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neher (Peter Neher)
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Projects (7)

User Details

User Since
Aug 1 2016, 12:10 PM (146 w, 2 d)

Recent Activity

Tue, Apr 23

neher committed rMITKb3f7dc19d888: Adapt default value (authored by neher).
Adapt default value
Tue, Apr 23, 3:44 PM
neher committed rMITK34a75a9ad325: Fiber cutting (authored by neher).
Fiber cutting
Tue, Apr 23, 2:39 PM

Apr 20 2019

neher committed rMITKda3906ce2fda: Catching zero fibers (authored by neher).
Catching zero fibers
Apr 20 2019, 12:28 PM
neher committed rMITK801d55171ea9: Filter zero (authored by neher).
Filter zero
Apr 20 2019, 12:03 PM

Apr 18 2019

neher committed rMITK64446163f12c: All new fit (authored by neher).
All new fit
Apr 18 2019, 3:10 PM
neher committed rMITK550e6206efe9: Normalizing system (authored by neher).
Normalizing system
Apr 18 2019, 3:07 PM
neher added a comment to T26285: [MITK Diffusion] Fiber fitting regularization.

Pushed new branch T26285-FitRegu.

Apr 18 2019, 3:07 PM · MITK
neher triaged T26285: [MITK Diffusion] Fiber fitting regularization as Normal priority.
Apr 18 2019, 3:04 PM · MITK
neher closed T26282: [MITK Diffusion] Missing icons as Resolved.
Apr 18 2019, 3:03 PM · MITK
neher committed rMITK1c7ee2a648a4: Merge branch 'T26282-Icons' (authored by neher).
Merge branch 'T26282-Icons'
Apr 18 2019, 2:33 PM
neher committed rMITK8b2397400371: Fix icons. Apparently only png is working. (authored by neher).
Fix icons. Apparently only png is working.
Apr 18 2019, 2:32 PM
neher committed rMITKfc363974d833: Distance as parameter (authored by neher).
Distance as parameter
Apr 18 2019, 11:25 AM
neher committed rMITKeb01007be3ca: wip (authored by neher).
wip
Apr 18 2019, 11:19 AM
neher committed rMITK43cb3e342755: Setting cmake file and qrc resources correctly (authored by neher).
Setting cmake file and qrc resources correctly
Apr 18 2019, 11:19 AM
neher added a comment to T26282: [MITK Diffusion] Missing icons.

Pushed new branch T26282-Icons.

Apr 18 2019, 11:18 AM · MITK

Apr 16 2019

neher triaged T26282: [MITK Diffusion] Missing icons as Normal priority.
Apr 16 2019, 1:20 PM · MITK
neher closed T25779: [MITK Diffusion] Streamline tractography parameter files as Resolved.
Apr 16 2019, 1:19 PM · MITK
neher committed rMD70525f253cfa: Tracking test data (authored by neher).
Tracking test data
Apr 16 2019, 11:16 AM
neher triaged T26281: [MITK Diffusion] Fiberfox: simulation without fibers, only VFMs as Wishlist priority.
Apr 16 2019, 10:10 AM · MITK
neher committed rMITK7fbef1887434: Merge branch 'T25779-StpFiles6' (authored by neher).
Merge branch 'T25779-StpFiles6'
Apr 16 2019, 9:56 AM

Apr 15 2019

neher committed rMITK166bffff1578: Max length param readf (authored by neher).
Max length param readf
Apr 15 2019, 11:37 AM
neher committed rMITK20e70f4dbb61: Merge branch 'T25779-StpFiles5' into T25779-StpFiles6 (authored by neher).
Merge branch 'T25779-StpFiles5' into T25779-StpFiles6
Apr 15 2019, 11:28 AM
neher committed rMITK6f6f6fc674ef: Loading of parameters (authored by neher).
Loading of parameters
Apr 15 2019, 11:28 AM
neher added a comment to T25779: [MITK Diffusion] Streamline tractography parameter files.

Pushed new branch T25779-StpFiles6.

Apr 15 2019, 11:28 AM · MITK

Apr 12 2019

neher committed rMITK6d6ff2576c91: Refactoring. Todo: reading and writing (authored by neher).
Refactoring. Todo: reading and writing
Apr 12 2019, 3:03 PM
neher committed rMITKd07cd498d92b: Check units (authored by neher).
Check units
Apr 12 2019, 2:32 PM
neher committed rMITKf3895f778a21: Tests passing (authored by neher).
Tests passing
Apr 12 2019, 2:11 PM
neher closed T26273: [MITK Diffusion] Probabilistic peak tracking as Resolved.
Apr 12 2019, 1:33 PM · MITK
neher committed rMITKe643e97a1b0c: Merge branch 'T25779-StpFiles4' into T25779-StpFiles5 (authored by neher).
Merge branch 'T25779-StpFiles4' into T25779-StpFiles5
Apr 12 2019, 1:12 PM
neher committed rMITK4f7a0699f9b2: Merge branch 'T25779-StpFiles3' into T25779-StpFiles4 (authored by neher).
Merge branch 'T25779-StpFiles3' into T25779-StpFiles4
Apr 12 2019, 1:12 PM
neher added a comment to T25779: [MITK Diffusion] Streamline tractography parameter files.

Pushed new branch T25779-StpFiles5.

Apr 12 2019, 1:11 PM · MITK
neher committed rMITK0b6cf889575e: Merge branch 'T26273-ProbPeaks' (authored by neher).
Merge branch 'T26273-ProbPeaks'
Apr 12 2019, 12:55 PM
neher committed rMITK6788ab1f30d3: Probabilistic peaks, prior flip in GUI (authored by neher).
Probabilistic peaks, prior flip in GUI
Apr 12 2019, 12:51 PM
neher renamed T26273: [MITK Diffusion] Probabilistic peak tracking from [MITK Diffusion] Probabilistoc Peak tracking to [MITK Diffusion] Probabilistic peak tracking.
Apr 12 2019, 8:07 AM · MITK
neher committed rMITK48bcc30ef83b: Added probabilistic peak tracking (authored by neher).
Added probabilistic peak tracking
Apr 12 2019, 8:02 AM
neher added a comment to T26273: [MITK Diffusion] Probabilistic peak tracking.

Pushed new branch T26273-ProbPeaks.

Apr 12 2019, 8:02 AM · MITK
neher triaged T26273: [MITK Diffusion] Probabilistic peak tracking as Normal priority.
Apr 12 2019, 7:59 AM · MITK

Apr 10 2019

neher closed T26261: Disable cv and vtk python tests as Resolved.
Apr 10 2019, 10:21 AM · MITK
neher committed rMITK744d520ddf8c: Merge branch 'T26261-PythonTest' (authored by neher).
Merge branch 'T26261-PythonTest'
Apr 10 2019, 10:19 AM
neher committed rMITK13d93c5bb6a5: Remove tests (authored by neher).
Remove tests
Apr 10 2019, 10:18 AM
neher added a comment to T26261: Disable cv and vtk python tests.

Pushed new branch T26261-PythonTest.

Apr 10 2019, 10:17 AM · MITK
neher triaged T26261: Disable cv and vtk python tests as Normal priority.
Apr 10 2019, 10:17 AM · MITK
neher added a comment to T26259: QmitkConvertToMultiLabelSegmentationAction only works once.

As a backup solution I added this functionality to the utilities view.

Apr 10 2019, 8:37 AM · MITK
neher committed rMITKe2343739cf33: Merge branch 'T26259-MlConversion' (authored by neher).
Merge branch 'T26259-MlConversion'
Apr 10 2019, 8:34 AM

Apr 9 2019

neher committed rMITK6e9f42810f82: Add multi label seg utility for conversion (authored by neher).
Add multi label seg utility for conversion
Apr 9 2019, 3:20 PM
neher added a comment to T26259: QmitkConvertToMultiLabelSegmentationAction only works once.

Pushed new branch T26259-MlConversion.

Apr 9 2019, 3:20 PM · MITK
neher triaged T26259: QmitkConvertToMultiLabelSegmentationAction only works once as Normal priority.
Apr 9 2019, 2:20 PM · MITK
neher triaged T26258: MITK and python only works with the specific python version the installer was created with as High priority.
Apr 9 2019, 2:06 PM · MITK

Apr 8 2019

neher closed T26257: [MITK Diffusion] Gradient rotation optional on load as Resolved.
Apr 8 2019, 5:01 PM · MITK
neher committed rMITK7523a72e4536: Merge branch 'T26257-OptionalGradientRotation' (authored by neher).
Merge branch 'T26257-OptionalGradientRotation'
Apr 8 2019, 4:54 PM
neher committed rMITK5148e255373b: Split mf from rotation matrix (authored by neher).
Split mf from rotation matrix
Apr 8 2019, 4:54 PM
neher committed rMITK96ec977079c8: Checking if matrix should be applied (authored by neher).
Checking if matrix should be applied
Apr 8 2019, 3:42 PM
neher added a comment to T26257: [MITK Diffusion] Gradient rotation optional on load.

Pushed new branch T26257-OptionalGradientRotation.

Apr 8 2019, 3:41 PM · MITK
neher added a comment to T26257: [MITK Diffusion] Gradient rotation optional on load.

Also make independent of measurement frame

Apr 8 2019, 3:34 PM · MITK
neher triaged T26257: [MITK Diffusion] Gradient rotation optional on load as Normal priority.
Apr 8 2019, 3:34 PM · MITK
neher committed rMITK4fefe0d753b7: Merge branch 'T25779-StpFiles2' into T25779-StpFiles3 (authored by neher).
Merge branch 'T25779-StpFiles2' into T25779-StpFiles3
Apr 8 2019, 2:23 PM
neher committed rMITK7444bea9335a: Tests (authored by neher).
Tests
Apr 8 2019, 2:23 PM
neher added a comment to T25779: [MITK Diffusion] Streamline tractography parameter files.

Pushed new branch T25779-StpFiles3.

Apr 8 2019, 2:23 PM · MITK
neher added a comment to T24778: OpenIGTlink does not build in superbuild [Ubuntu 18.04].

Is this mergeable now?

Apr 8 2019, 12:49 PM · Photoacoustics, Restricted Project, IGT, MITK
neher committed rMITKd923b82127e9: Skip test -e command (authored by neher).
Skip test -e command
Apr 8 2019, 11:21 AM
neher added a revision to T26252: Boost install error: Unknown Object (Differential Revision).
Apr 8 2019, 11:11 AM · MITK (2018-04-4)
neher committed rMITK94c615ca827e: Skip test -e command (authored by neher).
Skip test -e command
Apr 8 2019, 11:09 AM
neher added a comment to T26252: Boost install error.

Pushed new branch T26252-BoostError.

Apr 8 2019, 11:09 AM · MITK (2018-04-4)
neher added a project to T26252: Boost install error: MITK.
Apr 8 2019, 11:09 AM · MITK (2018-04-4)
neher triaged T26252: Boost install error as Normal priority.
Apr 8 2019, 11:07 AM · MITK (2018-04-4)

Apr 5 2019

neher committed rMITKa1b81591a0a1: Building. Now double-check everything (authored by neher).
Building. Now double-check everything
Apr 5 2019, 4:50 PM
neher committed rMITKf960441edc75: Merge branch 'T25779-StpFiles' into T25779-StpFiles2 (authored by neher).
Merge branch 'T25779-StpFiles' into T25779-StpFiles2
Apr 5 2019, 1:28 PM
neher committed rMITK37420551156c: Tracking pic (authored by neher).
Tracking pic
Apr 5 2019, 1:28 PM
neher added a comment to T25779: [MITK Diffusion] Streamline tractography parameter files.

Pushed new branch T25779-StpFiles2.

Apr 5 2019, 1:28 PM · MITK
neher edited projects for T25682: mitkBaseGeometry.cpp: Internal ITK matrix inversion error, cannot proceed., added: MITK (2018-04-4); removed MITK.
Apr 5 2019, 11:19 AM · MITK (2018-04-4)
neher committed rMITK6b4ea15d8155: Check if matrix is rotation. Safe calculate dominant axes. (authored by neher).
Check if matrix is rotation. Safe calculate dominant axes.
Apr 5 2019, 9:19 AM

Apr 4 2019

neher closed T26179: [MITK Diffusion] Fiberfox: account for partial fourier in ETL calculation as Invalid.
Apr 4 2019, 2:57 PM · MITK
neher closed T26123: [MITK Diffusion] Fiberfox output tick image as Resolved.
Apr 4 2019, 2:56 PM · MITK
neher closed T26234: [MITK Diffusion] Fiberfox TSE sequence as Resolved.
Apr 4 2019, 2:51 PM · MITK
neher committed rMITK198a079c6c37: Merge branch 'T26234-TSE' (authored by neher).
Merge branch 'T26234-TSE'
Apr 4 2019, 2:49 PM
neher committed rMITK340761862ae4: Adjust echo spacing and output tick and RF image (authored by neher).
Adjust echo spacing and output tick and RF image
Apr 4 2019, 2:49 PM
neher added a comment to T26234: [MITK Diffusion] Fiberfox TSE sequence.

Pushed new branch T26234-TSE.

Apr 4 2019, 2:48 PM · MITK
neher triaged T26234: [MITK Diffusion] Fiberfox TSE sequence as Normal priority.
Apr 4 2019, 2:18 PM · MITK
neher committed rMD70532cbb2c5b: Add data for corrupted rotation matrix check (authored by neher).
Add data for corrupted rotation matrix check
Apr 4 2019, 2:03 PM
neher added a comment to T25682: mitkBaseGeometry.cpp: Internal ITK matrix inversion error, cannot proceed..

I just realized that it is actually checked in SetIndexToWorldTransform :-D

Apr 4 2019, 10:59 AM · MITK (2018-04-4)
neher added a comment to T25682: mitkBaseGeometry.cpp: Internal ITK matrix inversion error, cannot proceed..

While I changed the matrix check, I left it at the current position in in the PlaneGeometry.
We should discuss if it is sensible to move this ckec and also it's applications to a different location, e.g. to SetIndexToWorldTransform of BaseGeometry.

Apr 4 2019, 10:45 AM · MITK (2018-04-4)
neher added a revision to T25682: mitkBaseGeometry.cpp: Internal ITK matrix inversion error, cannot proceed.: Unknown Object (Differential Revision).
Apr 4 2019, 10:42 AM · MITK (2018-04-4)
neher committed rMITKe2a1d71ddd26: Add tests if rotation matrix check and default dominant axes calculation work. (authored by neher).
Add tests if rotation matrix check and default dominant axes calculation work.
Apr 4 2019, 10:40 AM
neher committed rMITK223c1163e9ee: Check if matrix is rotation. Safe calculate dominant axes. (authored by neher).
Check if matrix is rotation. Safe calculate dominant axes.
Apr 4 2019, 10:01 AM
neher added a comment to T25682: mitkBaseGeometry.cpp: Internal ITK matrix inversion error, cannot proceed..

Pushed new branch T25682-DominantAxesError.

Apr 4 2019, 10:01 AM · MITK (2018-04-4)
neher closed T26217: [MITK Diffusion] Diffusion function collection reference bvalue as Resolved.
Apr 4 2019, 9:29 AM · MITK
neher committed rMITKbcf8a2eb2c9b: Merge branch 'T26217-FfRefBval' (authored by neher).
Merge branch 'T26217-FfRefBval'
Apr 4 2019, 9:18 AM
neher committed rMITK8d34836f609f: Catch 0 (authored by neher).
Catch 0
Apr 4 2019, 9:17 AM
neher added a comment to T26217: [MITK Diffusion] Diffusion function collection reference bvalue.

Pushed new branch T26217-FfRefBval.

Apr 4 2019, 9:16 AM · MITK
neher added a comment to T25682: mitkBaseGeometry.cpp: Internal ITK matrix inversion error, cannot proceed..

Does anyone know why the inverse is always calculated and not simply set to the transpose? After all, we are talking about rotation matrices.
In this context, the EnsurePerpendicularNormal method (https://phabricator.mitk.org/source/mitk/browse/master/Modules/Core/src/DataManagement/mitkPlaneGeometry.cpp$37) seems rather complex and also does not catch all cases since it only checks if axis 3 is perpendicular to 1&2 but not if 1&2 are perpendicular to each other. I would prefer to simply check if the matrix R is a rotation matrix by checking

  1. det(R) == 1?
  2. R*R^T = ID?
Apr 4 2019, 8:16 AM · MITK (2018-04-4)

Apr 3 2019

neher added a comment to T25682: mitkBaseGeometry.cpp: Internal ITK matrix inversion error, cannot proceed..

It's apparently an issue of the "dominantAxis" calculation. In some cases this does not make sense and yields the same index twice. Not sure what this "dominantAxis" is supposed to be anyway. Supposedly related to T22254.

Apr 3 2019, 4:12 PM · MITK (2018-04-4)

Apr 1 2019

neher triaged T26217: [MITK Diffusion] Diffusion function collection reference bvalue as Normal priority.
Apr 1 2019, 3:41 PM · MITK

Mar 28 2019

neher committed rMITKaf2ba67bb4ff: Refactoring (authored by neher).
Refactoring
Mar 28 2019, 3:01 PM
neher added a comment to T25779: [MITK Diffusion] Streamline tractography parameter files.

Pushed new branch T25779-StpFiles.

Mar 28 2019, 3:00 PM · MITK
neher closed T26207: [MITK Diffusion] Set seed value for randm phantoms explicitely as Resolved.
Mar 28 2019, 10:21 AM · MITK
neher committed rMITK4a757433206f: Merge branch 'T26207-RandomPhantomSeed' (authored by neher).
Merge branch 'T26207-RandomPhantomSeed'
Mar 28 2019, 9:42 AM
neher committed rMITK2dad735e8b31: User defined seed (authored by neher).
User defined seed
Mar 28 2019, 9:41 AM
neher added a comment to T26207: [MITK Diffusion] Set seed value for randm phantoms explicitely.

Pushed new branch T26207-RandomPhantomSeed.

Mar 28 2019, 9:41 AM · MITK
neher triaged T26207: [MITK Diffusion] Set seed value for randm phantoms explicitely as Normal priority.
Mar 28 2019, 9:40 AM · MITK

Mar 27 2019

neher closed T26168: Linux installer shell scripts error as Resolved.
Mar 27 2019, 9:56 AM · MITK