.. _fmritoolkit2025-theory-background-removal:

One more step before computing QSM but why?
===========================================

The phase 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, and we have no signal outside the brain, 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 (it is not only about high and low spatial frequency) and researchers have successfully developed various algorithms to separate the tissue fields from the background fields.

.. figure:: images/total_field_explain.png
   :align: center
   
   Figure 1: The total field we obtained from the first sub-panel is the summation of tissue and background magnetic fields.


Back to :ref:`fmritoolkit2025-exercise3`.