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I'm annotating CT scan slices(Nifti format) with ITK-snap. One slice contains two labels(Subarachnoid and Intraparenchymal) in the same area. Here is the original annotated image link: https://ibb.co/FJpyVZF Since two labels are overlapping, the intersection area in the slice should contain both labels. But it shows it only contains the label which has been drawn last. Since the Subarachnoid area was drawn last over the Intraparenchymal area, the final segmented image only shows it contains Subarachnoid in the intersection region. I'm attaching the annotated slice https://ibb.co/F3TrXtq and segmented slice https://ibb.co/sRgdndY to clear my point. What can I do to make the intersection area contain two labels?

Ornob Rahman
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ITK-SNAP uses binary label maps. That approach does not allow label overlap. Your options are:

  1. Use a different label map for each structure you are segmenting.
  2. Use a different segmentation representation. This will require use of different software. I recommend 3D Slicer.
Dženan
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  • I was able to overlap them by using 3D Slicer. I had to turn on the feature "allow overlapping" while I was editing. But as soon as I save the segmented series into one Nifti file, the mask became non-overlapping. Could you please tell me what is the right way to save or export the segmented series which may contain overlapping labels? – Ornob Rahman Mar 09 '22 at 09:34
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    One nifti file is the approach for non-overlapping labels. Slicer has a .seg.nrrd file which allows label overlaps. https://slicer.readthedocs.io/en/latest/user_guide/modules/segmentations.html – Dženan Mar 09 '22 at 15:56
  • From documentation: If segments in a segmentation do not overlap each other then segmentation is saved as a 3D volume node by default when the scene is saved (application menu: File / Save). If the segmentation contains overlapping segments then it is saved as a 4D volume: each 3D volume containing a set of non-overlapping segments. – Dženan Mar 09 '22 at 15:56
  • Could I use separate Nifti files for each separate label? Should not that be okay? – Ornob Rahman Mar 10 '22 at 05:23
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    Yes, you can totally use a separate NIFTI file for each label. – Dženan Mar 11 '22 at 15:05