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Fri, Nov 26

neher closed T27601: Fiber2DSliceThickness in fiber processing as Resolved.
Fri, Nov 26, 9:34 AM · MITK Diffusion
neher closed T27699: mitkCommandLineParser should allow arbitrary types with input/output flag as Resolved.
Fri, Nov 26, 9:34 AM · MITK
neher closed T28872: Diffusion registration crashes when two non-diffusion-weighted images are registered as Resolved.
Fri, Nov 26, 9:33 AM · MITK Diffusion
neher closed T27419: Fix dartclient documentation build as Resolved.
Fri, Nov 26, 9:33 AM · MITK Diffusion

Thu, Nov 25

neher closed T28875: Refactor ODF normalization for streamline tracking as Resolved.
Thu, Nov 25, 12:01 PM · MITK Diffusion
neher committed rMITKDIFF12917e7439e4: Merge branch 'T28875-OdfNormalization' (authored by neher).
Merge branch 'T28875-OdfNormalization'
Thu, Nov 25, 11:10 AM
neher added a comment to T28875: Refactor ODF normalization for streamline tracking.

Pushed new branch T28875-OdfNormalization.

Thu, Nov 25, 11:09 AM · MITK Diffusion
neher committed rMITKDIFFe1364c9083b6: Using sharpening for tensor tracking. No min-max sharpening (authored by neher).
Using sharpening for tensor tracking. No min-max sharpening
Thu, Nov 25, 11:09 AM
neher committed rMDf47f5098b8b0: Update streamline tracking reference (authored by neher).
Update streamline tracking reference
Thu, Nov 25, 11:09 AM
neher triaged T28875: Refactor ODF normalization for streamline tracking as High priority.
Thu, Nov 25, 9:33 AM · MITK Diffusion

Mon, Nov 22

neher committed rMITKDIFF1bc1f9c63130: Merge branch 'T28872-Registration' (authored by neher).
Merge branch 'T28872-Registration'
Mon, Nov 22, 12:45 PM
neher committed rMITKDIFF93ad4096f56e: Ctaching non diff images (authored by neher).
Ctaching non diff images
Mon, Nov 22, 12:39 PM
neher added a comment to T28872: Diffusion registration crashes when two non-diffusion-weighted images are registered.

Pushed new branch T28872-Registration.

Mon, Nov 22, 12:39 PM · MITK Diffusion
neher triaged T28872: Diffusion registration crashes when two non-diffusion-weighted images are registered as Normal priority.
Mon, Nov 22, 11:14 AM · MITK Diffusion

Fri, Nov 19

neher committed rMITKDIFF0ea02355d8f3: Merge branch 'T28867-FiberfoxTest' (authored by neher).
Merge branch 'T28867-FiberfoxTest'
Fri, Nov 19, 11:11 AM
neher committed rMITKDIFF0b82b32bd2e8: Outputting gradient index (authored by neher).
Outputting gradient index
Fri, Nov 19, 11:11 AM
neher added a comment to T28867: Fiberfox test randomly fails.

Pushed new branch T28867-FiberfoxTest.

Fri, Nov 19, 11:11 AM · MITK Diffusion
neher triaged T28867: Fiberfox test randomly fails as High priority.
Fri, Nov 19, 11:10 AM · MITK Diffusion
neher closed T28831: dMRI nonlocal means denoising crashes as Wontfix.
Fri, Nov 19, 11:09 AM · MITK Diffusion
neher reopened T28831: dMRI nonlocal means denoising crashes as "Open".
Fri, Nov 19, 11:08 AM · MITK Diffusion
neher closed T28831: dMRI nonlocal means denoising crashes as Wontfix.
Fri, Nov 19, 11:07 AM · MITK Diffusion

Thu, Nov 18

neher lowered the priority of T26413: Nifti2 support from Normal to Wishlist.
Thu, Nov 18, 3:35 PM · MITK
neher closed T26960: Fiber mapper test fails as Resolved.
Thu, Nov 18, 3:34 PM · MITK Diffusion
neher added a comment to T28831: dMRI nonlocal means denoising crashes.

I think there is a bug in the itk filter. itkPatchBasedDenoisingImageFilter normalizes the patch weights to center weigh=1, i.e. the other weights might very well become > 1. In a next step it is asserted that the weights are <=1, leading to a crash (PatchBasedDenoisingBaseImageFilter<TInputImage, TOutputImage>
::SetPatchWeights).

Thu, Nov 18, 3:09 PM · MITK Diffusion
neher closed T28863: Fix diffusion property serializer test as Resolved.
Thu, Nov 18, 2:13 PM · MITK Diffusion
neher committed rMITKDIFF71a5dfd31e51: Merge branch 'T28863-DiffPropSerializerTest' (authored by neher).
Merge branch 'T28863-DiffPropSerializerTest'
Thu, Nov 18, 2:13 PM
neher committed rMITKDIFF75730eed4594: Adapted to VectorPropertySerializerTest (authored by neher).
Adapted to VectorPropertySerializerTest
Thu, Nov 18, 2:12 PM
neher added a comment to T28863: Fix diffusion property serializer test.

Pushed new branch T28863-DiffPropSerializerTest.

Thu, Nov 18, 2:12 PM · MITK Diffusion
neher triaged T28863: Fix diffusion property serializer test as Normal priority.
Thu, Nov 18, 2:11 PM · MITK Diffusion
neher closed T28832: Headmotion correction fails as Invalid.
Thu, Nov 18, 12:44 PM · MITK Diffusion
neher added a comment to T28832: Headmotion correction fails.

can't reproduce

Thu, Nov 18, 12:44 PM · MITK Diffusion
neher committed rMDccd7110f0dbd: Update fiber rendering test data (authored by neher).
Update fiber rendering test data
Thu, Nov 18, 12:25 PM

Wed, Nov 17

neher closed T28859: Fix connectomics test as Resolved.
Wed, Nov 17, 2:49 PM · MITK Diffusion
neher committed rMITKDIFFcd0e2e751ca3: Merge branch 'T28859-ConnectomicsReader' (authored by neher).
Merge branch 'T28859-ConnectomicsReader'
Wed, Nov 17, 2:48 PM
neher committed rMITKDIFFe5b1395a9542: Fix error handling (authored by neher).
Fix error handling
Wed, Nov 17, 2:48 PM
neher added a comment to T28859: Fix connectomics test.

Pushed new branch T28859-ConnectomicsReader.

Wed, Nov 17, 2:48 PM · MITK Diffusion
neher triaged T28859: Fix connectomics test as Normal priority.
Wed, Nov 17, 2:46 PM · MITK Diffusion
neher closed T28858: Fix fiber fit test as Resolved.
Wed, Nov 17, 1:36 PM · MITK Diffusion
neher committed rMITKDIFFa74b258e0e97: Merge branch 'T28858-FiberFitTest' (authored by neher).
Merge branch 'T28858-FiberFitTest'
Wed, Nov 17, 1:35 PM
neher committed rMITKDIFFe0b0bfed50bf: Recognizing nrrd files as peak images (authored by neher).
Recognizing nrrd files as peak images
Wed, Nov 17, 1:34 PM
neher added a comment to T28858: Fix fiber fit test.

Pushed new branch T28858-FiberFitTest.

Wed, Nov 17, 1:34 PM · MITK Diffusion
neher triaged T28858: Fix fiber fit test as Normal priority.
Wed, Nov 17, 1:33 PM · MITK Diffusion
neher committed rMD2e978b73f845: Update fiber generation test files (authored by neher).
Update fiber generation test files
Wed, Nov 17, 1:32 PM
neher committed rMITKDIFF7f2663073b8a: Merge branch 'T28857-FiberSegDistance' (authored by neher).
Merge branch 'T28857-FiberSegDistance'
Wed, Nov 17, 1:12 PM
neher committed rMITKDIFF689205e1fcfa: Add new filter and miniapp (authored by neher).
Add new filter and miniapp
Wed, Nov 17, 1:12 PM
neher closed T28857: Create cmd app to calculate distances from fiber bundles to segmentations as Resolved.
Wed, Nov 17, 11:19 AM · MITK Diffusion
neher added a comment to T28857: Create cmd app to calculate distances from fiber bundles to segmentations.

Pushed new branch T28857-FiberSegDistance.

Wed, Nov 17, 11:18 AM · MITK Diffusion
neher triaged T28857: Create cmd app to calculate distances from fiber bundles to segmentations as High priority.
Wed, Nov 17, 11:17 AM · MITK Diffusion

Fri, Nov 12

neher added a comment to T28849: Remove fiber parts only removes parts if point inside mask.

Maybe transform mask to polydata and use vtkIntersectionPolyDataFilter

Fri, Nov 12, 1:01 PM · MITK
neher triaged T28849: Remove fiber parts only removes parts if point inside mask as Normal priority.
Fri, Nov 12, 1:00 PM · MITK

Wed, Nov 3

neher created T28832: Headmotion correction fails.
Wed, Nov 3, 1:45 PM · MITK Diffusion
neher edited projects for T28831: dMRI nonlocal means denoising crashes, added: MITK Diffusion; removed MITK.
Wed, Nov 3, 1:44 PM · MITK Diffusion
neher lowered the priority of T26960: Fiber mapper test fails from High to Normal.
Wed, Nov 3, 1:21 PM · MITK Diffusion
neher triaged T28831: dMRI nonlocal means denoising crashes as High priority.
Wed, Nov 3, 1:21 PM · MITK Diffusion

Oct 29 2021

neher committed rMITKDIFF0be09e9979d5: Merge branch 'T28772-ShaderIssues' (authored by neher).
Merge branch 'T28772-ShaderIssues'
Oct 29 2021, 2:43 PM
neher committed rMITKDIFF1f99fb547c71: Workaround using 2 clipping planes (authored by neher).
Workaround using 2 clipping planes
Oct 29 2021, 2:42 PM
neher added a comment to T28772: 2D fiber mapper and VTK9.

Pushed new branch T28772-ShaderIssues.

Oct 29 2021, 2:42 PM · MITK Diffusion
neher closed T28017: Update to vtk 9 as Resolved.
Oct 29 2021, 2:42 PM · MITK Diffusion
neher committed rMITKDIFFc60e14576a49: Merge branch 'T28017-FinalizeCompatibilityWithMitk' (authored by neher).
Merge branch 'T28017-FinalizeCompatibilityWithMitk'
Oct 29 2021, 2:41 PM

Oct 27 2021

neher added a comment to T28772: 2D fiber mapper and VTK9.

I tried to create an artificial fiberbundle using Fiberfox. The result looks fine in 2D and 3D.

Oct 27 2021, 6:25 PM · MITK Diffusion
neher added a comment to T28772: 2D fiber mapper and VTK9.

Original description of the issue by Nil Goyette:

Oct 27 2021, 6:21 PM · MITK Diffusion
neher triaged T28772: 2D fiber mapper and VTK9 as High priority.
Oct 27 2021, 6:18 PM · MITK Diffusion
neher added a comment to T28017: Update to vtk 9.

Pushed new branch T28017-FinalizeCompatibilityWithMitk.

Oct 27 2021, 2:24 PM · MITK Diffusion
neher committed rMITKDIFFed820764c686: Buildable. To-do: testing and 2D mapper fixing (authored by neher).
Buildable. To-do: testing and 2D mapper fixing
Oct 27 2021, 2:24 PM

Feb 16 2021

neher added a comment to T28109: Check correct association of Segs with origin DICOM.

Missing tags in the Seg, so it is an error in the file.

Feb 16 2021, 6:56 AM · Kaapana (internal)
neher closed T28109: Check correct association of Segs with origin DICOM as Resolved.

This should be resolved.

Feb 16 2021, 6:55 AM · Kaapana (internal)
neher closed T28053: DICOM Seg not associated with source DICOM as Resolved.

This should be resolved.

Feb 16 2021, 6:55 AM · Kaapana (internal)

Feb 15 2021

neher closed T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices as Resolved.
Feb 15 2021, 9:51 AM · MITK

Feb 8 2021

neher created T28285: DICOM with 'ä' in filename not readable on Windows.
Feb 8 2021, 2:06 PM · MITK (v2022.04)

Feb 4 2021

neher committed rMITKab89919a514c: Interpolator as parameter (authored by neher).
Interpolator as parameter
Feb 4 2021, 2:15 PM
neher committed rMITK18a737ca6a88: Remove unneccesary cast. Update help text. (authored by neher).
Remove unneccesary cast. Update help text.
Feb 4 2021, 2:15 PM
neher committed rMITKae90d3d48c7b: Interpolator as parameter (authored by neher).
Interpolator as parameter
Feb 4 2021, 2:15 PM

Feb 1 2021

neher placed T27487: Multi-slice screenshots up for grabs.
Feb 1 2021, 5:40 PM · MITK
neher added a comment to T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices.

Who should I assign as reviewer for this?

Feb 1 2021, 10:44 AM · MITK
neher added a comment to T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices.

Pushed new branch to rMITK MITK: feature/T28230-ResampleImageToReference.

Feb 1 2021, 9:58 AM · MITK

Jan 29 2021

neher added a comment to T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices.

I added the functionality to choose the interpolator. I forgot how to merge it :) Arcanist? And land on develop?

Jan 29 2021, 3:47 PM · MITK
neher added a comment to T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices.

Pushed new branch to rMITK MITK: T28230-ResampleImageToReference.

Jan 29 2021, 3:21 PM · MITK
neher added a comment to T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices.

These parameter descriptions don't really make sense, no?

Jan 29 2021, 2:36 PM · MITK
neher added a comment to T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices.

For RACOON we need it in the next weeks. Sooner is better of course :)
We could simply adapt CLResampleImageToReference to optionally use NN. Should be easy enough. I will take a look today.

Jan 29 2021, 2:07 PM · MITK

Jan 28 2021

neher closed T27974: Sarah requires an MITK installer containing the mitk file converter as Resolved.
Jan 28 2021, 9:51 AM · Missing Info, MITK
neher created T28232: Shapemodels.
Jan 28 2021, 9:47 AM · Kaapana (internal), Request for Discussion, MITK
neher added a comment to T28230: Issue with DICOM SEG -> NIFTI conversion: missing empty slices.

As far as I know, this is crucial for the RACOON project. So for the Kaapana side, this has a high priority.

Jan 28 2021, 9:33 AM · MITK

Jan 20 2021

neher added a comment to T28039: DICOM Seg loading error.

Sure. Could you point me to the nightly installers again? @nolden

Jan 20 2021, 9:59 AM · MITK (v2021.10)

Jan 18 2021

neher committed rMITKDIFF58b42eb2204e: Merge branch 'T28017-VTK9-CodeIssues2' (authored by neher).
Merge branch 'T28017-VTK9-CodeIssues2'
Jan 18 2021, 3:44 PM
neher committed rMITKDIFFa1bbe1077655: Final changes for dependency upgrade compatibility (authored by neher).
Final changes for dependency upgrade compatibility
Jan 18 2021, 3:20 PM
neher added a comment to T28017: Update to vtk 9.

Pushed new branch T28017-VTK9-CodeIssues2.

Jan 18 2021, 3:20 PM · MITK Diffusion

Jan 14 2021

neher added a comment to T28017: Update to vtk 9.

Fiber mapper issue: https://vtk.org/doc/nightly/html/classvtkOpenGLPolyDataMapper.html#a80cc4bf99b408c63cad0a59c0388ffae

Jan 14 2021, 4:47 PM · MITK Diffusion
neher committed rMITKDIFF79272f527e51: Merge branch 'T28017-VTK9-CodeIssues' (authored by neher).
Merge branch 'T28017-VTK9-CodeIssues'
Jan 14 2021, 4:42 PM
neher committed rMITKDIFFdd4062dbe8b6: Solved tinyxml update issues (authored by neher).
Solved tinyxml update issues
Jan 14 2021, 4:42 PM

Dec 14 2020

neher triaged T28109: Check correct association of Segs with origin DICOM as High priority.
Dec 14 2020, 12:21 PM · Kaapana (internal)

Dec 3 2020

neher created T28053: DICOM Seg not associated with source DICOM.
Dec 3 2020, 10:24 AM · Kaapana (internal)

Dec 2 2020

neher added a comment to T28039: DICOM Seg loading error.

Here you go with the CT. Actually the archive contains two CT images, not sure which one is the matching one :)
https://hub.dkfz.de/s/MDWwGHQxJcWgrzN

Dec 2 2020, 1:28 PM · MITK (v2021.10)
neher added a comment to T28039: DICOM Seg loading error.

@nolden, Jonas already tried it with the reference CT. Does not work since some tag that Ohif uses to link the seg to the ct is missing.

Dec 2 2020, 1:27 PM · MITK (v2021.10)
neher added a comment to T28039: DICOM Seg loading error.
In T28039#215328, @kast wrote:

Hi,
we tried to import our DICOM Seg in the MITK WB and this did not work. I think it makes sense if we schedule a short meeting. What do you think?

Dec 2 2020, 6:28 AM · MITK (v2021.10)

Nov 30 2020

neher added a comment to T28039: DICOM Seg loading error.

Forgot the error message :)
Error occurs directly when loading the file.

Nov 30 2020, 1:31 PM · MITK (v2021.10)
neher triaged T28039: DICOM Seg loading error as High priority.
Nov 30 2020, 1:30 PM · MITK (v2021.10)

Nov 26 2020

neher committed rMITKDIFF7377ebb4907d: Merge branch 'T28017-VTK9' (authored by neher).
Merge branch 'T28017-VTK9'
Nov 26 2020, 3:09 PM
neher committed rMITKDIFFf6421a87b933: cell array nextcell (authored by neher).
cell array nextcell
Nov 26 2020, 3:09 PM
neher committed rMITKDIFF96cc00455433: update vtk connectomics (authored by neher).
update vtk connectomics
Nov 26 2020, 3:09 PM
neher committed rMITKDIFFeef11174f790: Merge branch 'T28017-VTK9' (authored by neher).
Merge branch 'T28017-VTK9'
Nov 26 2020, 3:09 PM