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Maniphest T2210

Allow segmentation on reoriented 2D slices
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Assigned To
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Authored By
maleike
Jul 9 2009, 10:55 AM
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Referenced Files
F255: contour_reoriented-svn20100.patch
Feb 22 2010, 12:09 PM
F254: mitkOverwriteSliceImageFilter.cpp
Oct 5 2009, 7:43 AM
F253: mitkOverwriteSliceImageFilter.h
Oct 5 2009, 7:43 AM
F252: mitkContourTool.cpp
Oct 5 2009, 7:42 AM
F251: mitkSegTool2D.cpp
Oct 5 2009, 7:42 AM
Subscribers
• fetzer
• heimann
maleike
• martelli
nolden

Description

Chiara R and Xavier P offerd on mitk-users to modify the 2D segmentation tools (derived from mitk::SegTool2D) in a way that it would be possible to segment images in 2D slices which are not parallel to the main image axes.

Xavier already sent in a first piece of code, which I tried to integrate. Unfortunately, segmentation on rotated slices did not work as expected. Also, a couple of code issues arised:

  • Why not make it two different "write a 2D slice back into a volume" filter? Looks reasonable to me, since there are two "extract a slice" filters.
  • Do the return values of the helper methods in SegTool2D still make sense? Esp. DetermineAffectedImageSlice?
  • How will undo be handled? It should be handled, since all other operations support undo.
  • MITK style guide allows no tabs in code, should be replaced by two spaces
  • Please try to develop or generate patches against the most recent SVN version from http://svn2.mitk.org/trunk/mitk . This makes it easier to merge your modifications.

A prototype can of course be implemented as a proof-of-concept. However I would like to maintain a reasonable and clean code structure, so we should get clear about the above issues before changing the implementation.

We can use this platform (Bugzilla) to discuss all issues. If neccessary we split this bug up into smaller dependent ones. Also we can add attachments (design sketches, patches, etc.).

Related Objects

Event Timeline

maleike added projects: MITK, Bugzilla.Jul 9 2009, 10:55 AM
maleike added a subscriber: maleike.Oct 5 2009, 7:42 AM

mitkSegTool2D.cpp

mitkSegTool2D.cpp8 KBDownload

maleike added a comment.Oct 5 2009, 7:42 AM

mitkContourTool.cpp

mitkContourTool.cpp6 KBDownload

maleike added a comment.Oct 5 2009, 7:43 AM

mitkOverwriteSliceImageFilter.h

mitkOverwriteSliceImageFilter.h4 KBDownload

maleike added a comment.Oct 5 2009, 7:43 AM

mitkOverwriteSliceImageFilter.cpp

mitkOverwriteSliceImageFilter.cpp13 KBDownload

maleike added a comment.Jan 13 2010, 4:59 PM

this sounds unrealistic for the 1.0 release:

  • nobody to implement it
  • there are quite some errors to fix before features can be started
• martelli added a subscriber: • martelli.Feb 22 2010, 12:07 PM

Hi,
My name is Yves and I work with Chiara and Xavi. We are in the process of updating our MITK. For that I updated the code for the contour on reoriented slice that I attach as a patch created with Tortoise SVN ('contour_reoriented.patch', compared to MITK svn 20100).
The changes follow some advices from Tobias on the mailing list (topic:"Geometry problem with mitk 0.12"). The code works but still, in the OverwriteSliceImageFilter, I added a one pixel shift that I do not see any justification for.
Regards,
Yves

• martelli added a comment.Feb 22 2010, 12:09 PM

See message above.

contour_reoriented-svn20100.patch21 KBDownload

• heimann added a subscriber: • heimann.Jun 30 2010, 5:35 PM

Working on this, I'm getting problems with incorrect world2index and index2world transforms. There should be a test case in MITK to ensure that these work reliably.

• heimann added a comment.Jan 19 2011, 9:49 PM

Andreas Fetzer is working on this now.

• heimann added a comment.Jan 19 2011, 9:51 PM

A first version is in the current SVN.

nolden added a subscriber: nolden.Jul 27 2011, 2:42 PM

Resetting all bugs without active assignee flag to "CONFIRMED". Change status to IN_PROGRESS if you are working on it.

• fetzer added a subscriber: • fetzer.Aug 11 2011, 4:36 PM

Duplicated to T6417. It is now possible to segment images in rotated slices.

xplanes mentioned this in T4276: Allow to choose the pixel value for the ROI and added a flag to erase only the pixels with a specified pixel value.Jun 11 2010, 5:49 PM
kislinsk closed this task as a duplicate of T6417: Allow contouring for rotated slices.Aug 1 2016, 10:47 PM
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