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Oct 11 2023

a178n updated subscribers of T30220: SAM tool: Custom NRRD writer not working as expected in Ubuntu.
Oct 11 2023, 9:15 AM · MITK (v2023.12)
a178n added a comment to T30220: SAM tool: Custom NRRD writer not working as expected in Ubuntu.

This is the sample NRRD file written by the above mentioned writer function. It can't be opened in Python or by

.
Error log:

Exception occurred when reading file /tmp/mitk-sam-OBvksy/sam-in-QOdQsN/3111588501110146159.nrrd:
/home/user1/DKFZ/nnUNet_work/MITK_nnunet/build/ep/src/ITK/Modules/IO/NRRD/src/itkNrrdImageIO.cxx:292:
itk::ERROR: NrrdImageIO(0x561dd4b8c4b0): ReadImageInformation: Error reading /tmp/mitk-sam-OBvksy/sam-in-QOdQsN/3111588501110146159.nrrd:
[nrrd] nrrdLoad: trouble reading "/tmp/mitk-sam-OBvksy/sam-in-QOdQsN/3111588501110146159.nrrd"
[nrrd] nrrdRead: trouble
[nrrd] _nrrdRead: trouble reading NRRD file
[nrrd] _nrrdFormatNRRD_read: trouble parsing space origin info |(-185,04367065429688,-161,31900024414062)|
[nrrd] _nrrdReadNrrdParse_space_origin: couldn't parse origin "(-185,04367065429688,-161,31900024414062)"
[nrrd] _nrrdSpaceVectorParse: space dimension is 2, but seem to have 4 coefficients
Oct 11 2023, 9:15 AM · MITK (v2023.12)

Oct 10 2023

a178n triaged T30220: SAM tool: Custom NRRD writer not working as expected in Ubuntu as Normal priority.
Oct 10 2023, 3:01 PM · MITK (v2023.12)
floca edited projects for T29454: Clarify the versions/editions we publish as installer, added: MITK (v2023.12); removed MITK (v2023.04).
Oct 10 2023, 12:07 PM · MITK (v2024.06), Request for Discussion
floca edited projects for T29454: Clarify the versions/editions we publish as installer, added: MITK (v2023.04); removed MITK.
Oct 10 2023, 12:06 PM · MITK (v2024.06), Request for Discussion
kislinsk added a comment to T30155: Bounding boxes / ROIs in MITK.

Pushed new branch to rMITK MITK: feature/T30155-ROI.

Oct 10 2023, 10:26 AM · MITK (v2024.06)

Oct 6 2023

kompan committed rMITK5bc15d6dbdcf: Invoke progress event after member variable m_progress has been updated. (authored by kompan).
Invoke progress event after member variable m_progress has been updated.
Oct 6 2023, 7:32 AM
kompan committed rMITK4218f3bb744d: Invoke progress event after member variable m_progress has been updated. (authored by kompan).
Invoke progress event after member variable m_progress has been updated.
Oct 6 2023, 7:32 AM

Oct 5 2023

kislinsk committed rMITK0dd98a1e2c63: Reduce amount of CMake warnings in MITK (authored by kislinsk).
Reduce amount of CMake warnings in MITK
Oct 5 2023, 7:53 AM
kislinsk committed rMITK41dfe5a9500e: Use same minimum required CMake version in CppMicroServices as in MITK (authored by kislinsk).
Use same minimum required CMake version in CppMicroServices as in MITK
Oct 5 2023, 7:53 AM
kislinsk closed T30216: Reduce amount of CMake warnings in MITK as Resolved by committing rMITK0dd98a1e2c63: Reduce amount of CMake warnings in MITK.
Oct 5 2023, 7:53 AM · MITK (v2023.12)
kislinsk committed rMITK5b2d8742ef90: Use DOWNLOAD_EXTRACT_TIMESTAMP option in ExternalProject_Add() (authored by kislinsk).
Use DOWNLOAD_EXTRACT_TIMESTAMP option in ExternalProject_Add()
Oct 5 2023, 7:53 AM
kislinsk committed rMITK6f217eeec8ad: Use Boost_ROOT instead of BOOST_ROOT (authored by kislinsk).
Use Boost_ROOT instead of BOOST_ROOT
Oct 5 2023, 7:53 AM

Oct 4 2023

a178n added a comment to T30215: [SEG] Support TotalSegmentatorV2.

Pushed new branch to rMITK MITK: feature/T30215-totalseg-v2-update.

Oct 4 2023, 5:25 PM · MITK (v2024.06)
kislinsk added a revision to T30216: Reduce amount of CMake warnings in MITK: Unknown Object (Differential Revision).
Oct 4 2023, 2:25 PM · MITK (v2023.12)
kislinsk triaged T30216: Reduce amount of CMake warnings in MITK as Normal priority.
Oct 4 2023, 2:21 PM · MITK (v2023.12)
a178n renamed T30215: [SEG] Support TotalSegmentatorV2 from Support TotalSegmentatorV2 to [SEG] Support TotalSegmentatorV2.
Oct 4 2023, 2:15 PM · MITK (v2024.06)
kislinsk added a comment to T30214: Merge a few external GitHub pull requests.

Deleted branch from rMITK MITK: bugfix/T30214-MergeAFewGitHubPullRequests.

Oct 4 2023, 10:52 AM · MITK
kislinsk closed T30214: Merge a few external GitHub pull requests as Resolved.
Oct 4 2023, 10:51 AM · MITK
kislinsk added a comment to T30214: Merge a few external GitHub pull requests.
Oct 4 2023, 10:46 AM · MITK
SSingh committed rMITKa578ff5ff700: Do not include uic generated file in header (authored by SSingh).
Do not include uic generated file in header
Oct 4 2023, 10:45 AM
kislinsk committed rMITKb6c834d52bd1: Merge remote-tracking branch 'Namdhari/fix-QmitkLevelWindowWidget-header' into… (authored by kislinsk).
Merge remote-tracking branch 'Namdhari/fix-QmitkLevelWindowWidget-header' into…
Oct 4 2023, 10:45 AM
kislinsk committed rMITK1bcdb33ad6b8: Include generated UI header files from build directory (authored by kislinsk).
Include generated UI header files from build directory
Oct 4 2023, 10:45 AM
kislinsk committed rMITK394322b1ced1: Merge branch 'bugfix/T30214-MergeAFewGitHubPullRequests' into develop (authored by kislinsk).
Merge branch 'bugfix/T30214-MergeAFewGitHubPullRequests' into develop
Oct 4 2023, 10:45 AM
kislinsk committed rMITK8d282a26a9b5: Merge remote-tracking branch 'pankaj-r-zero/pankaj-T26399' into bugfix/T30214… (authored by kislinsk).
Merge remote-tracking branch 'pankaj-r-zero/pankaj-T26399' into bugfix/T30214…
Oct 4 2023, 10:25 AM
pankaj-r-zero <prawat@msystechnologies.com> committed rMITKa9cc87505757: Workbench crash on simple tree model update. (authored by pankaj-r-zero <prawat@msystechnologies.com>).
Workbench crash on simple tree model update.
Oct 4 2023, 10:25 AM
kislinsk committed rMITK1f3d06c69769: Merge branch 'bugfix/T30214-MergeAFewGitHubPullRequests' into develop (authored by kislinsk).
Merge branch 'bugfix/T30214-MergeAFewGitHubPullRequests' into develop
Oct 4 2023, 10:25 AM
kislinsk added a comment to T30214: Merge a few external GitHub pull requests.

Merged GitHub pull request https://github.com/MITK/MITK/pull/265 (Fix typos in Plugins subdirectory).

Oct 4 2023, 10:04 AM · MITK
kislinsk committed rMITK68d2a736ceff: Merge remote-tracking branch 'luzpaz/typos/Plugins' into bugfix/T30214… (authored by kislinsk).
Merge remote-tracking branch 'luzpaz/typos/Plugins' into bugfix/T30214…
Oct 4 2023, 10:02 AM
luzpaz <luzpaz@users.noreply.github.com> committed rMITKb86ac6a5f58d: Fix typos in Plugins subdirectory (authored by luz paz <luzpaz@pm.me>).
Fix typos in Plugins subdirectory
Oct 4 2023, 10:02 AM
kislinsk committed rMITK12773d72a3b5: Fix parameter name in documentation (authored by kislinsk).
Fix parameter name in documentation
Oct 4 2023, 10:02 AM
kislinsk committed rMITK432e88952209: Merge branch 'bugfix/T30214-MergeAFewGitHubPullRequests' into develop (authored by kislinsk).
Merge branch 'bugfix/T30214-MergeAFewGitHubPullRequests' into develop
Oct 4 2023, 10:02 AM
kislinsk added a comment to T30214: Merge a few external GitHub pull requests.

Merged T22990: SlicedGeometry3D crash when volume is rotated by 45 degrees (GitHub pull request: https://github.com/MITK/MITK/pull/203).

Oct 4 2023, 9:17 AM · MITK
espak committed rMITKb2ede367f92a: Fix for determining axes corresponding to given orientations (authored by espak).
Fix for determining axes corresponding to given orientations
Oct 4 2023, 9:16 AM
kislinsk committed rMITKcf129df95b7f: Merge remote-tracking branch 'NifTK/T22990-map-axes-to-orientations' into… (authored by kislinsk).
Merge remote-tracking branch 'NifTK/T22990-map-axes-to-orientations' into…
Oct 4 2023, 9:16 AM
kislinsk committed rMITK7c5e1594909a: Merge branch 'bugfix/T30214-MergeAFewGitHubPullRequests' into develop (authored by kislinsk).
Merge branch 'bugfix/T30214-MergeAFewGitHubPullRequests' into develop
Oct 4 2023, 9:16 AM
kislinsk added a comment to T30214: Merge a few external GitHub pull requests.

Pushed new branch to rMITK MITK: bugfix/T30214-MergeAFewGitHubPullRequests.

Oct 4 2023, 9:15 AM · MITK
kislinsk changed the status of T22990: SlicedGeometry3D crash when volume is rotated by 45 degrees from Wontfix to Resolved.
Oct 4 2023, 9:14 AM · Auto-closed, Pull Request, MITK
kislinsk changed the status of T22990: SlicedGeometry3D crash when volume is rotated by 45 degrees, a subtask of T30214: Merge a few external GitHub pull requests, from Wontfix to Resolved.
Oct 4 2023, 9:14 AM · MITK
kislinsk added a parent task for T22990: SlicedGeometry3D crash when volume is rotated by 45 degrees: T30214: Merge a few external GitHub pull requests.
Oct 4 2023, 9:14 AM · Auto-closed, Pull Request, MITK
kislinsk added a subtask for T30214: Merge a few external GitHub pull requests: T22990: SlicedGeometry3D crash when volume is rotated by 45 degrees.
Oct 4 2023, 9:14 AM · MITK
a178n triaged T30215: [SEG] Support TotalSegmentatorV2 as Normal priority.
Oct 4 2023, 8:24 AM · MITK (v2024.06)
kislinsk triaged T30214: Merge a few external GitHub pull requests as Normal priority.
Oct 4 2023, 7:48 AM · MITK

Sep 29 2023

kislinsk added a comment to T30213: Poco fails to build if the library names of OpenSSL are not libcrypto.lib and libssl.lib.

Deleted branch from rMITK MITK: bugfix/T30213-PocoOpenSSL.

Sep 29 2023, 2:53 PM · MITK (v2023.12)
kislinsk committed rMITK8ab436927e00: Fix CMake build of Poco Crypto with custom libcrypto.lib names (authored by kislinsk).
Fix CMake build of Poco Crypto with custom libcrypto.lib names
Sep 29 2023, 2:53 PM
kislinsk closed T30213: Poco fails to build if the library names of OpenSSL are not libcrypto.lib and libssl.lib as Resolved by committing rMITK859410e34da9: Fix CMake build of Poco Crypto with custom libcrypto.lib names.
Sep 29 2023, 2:53 PM · MITK (v2023.12)
kislinsk committed rMITK859410e34da9: Fix CMake build of Poco Crypto with custom libcrypto.lib names (authored by kislinsk).
Fix CMake build of Poco Crypto with custom libcrypto.lib names
Sep 29 2023, 2:53 PM

Sep 28 2023

kislinsk placed T29225: Rule Checker for FlowBench up for grabs.
Sep 28 2023, 3:29 PM · MITK
kislinsk added a comment to T30213: Poco fails to build if the library names of OpenSSL are not libcrypto.lib and libssl.lib.

Pushed new branch to rMITK MITK: bugfix/T30213-PocoOpenSSL.

Sep 28 2023, 3:23 PM · MITK (v2023.12)
kislinsk added a revision to T30213: Poco fails to build if the library names of OpenSSL are not libcrypto.lib and libssl.lib: Unknown Object (Differential Revision).
Sep 28 2023, 11:57 AM · MITK (v2023.12)
kislinsk updated the task description for T30213: Poco fails to build if the library names of OpenSSL are not libcrypto.lib and libssl.lib.
Sep 28 2023, 11:01 AM · MITK (v2023.12)
kislinsk triaged T30213: Poco fails to build if the library names of OpenSSL are not libcrypto.lib and libssl.lib as High priority.
Sep 28 2023, 11:00 AM · MITK (v2023.12)

Sep 27 2023

floca added a comment to T30207: Add org.mitk.gui.qt.dicominspector to release.

I think in doubt I would just move but not merge it for now. If we see that it is needed or wanted we can make the effort and merge it. It would be better than not offering this feature at all.

Sep 27 2023, 11:01 AM · Request for Discussion, MITK (v2023.12)
floca added a project to T30207: Add org.mitk.gui.qt.dicominspector to release: Request for Discussion.

The dicom inspector has one additional dependency to module MITKDICOM. Therefore if we merge the inspector plugins also our normal inspector could only be build if DICOM module is activated. (Which it currently is per default).

Sep 27 2023, 10:56 AM · Request for Discussion, MITK (v2023.12)
floca claimed T30210: [SEG] Add dedicated reader for label image stack support.
Sep 27 2023, 10:50 AM · Moved to git.dkfz.de, MITK (v2024.12)
floca claimed T30209: [SEG] Add a writer for label image stack support.
Sep 27 2023, 10:49 AM · Moved to git.dkfz.de, MITK (v2024.12)
floca claimed T27718: Miniapp for basic DICOM testing.
Sep 27 2023, 10:39 AM · MITK (v2023.12), Kaapana (internal)

Sep 26 2023

kompan added a comment to T27813: Curve Description Parameters View progress bar 99%.

In fact, this problem occurs not just for the progress bar, but the progress itself, e.g. also in the info box 1 is currently never reached even if the descriptive parameter calculation process is finished. The reason for this bug is that the progress is stored in a member variable which is updated after the progress event is invoked. Therefore, the progress variable is always lagging one update behind. This is fixed by changing the order of the called functions.
The fix is done for the descriptive parameter calculation, but also for the pixel and ROI-wise fitting.

Sep 26 2023, 9:19 AM · MITK (v2023.12)

Sep 20 2023

kompan removed a project from T30168: Fail to load NIFTI images due to error "itk only supports orthonormal direction cosines": Request for Discussion.

Discussion result: Use permissive mode always switched on. No preferences needed.

Sep 20 2023, 11:57 AM · Moved to git.dkfz.de, MITK
kompan removed a project from T30186: PixelDumper view in MITK release: Request for Discussion.

Discussion result: Feature is useful but not as plugin on its own but instead as part of the statistics plugin (as an additional button like copy to clipboard).

Sep 20 2023, 11:37 AM · Moved to git.dkfz.de, MITK
kompan removed a project from T30205: Check and update perfusion user manual: Request for Discussion.
Sep 20 2023, 11:29 AM · MITK (v2024.06)
kompan added a comment to T30205: Check and update perfusion user manual.

Integrate into F1 help. Make MITK ModelFit Webpage deprecated for manual section with link to doxygen documentation.

Sep 20 2023, 11:29 AM · MITK (v2024.06)
kompan moved T30205: Check and update perfusion user manual from Backlog to MITK Meeting on the Request for Discussion board.
Sep 20 2023, 11:25 AM · MITK (v2024.06)
kompan moved T30186: PixelDumper view in MITK release from Backlog to MITK Meeting on the Request for Discussion board.
Sep 20 2023, 11:25 AM · Moved to git.dkfz.de, MITK
kompan moved T30168: Fail to load NIFTI images due to error "itk only supports orthonormal direction cosines" from Backlog to MITK Meeting on the Request for Discussion board.
Sep 20 2023, 11:24 AM · Moved to git.dkfz.de, MITK
kompan removed a project from T30207: Add org.mitk.gui.qt.dicominspector to release: Request for Discussion.
Sep 20 2023, 11:19 AM · Request for Discussion, MITK (v2023.12)
kompan added a comment to T30207: Add org.mitk.gui.qt.dicominspector to release.

It is a useful feature and should be part of the next release.
Open to dos:

  • Checklist
  • check dependencies of the view. If the view does not have more dependencies then our property inspector should be merged.
Sep 20 2023, 11:18 AM · Request for Discussion, MITK (v2023.12)
kompan added a project to T30205: Check and update perfusion user manual: Request for Discussion.
Sep 20 2023, 9:56 AM · MITK (v2024.06)

Sep 19 2023

floca added a project to T30186: PixelDumper view in MITK release: Request for Discussion.
Sep 19 2023, 11:39 AM · Moved to git.dkfz.de, MITK
floca updated the task description for T30186: PixelDumper view in MITK release.
Sep 19 2023, 11:38 AM · Moved to git.dkfz.de, MITK
floca added a comment to T30186: PixelDumper view in MITK release.

Is there some additional functionality involved or could we just add it as another MIME type for images instead of a dedicated plugin?

Yes there is. As only (potentially) the pixel values of image parts with an mask should be exported. And you can select multiple image (as long as they have the same geometry), there pixel values will be exported into the same table.

Sep 19 2023, 11:38 AM · Moved to git.dkfz.de, MITK

Sep 15 2023

kompan closed T30199: Update checklist for Perfusion Curve Description Parameters as Resolved.
Sep 15 2023, 9:43 AM · MITK (v2023.12)
kompan removed a project from T27813: Curve Description Parameters View progress bar 99%: Cleared.
Sep 15 2023, 9:41 AM · MITK (v2023.12)

Sep 11 2023

floca placed T29392: [SEG] Add dedicated writer to store multi-label images in nifti up for grabs.
Sep 11 2023, 3:01 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca triaged T30210: [SEG] Add dedicated reader for label image stack support as Normal priority.
Sep 11 2023, 3:00 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca updated the task description for T30209: [SEG] Add a writer for label image stack support.
Sep 11 2023, 2:36 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca triaged T30209: [SEG] Add a writer for label image stack support as Normal priority.
Sep 11 2023, 2:36 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca triaged T30208: [SEG] Add support to read/write stack of label images from/to a mitk label image as Normal priority.
Sep 11 2023, 2:34 PM · Moved to git.dkfz.de, MITK (v2024.12)
floca renamed T29392: [SEG] Add dedicated writer to store multi-label images in nifti from [Segmentation] Add dedicated writer to store multi-label images in nifti to [SEG] Add dedicated writer to store multi-label images in nifti.
Sep 11 2023, 1:58 PM · Moved to git.dkfz.de, MITK (v2024.12)
kompan committed rMITK95e0615a3793: Change parameter naming in mitkPixelBasedParameterFitImageGeneratorTest. (authored by kompan).
Change parameter naming in mitkPixelBasedParameterFitImageGeneratorTest.
Sep 11 2023, 1:47 PM
kompan committed rMITKb824dbbec5ff: Change parameter naming in mitkROIBasedParameterFitImageGeneratorTest. (authored by kompan).
Change parameter naming in mitkROIBasedParameterFitImageGeneratorTest.
Sep 11 2023, 1:47 PM
kompan committed rMITKeeb86dcd4844: Change parameter naming in mitkPixelBasedParameterFitImageGeneratorTest. (authored by kompan).
Change parameter naming in mitkPixelBasedParameterFitImageGeneratorTest.
Sep 11 2023, 1:47 PM
floca moved T30207: Add org.mitk.gui.qt.dicominspector to release from Backlog to MITK Meeting on the Request for Discussion board.
Sep 11 2023, 11:43 AM · Request for Discussion, MITK (v2023.12)
floca triaged T30207: Add org.mitk.gui.qt.dicominspector to release as Normal priority.
Sep 11 2023, 11:43 AM · Request for Discussion, MITK (v2023.12)
kompan triaged T30206: Parameter naming in mitkPixelBasedParameterFitImageGeneratorTest and mitkROIBasedParameterFitImageGenerator as Normal priority.
Sep 11 2023, 11:05 AM · MITK (v2024.06)
kompan committed rMD3eca5ef9341b: Correct y-axis name of Exponential Saturation Model. (authored by kompan).
Correct y-axis name of Exponential Saturation Model.
Sep 11 2023, 10:45 AM
kompan committed rMDae0b52a4a89b: Correct function string for Exponential Decay Model. (authored by kompan).
Correct function string for Exponential Decay Model.
Sep 11 2023, 10:45 AM
kompan triaged T30205: Check and update perfusion user manual as Normal priority.
Sep 11 2023, 8:14 AM · MITK (v2024.06)
kompan triaged T30204: Improve visibility between help files for perfusion as Normal priority.
Sep 11 2023, 8:10 AM · Moved to git.dkfz.de, MITK (v2024.12), Request for Discussion
kompan moved T30202: Provide checklist for ModelFit Generic Data Fitting from Backlog to Tests/Checklists on the MITK (v2023.12) board.
Sep 11 2023, 8:01 AM · MITK (v2024.06)
kompan moved T30203: Provide checklist for Fit Generator Demo from Backlog to Tests/Checklists on the MITK (v2023.12) board.
Sep 11 2023, 8:01 AM · MITK (v2024.06)
kompan triaged T30203: Provide checklist for Fit Generator Demo as Normal priority.
Sep 11 2023, 8:01 AM · MITK (v2024.06)
kompan triaged T30202: Provide checklist for ModelFit Generic Data Fitting as Normal priority.
Sep 11 2023, 8:00 AM · MITK (v2024.06)
kompan moved T30201: Provide checklist for ModelFit Inspector View from Backlog to Tests/Checklists on the MITK (v2023.12) board.
Sep 11 2023, 7:56 AM · MITK (v2024.06)
kompan triaged T30201: Provide checklist for ModelFit Inspector View as Normal priority.
Sep 11 2023, 7:48 AM · MITK (v2024.06)
kompan moved T30200: Update checklist for Perfusion DCE MRI Perfusion Datafit from Backlog to Tests/Checklists on the MITK (v2023.12) board.
Sep 11 2023, 7:46 AM · MITK (v2024.06)
kompan triaged T30200: Update checklist for Perfusion DCE MRI Perfusion Datafit as Normal priority.
Sep 11 2023, 7:46 AM · MITK (v2024.06)
kompan moved T30199: Update checklist for Perfusion Curve Description Parameters from Backlog to Tests/Checklists on the MITK (v2023.12) board.
Sep 11 2023, 7:45 AM · MITK (v2023.12)
kompan triaged T30199: Update checklist for Perfusion Curve Description Parameters as Normal priority.
Sep 11 2023, 7:45 AM · MITK (v2023.12)
kompan moved T30198: Update checklist for Perfusion Concentration Curve Converter from Backlog to Tests/Checklists on the MITK (v2023.12) board.
Sep 11 2023, 7:43 AM · MITK (v2023.12)