thomass (Sarina Thomas)
User

Projects (12)
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2020
Milestone
BVM
Tag
CSI-HD
Project
d:cipher
Group
Deep Learning
Group

User Details

User Since: Aug 1 2016, 12:10 PM (205 w, 9 h)

Recent Activity
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Fri, Jul 3

thomass added a comment to T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.

Plugin name	dynamic timestep =0	dynamic timestep != 0	static t=0	static t =2
Threshold	performs segmentation on all timesteps	performs segmentation on all timesteps	performs segmentation on timestep 0	performs segmentation on timestep 0
UL threshold	performs segmentation on all timesteps	performs segmentation on all timesteps	performs segmentation on timestep 0	performs segmentation on timestep 0
Otsu	performs static 3D seg on the selected timestep performs static 3D seg on the selected timestep > it only matters which time point is selected not on which it was created
Fast Marching	it doesn't matter on which timesteps the seeds are selected, they all account for initial image / performs segmentation only on the timestep selected, others are blank
Watershed	segmentation cannot be produced with US4DCyl / LinearModel / performs static 3D seg on the selected timestep		performs segmentation on timestep 0	performs segmentation on timestep 2 / it only matters which time point is selected not on which it was created
Picking	Creates a 3D segmentation with picked region and deletes all other segmentations (in all timesteps)

Fri, Jul 3, 2:19 PM · Restricted Project, Cleared, MITK (2020)

thomass claimed T27507: Check the current behavior of the segmentation tools according static and dynamic 4D segmentation.

Fri, Jul 3, 11:08 AM · Restricted Project, Cleared, MITK (2020)

Tue, Jun 30

thomass added a revision to T26974: [Segmentation] Region Growing 3D with 4D dataset not working: Unknown Object (Differential Revision).

Tue, Jun 30, 11:26 AM · MITK (2020)

Thu, Jun 25

thomass added a comment to T25825: [Segmentation] Crash using Watershed on different time steps.

But the 3d segmentation has only 1 timestep with duration = sum of durations of all 4D image timesteps, right?

Thu, Jun 25, 1:44 PM · MITK (2020)

Fri, Jun 19

thomass removed a project from T26974: [Segmentation] Region Growing 3D with 4D dataset not working: Missing Info.

Fri, Jun 19, 3:27 PM · MITK (2020)

thomass added a comment to T26974: [Segmentation] Region Growing 3D with 4D dataset not working.

The error described above results from the function add seed that currently takes 3D images only. It can be solved with using a timeselector to crop the current time step and set a 3D seed.
However, the task is related to the discussion on time points versus time steps and should be revised accordingly.

Fri, Jun 19, 3:18 PM · MITK (2020)

thomass added a comment to T27477: [Segmentation] Selection concept displays 'Favorite node list' by default leading to user confusion .

When the workbench is started from scratch it works.

Fri, Jun 19, 11:34 AM · Cleared, MITK (2020)

thomass claimed T26974: [Segmentation] Region Growing 3D with 4D dataset not working.

Fri, Jun 19, 9:49 AM · MITK (2020)

Tue, Jun 16

thomass added a comment to T27477: [Segmentation] Selection concept displays 'Favorite node list' by default leading to user confusion .

I used a master that was three weeks old, I will double check on the current develop

Tue, Jun 16, 10:17 AM · Cleared, MITK (2020)

Wed, Jun 10

thomass moved T27477: [Segmentation] Selection concept displays 'Favorite node list' by default leading to user confusion from Backlog to Segmentation on the MITK (2020) board.

Wed, Jun 10, 10:52 AM · Cleared, MITK (2020)

thomass triaged T27477: [Segmentation] Selection concept displays 'Favorite node list' by default leading to user confusion as High priority.

Wed, Jun 10, 10:47 AM · Cleared, MITK (2020)

thomass added a comment to T25825: [Segmentation] Crash using Watershed on different time steps.

Works for dynamic (4D) segmentations
Could not be reproduced for static segmentations since the workbench crashes during the creation of a static segmentation (related to T27476)

Wed, Jun 10, 9:45 AM · MITK (2020)

thomass added a comment to T27476: [Segmentation] Crash if new segmentation is created with timestep different than 0.

Works for timestep 0
Independent from segmentation tool so might be a problem of the selection concept not the segmentation

Wed, Jun 10, 9:40 AM · MITK (2020)

thomass updated the task description for T27476: [Segmentation] Crash if new segmentation is created with timestep different than 0.

Wed, Jun 10, 9:36 AM · MITK (2020)

thomass triaged T27476: [Segmentation] Crash if new segmentation is created with timestep different than 0 as High priority.

Wed, Jun 10, 9:34 AM · MITK (2020)

Mon, Jun 8

thomass added a project to T26974: [Segmentation] Region Growing 3D with 4D dataset not working: Missing Info.

@gaoh: Can you tell what you mean by dynamic mask?

Mon, Jun 8, 2:29 PM · MITK (2020)

thomass lowered the priority of T27067: ImageCropper cannot crop some images (4d?) from High to Normal.

I will leave the task open since the handling in the respective class might need further refactoring to fully understand the behavior (as also mentioned by @kalali in the D279 review).
I remove the MITK2020 tag for now since the mentioned bug is resolved by the fix in D279.

Mon, Jun 8, 2:14 PM · MITK

thomass committed rMITKae05e678acfd: <<Allow 4D image handling in Boundingshapecropper> (authored by thomass).

<<Allow 4D image handling in Boundingshapecropper>

Mon, Jun 8, 2:05 PM

thomass added a comment to T27439: [Segmentation] Support of Mask/Segmentations that are cropped / do not cover the whole image grid.

Task T26596 is mentioned but does not correlate with the Topic asaik...maybe transposed digits in the task number?

Mon, Jun 8, 11:52 AM · MITK

May 26 2020

thomass updated the task description for T27444: [Registration] Manipulator crashes on Start Manual Registration.

May 26 2020, 12:55 PM · MITK (2020)

thomass moved T27444: [Registration] Manipulator crashes on Start Manual Registration from Backlog to Registration on the MITK (2020) board.

May 26 2020, 12:54 PM · MITK (2020)

thomass triaged T27444: [Registration] Manipulator crashes on Start Manual Registration as High priority.

May 26 2020, 12:53 PM · MITK (2020)

Apr 23 2020

thomass committed rMITK3df935e97fdb: initial commit (authored by thomass).

initial commit

Apr 23 2020, 8:20 AM

Apr 22 2020

thomass added a revision to T27067: ImageCropper cannot crop some images (4d?): Unknown Object (Differential Revision).

Apr 22 2020, 1:05 PM · MITK

Apr 15 2020

thomass added a comment to T27067: ImageCropper cannot crop some images (4d?).

The reason seems to be that a BoundingShape as such is 3D with an index of size=3 that does not equal the index array of the 4D image. I will test the fix for other images to make sure.

Apr 15 2020, 12:23 PM · MITK

thomass committed rMITKea9929dd148e: correct index for cropping a 4d image with a 3d bounding box (authored by thomass).

correct index for cropping a 4d image with a 3d bounding box

Apr 15 2020, 12:20 PM

thomass added a comment to T27067: ImageCropper cannot crop some images (4d?).

Pushed new branch T27067-ImageCropperCorrect4D.

Apr 15 2020, 12:20 PM · MITK

thomass claimed T27067: ImageCropper cannot crop some images (4d?).

Apr 15 2020, 11:40 AM · MITK

thomass closed T23551: MITK does not support Dicom Subgroup Tags as Resolved.

This was also communicated to Siemens and only occured when loading their early stage clinical prototype data. Can not be reproduced with the newer data. The task can be closed for now.

Apr 15 2020, 8:11 AM · MITK