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Jan 26 2022

neher committed rMITKDIFFbaa78614307d: added basic segment creation (authored by neher).

added basic segment creation

Jan 26 2022, 1:17 PM

neher added a comment to T28947: tract rad.

Pushed new branch T28947-TractRad.

Jan 26 2022, 1:17 PM · MITK Diffusion

neher triaged T28947: tract rad as Wishlist priority.

Jan 26 2022, 12:28 PM · MITK Diffusion

Jan 7 2022

neher closed T28901: Finalize distance to surface cmdapp as Resolved.

Jan 7 2022, 8:53 AM · MITK Diffusion

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

A new PhD student who is starting in February will work on MITK Diffusion again. He will also look into this.

Jan 7 2022, 8:52 AM · MITK Diffusion

Jan 4 2022

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

Hi Nil. Thank you for testing! Did you directly compare the dataset performance with the old shader version? Just to make sure it's actually an issue with the clipping planes.

Jan 4 2022, 8:57 AM · MITK Diffusion

Dec 15 2021

neher closed T28867: Fiberfox test randomly fails as Wontfix.

Dec 15 2021, 11:03 AM · MITK Diffusion

neher committed rMITKDIFFb1bf62d1c76f: Merge branch 'T28901-DistanceToSurface' (authored by neher).

Merge branch 'T28901-DistanceToSurface'

Dec 15 2021, 10:17 AM

neher committed rMITKDIFF71ac9a636bbc: Added distance image output (authored by neher).

Added distance image output

Dec 15 2021, 10:16 AM

Dec 3 2021

neher committed rMITKDIFF329fc713a91a: Merge branch 'T28901-DistanceToSurface' (authored by neher).

Merge branch 'T28901-DistanceToSurface'

Dec 3 2021, 11:37 AM

neher committed rMITKDIFF45102e009f00: Printing volume statistics (authored by neher).

Printing volume statistics

Dec 3 2021, 11:36 AM

neher added a comment to T28901: Finalize distance to surface cmdapp.

Pushed new branch T28901-DistanceToSurface.

Dec 3 2021, 11:36 AM · MITK Diffusion

neher triaged T28901: Finalize distance to surface cmdapp as Normal priority.

Dec 3 2021, 11:26 AM · MITK Diffusion

Dec 1 2021

neher closed T28890: Fix probability normalization in prob tracking as Resolved.

Dec 1 2021, 11:49 AM · MITK Diffusion

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