One more step before computing QSM but why?

In the last exercise, it seems like the brain structures are hidding behind something. Why are these tissue contrasts ‘hidden’ in our images?

The data contains not only the phase generated by the brain tissues but also by the scanner hardware imperfection and fields generated at air/tissue interfaces such as sinuses and ear canals.

These non-tissue fields, or so-called background fields, can be one or two order(s) of magnitude stronger than the tissue fields and affects the global brain tissues.

Since we are only interested in the magnetic fields generated by the brain tissues, we have to remove these background fields before computing the QSM map. However, the background fields and tissue fields co-exist across the whole brain.

Luckily, the background fields have different mathematical properties and researchers have successfully developed various algorithms to separate the tissue fields from the background fields.

Back to Exercise 3.