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Dec 1 2021

neher committed rMITKDIFF2830a040a0b2: Merge branch 'T28890-StreamlineProbs' (authored by neher).

Merge branch 'T28890-StreamlineProbs'

Dec 1 2021, 11:22 AM

neher committed rMITKDIFFf6cc01a12291: Normalizing proabilities after directional weightin (authored by neher).

Normalizing proabilities after directional weightin

Dec 1 2021, 11:22 AM

neher added a comment to T28890: Fix probability normalization in prob tracking.

Pushed new branch T28890-StreamlineProbs.

Dec 1 2021, 11:22 AM · MITK Diffusion

neher triaged T28890: Fix probability normalization in prob tracking as Normal priority.

Dec 1 2021, 11:15 AM · MITK Diffusion

neher committed rMD7ed1d6623170: Update prob tracking reference (authored by neher).

Update prob tracking reference

Dec 1 2021, 11:15 AM

Nov 30 2021

neher created T28881: 3D interpolation mesh has inverted normals.

Nov 30 2021, 9:33 AM · Auto-closed, MITK

Nov 26 2021

neher closed T27601: Fiber2DSliceThickness in fiber processing as Resolved.

Nov 26 2021, 9:34 AM · MITK Diffusion

neher closed T27699: mitkCommandLineParser should allow arbitrary types with input/output flag as Resolved.

Nov 26 2021, 9:34 AM · MITK

neher closed T28872: Diffusion registration crashes when two non-diffusion-weighted images are registered as Resolved.

Nov 26 2021, 9:33 AM · MITK Diffusion

neher closed T27419: Fix dartclient documentation build as Resolved.

Nov 26 2021, 9:33 AM · MITK Diffusion

Nov 25 2021

neher closed T28875: Refactor ODF normalization for streamline tracking as Resolved.

Nov 25 2021, 12:01 PM · MITK Diffusion

neher committed rMITKDIFF12917e7439e4: Merge branch 'T28875-OdfNormalization' (authored by neher).

Merge branch 'T28875-OdfNormalization'

Nov 25 2021, 11:10 AM

neher added a comment to T28875: Refactor ODF normalization for streamline tracking.

Pushed new branch T28875-OdfNormalization.

Nov 25 2021, 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

Nov 25 2021, 11:09 AM

neher committed rMDf47f5098b8b0: Update streamline tracking reference (authored by neher).

Update streamline tracking reference

Nov 25 2021, 11:09 AM

neher triaged T28875: Refactor ODF normalization for streamline tracking as High priority.

Nov 25 2021, 9:33 AM · MITK Diffusion

Nov 22 2021

neher committed rMITKDIFF1bc1f9c63130: Merge branch 'T28872-Registration' (authored by neher).

Merge branch 'T28872-Registration'

Nov 22 2021, 12:45 PM

neher committed rMITKDIFF93ad4096f56e: Ctaching non diff images (authored by neher).

Ctaching non diff images

Nov 22 2021, 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.

Nov 22 2021, 12:39 PM · MITK Diffusion

neher triaged T28872: Diffusion registration crashes when two non-diffusion-weighted images are registered as Normal priority.

Nov 22 2021, 11:14 AM · MITK Diffusion

Nov 19 2021

neher committed rMITKDIFF0ea02355d8f3: Merge branch 'T28867-FiberfoxTest' (authored by neher).

Merge branch 'T28867-FiberfoxTest'

Nov 19 2021, 11:11 AM

neher committed rMITKDIFF0b82b32bd2e8: Outputting gradient index (authored by neher).

Outputting gradient index

Nov 19 2021, 11:11 AM

neher added a comment to T28867: Fiberfox test randomly fails.

Pushed new branch T28867-FiberfoxTest.

Nov 19 2021, 11:11 AM · MITK Diffusion

neher triaged T28867: Fiberfox test randomly fails as High priority.

Nov 19 2021, 11:10 AM · MITK Diffusion

neher closed T28831: dMRI nonlocal means denoising crashes as Wontfix.

Nov 19 2021, 11:09 AM · MITK Diffusion

neher reopened T28831: dMRI nonlocal means denoising crashes as "Open".

Nov 19 2021, 11:08 AM · MITK Diffusion

neher closed T28831: dMRI nonlocal means denoising crashes as Wontfix.

Nov 19 2021, 11:07 AM · MITK Diffusion

Nov 18 2021

neher lowered the priority of T26413: Nifti2 support from Normal to Wishlist.

Nov 18 2021, 3:35 PM · Auto-closed, Missing Info, MITK

neher closed T26960: Fiber mapper test fails as Resolved.

Nov 18 2021, 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).

Nov 18 2021, 3:09 PM · MITK Diffusion

neher closed T28863: Fix diffusion property serializer test as Resolved.

Nov 18 2021, 2:13 PM · MITK Diffusion

neher committed rMITKDIFF71a5dfd31e51: Merge branch 'T28863-DiffPropSerializerTest' (authored by neher).

Merge branch 'T28863-DiffPropSerializerTest'

Nov 18 2021, 2:13 PM

neher committed rMITKDIFF75730eed4594: Adapted to VectorPropertySerializerTest (authored by neher).

Adapted to VectorPropertySerializerTest

Nov 18 2021, 2:12 PM

neher added a comment to T28863: Fix diffusion property serializer test.

Pushed new branch T28863-DiffPropSerializerTest.

Nov 18 2021, 2:12 PM · MITK Diffusion

neher triaged T28863: Fix diffusion property serializer test as Normal priority.

Nov 18 2021, 2:11 PM · MITK Diffusion

neher closed T28832: Headmotion correction fails as Invalid.

Nov 18 2021, 12:44 PM · MITK Diffusion

neher added a comment to T28832: Headmotion correction fails.

can't reproduce

Nov 18 2021, 12:44 PM · MITK Diffusion

neher committed rMDccd7110f0dbd: Update fiber rendering test data (authored by neher).

Update fiber rendering test data

Nov 18 2021, 12:25 PM

Nov 17 2021

neher closed T28859: Fix connectomics test as Resolved.

Nov 17 2021, 2:49 PM · MITK Diffusion

neher committed rMITKDIFFcd0e2e751ca3: Merge branch 'T28859-ConnectomicsReader' (authored by neher).

Merge branch 'T28859-ConnectomicsReader'

Nov 17 2021, 2:48 PM

neher committed rMITKDIFFe5b1395a9542: Fix error handling (authored by neher).

Fix error handling

Nov 17 2021, 2:48 PM

neher added a comment to T28859: Fix connectomics test.

Pushed new branch T28859-ConnectomicsReader.

Nov 17 2021, 2:48 PM · MITK Diffusion

neher triaged T28859: Fix connectomics test as Normal priority.

Nov 17 2021, 2:46 PM · MITK Diffusion

neher closed T28858: Fix fiber fit test as Resolved.

Nov 17 2021, 1:36 PM · MITK Diffusion

neher committed rMITKDIFFa74b258e0e97: Merge branch 'T28858-FiberFitTest' (authored by neher).

Merge branch 'T28858-FiberFitTest'

Nov 17 2021, 1:35 PM

neher committed rMITKDIFFe0b0bfed50bf: Recognizing nrrd files as peak images (authored by neher).

Recognizing nrrd files as peak images

Nov 17 2021, 1:34 PM

neher added a comment to T28858: Fix fiber fit test.

Pushed new branch T28858-FiberFitTest.

Nov 17 2021, 1:34 PM · MITK Diffusion

neher triaged T28858: Fix fiber fit test as Normal priority.

Nov 17 2021, 1:33 PM · MITK Diffusion

neher committed rMD2e978b73f845: Update fiber generation test files (authored by neher).

Update fiber generation test files

Nov 17 2021, 1:32 PM

neher committed rMITKDIFF7f2663073b8a: Merge branch 'T28857-FiberSegDistance' (authored by neher).

Merge branch 'T28857-FiberSegDistance'

Nov 17 2021, 1:12 PM

neher committed rMITKDIFF689205e1fcfa: Add new filter and miniapp (authored by neher).

Add new filter and miniapp

Nov 17 2021, 1:12 PM

neher closed T28857: Create cmd app to calculate distances from fiber bundles to segmentations as Resolved.

Nov 17 2021, 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.

Nov 17 2021, 11:18 AM · MITK Diffusion

neher triaged T28857: Create cmd app to calculate distances from fiber bundles to segmentations as High priority.

Nov 17 2021, 11:17 AM · MITK Diffusion

Nov 12 2021

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

Maybe transform mask to polydata and use vtkIntersectionPolyDataFilter

Nov 12 2021, 1:01 PM · MITK Diffusion

neher triaged T28849: Remove fiber parts only removes parts if point inside mask as Normal priority.

Nov 12 2021, 1:00 PM · MITK Diffusion

Nov 3 2021

neher created T28832: Headmotion correction fails.

Nov 3 2021, 1:45 PM · MITK Diffusion

neher edited projects for T28831: dMRI nonlocal means denoising crashes, added: MITK Diffusion; removed MITK.

Nov 3 2021, 1:44 PM · MITK Diffusion

neher lowered the priority of T26960: Fiber mapper test fails from High to Normal.

Nov 3 2021, 1:21 PM · MITK Diffusion

neher triaged T28831: dMRI nonlocal means denoising crashes as High priority.

Nov 3 2021, 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 · Checklist, MITK (v2022.10)

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 · Auto-closed, 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 · Auto-closed, 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 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)

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