r).
Add --no-halt option to dcmsend command
Thu, May 27, 2:22 PM

Wed, May 26

floca committed rKAAPANA536ab655cca4: Fixed incorrect reference to DSdSO project (authored by floca).
Fixed incorrect reference to DSdSO project
Wed, May 26, 9:35 PM
floca committed rKAAPANA507933f49717: Fixed some markdown style errors (authored by floca).
Fixed some markdown style errors
Wed, May 26, 7:35 PM
floca committed rKAAPANA4b3479869d55: Merge branch 'feature/T28486-Add_project_acknowledgements' into develop (authored by floca).
Merge branch 'feature/T28486-Add_project_acknowledgements' into develop
Wed, May 26, 7:30 PM
floca committed rKAAPANAe6166a42b033: Added project acknowledgments (authored by floca).
Added project acknowledgments
Wed, May 26, 6:04 PM
s434n triaged T28510: [Segmentation Utilities] Switched definitions in documentation as Normal priority.
Wed, May 26, 5:19 PM · MITK
k656s added a member for NLP: s539y.
Wed, May 26, 2:13 PM

Tue, May 25

k656s committed rKAAPANA021dcff1aaab: updated racoon guide, added nuser-anagement and certificate installation (authored by k656s).
updated racoon guide, added nuser-anagement and certificate installation
Tue, May 25, 4:39 PM
k656s committed rKAAPANAb60079985c0b: updated racoon guide, added nuser-anagement and certificate installation (authored by k656s).
updated racoon guide, added nuser-anagement and certificate installation
Tue, May 25, 4:31 PM
k656s committed rKAAPANA8b605f2833b7: updated racoon guide, added nuser-anagement and certificate installation (authored by k656s).
updated racoon guide, added nuser-anagement and certificate installation
Tue, May 25, 4:31 PM
isensee updated the task description for T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations.
Tue, May 25, 11:14 AM · MITK (v2021.10)
isensee created T28500: Multilabel Segmentation Utilities do not work for multilabel segmentations.
Tue, May 25, 11:13 AM · MITK (v2021.10)
gaoh closed T28380: [MultLabel Segmentation, MITK FlowBench] Segmentation not recognized as segmentation in Release v2021.02 as Resolved.
Tue, May 25, 9:26 AM · MITK
gaoh committed rKAAPANA239de918931c: Changed to current workbench, due to T28380, and also changed the flowbench to… (authored by gaoh).
Changed to current workbench, due to T28380, and also changed the flowbench to…
Tue, May 25, 9:26 AM

Mon, May 24

floca claimed T27684: [Segmentation] Improve Region Growing 2D algorithm and interaction.
Mon, May 24, 12:26 PM · MITK (v2021.10)