This video shows how to segment spine (each vertebra as a separate object) in CT images using 3D Slicer's Segment Editor tool. All used tools and data set is open-source and freely usable without restrictions.
Download 3D Slicer: https://download.slicer.org
Download sample data set: http://medicaldecathlon.com/ (Task03-Liver, data set imagesTr\liver_100.nii.gz)
Hole filling code snippet: https://gist.github.com/lassoan/0f45db8bae792ea19ccad36ceefbf52d
Any questions? Write to the Slicer forum: https://discourse.slicer.org
