How to overlap two label to make mask for segmentation in ITK-snap?

Question

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?

Answer 1

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.