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Maniphest T27330

Otsu Segmentation using Diffusion Weighted data
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Description

MITK Version: v2018.02.2
OS: Mac

What I am trying to accomplish: Create a segmentation based off the B0 data (component 0) which I can apply to all diffusion directions after rigidly registering the data to the B0.

Steps to reproduce error:

  1. Load Diffusion DICOMs as diffusion weighted images into MITK (128 x 128 x 128 volume with 1 B0 and 30 gradient directions)
  2. Load Segmentation panell and create new segmentation for imported dataset
  3. Select 3D tools tab and select Otsu
  4. Run Otsu and receive this error:

"itkOtsuFilter error: image dimension must be in {2, 3} and no RGB images can be handled."

Event Timeline

TE_Cork created this task.Apr 17 2020, 7:22 PM
kislinsk triaged this task as Wishlist priority.Apr 18 2020, 9:29 AM
kislinsk added subscribers: neher, kislinsk.

@neher Is it possible to extract a component of B0 data into a separate image so it can be used in segmentation?

neher added a comment.Apr 18 2020, 9:34 AM

Sure. B0 extraction is available in the diffusion preprocessing view.

TE_Cork added a comment.Apr 18 2020, 9:40 AM

Is that B0 extraction feature only available in MITK Diffusion? I think that software was Windows and Linux only, right?

neher added a comment.Apr 18 2020, 11:01 AM

Yes, it is. Mac is still work in progress. As an alternative I recommend teem-unu for nrrd image operations. Not sure about Mac there too though.

kislinsk closed this task as Wontfix.Apr 29 2022, 1:44 PM
kislinsk added a project: Auto-closed.

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