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Segmentation: Add-Tool contouring on specific data sets fails on rotated planes.
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Apr 6 2016, 2:49 PM
Referenced Files
F1314: imagemask.png
Apr 13 2016, 2:55 PM
F1313: contour.png
Apr 13 2016, 2:54 PM


Segmentation on rotated sliced does not work for specific datasets :


3M3 Demodaten:
.../Organsegmentierung (Daniel M.)/WholeBody.pic.gz
.../Organsegmentierung (Daniel M.)/DataSet_Heart_Diastole.pic
.../Registrierung ( Daniel S. )/Organsegmentierung (Daniel M.)/DataSet_Heart_Systole.pic

Steps to reproduce:

  1. Load any of the mentioned figures
  2. Make a segmentation with the Add-Tool on a rotated slice

Result: Either no contour is shown on the respective slice or the contour is heavily misplaced.

I assume that actually all MR data sets in the folder are affected. Maybe the data sets have a strange geometry?

I tested older versions of mitk (2014.10) and it didn't work there as well, so it seems to be a very old bug.

Event Timeline

Just for documentation:
Hongzhi Lan,, reported a related issue on the MITK Mailing List on 6th April 2016:

I created a group planegeometries with different orientations (so, not evenly spaced) in a slicedgeometry3d, and used it to update the SliceNavigationController for one of the renderwindows in QmitkStdMultiWidget. Now I can get correct reslices for the image, but when I tried to use MITK segmentation tools on a reslice, the contour drawn was at right location, but when it was converted to binary image in 3D volume, the image mask shifted to a different location and had different sizes (see attachment). I was wondering what the reason could be. During the converting from contour to image mask, the display geometry was used. I guess the cause might be from display geometry. But since the image reslices were correct to me, it seemed the display geometry was ok.

+ See attached screenshots

kislinsk added a subscriber: kislinsk.

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