.. _SEPIA101-index:

SEPIA 101 - First QSM with SEPIA
================================

Objectives
----------

- Understanding the background of magnetic susceptibility contrast
- Gaining experience in basic QSM post-processing in SEPIA framework

Target Audience
^^^^^^^^^^^^^^^

- who is new to SEPIA
- who wants to know some basic knowledge about QSM

Estimated Time
^^^^^^^^^^^^^^

About 1 hour

Prerequisite
------------

Please install SEPIA in the Matlab environment. You can find the information about the installation procedures in :ref:`gettingstart-installation`.

Introduction  
------------

In this tutorial, we will go through the standard processing pipeline for quantitative susceptibility mapping (QSM), a novel contrast mechanism that uses to study tissue magnetic properties, in SEPIA framework. 

.. toctree::
   :maxdepth: 1

   Theory_qsmphysics

.. figure:: images/qsm_model_flow.png
   :align: center
   
   Figure 1: QSM theory. A magnetic source generates a secondary magnetic field inside the MRI scanner, which will eventually alter the signal phase we measured. Decoding the phase data allows us to detect the molecular environment of the brain tissues.  

Exercises
---------

Let's begin with the following exercises that will take you from the phase data to the susceptibility maps!

.. toctree::
   :maxdepth: 1
   :name: toc-tutorial-sepia101

   Exercise1
   Exercise2
   Exercise3
   Exercise4