Different brain structures have different tissue characteristics which results in various signal intensities. The signal intensities for different brain structures often overlap. Also, some non-brain tissues such as in the neck and scalp have the same intensities as brain tissues.
The thalamus, (the dark green structure shown above) is a central grey-matter structure that has an intermediate average intensity because it is actually a mixture of grey and white matter. The bottom border of the thalamus is very difficult to locate because it separates the thalamus from grey-matter structures that have very similar intensities. The thalamus is important to segment because it is a very interesting structure to brain researchers.