SEPIA Documentation

Welcome to the SEPIA documentation! Here you can find all the documents related to SEPIA.

SEPIA provides a graphical user interface (GUI) in Matlab to build data processing pipelines related to quantitative susceptibility mapping (QSM).

SEPIA is designed to solve two issues we encountered in QSM:

1. Using algorithms from toolboxes developed by different research groups,
2. Having a platform such that we can quickly adjust (and remember) parameters of each algorithm.

The purpose of SEPIA is to provide a platform for easy access to different QSM processing methods in the field. It provides interfaces to use the following three toolboxes freely available online for academic purposes, i.e.

1. MEDI toolbox
2. STI Suite
3. FANSI toolbox
4. SEGUE

Through SEPIA we hope researchers who are not coming from the field could also be able to use QSM for their research. For those more experienced researchers, we also hope this tool can simplify your workflow.

Table of Contents

Getting started

• Installation/Setp up
• Data Preparation
• SEPIA header
• SEPIA Output Files
• Release note

Graphical User Interface (GUI)

• SEPIA (One-stop QSM processing)
• Phase Unwarpping Standalone
• Background Magnetic Field Removal Standalone
• QSM Standalone

Supported algorithms in SEPIA

• Phase Unwarpping Algorithms
• Background Magnetic Field Removal Algorithms
• QSM Algorithms
• Lookup table of algorithm parameters

Demonstration

• Choosing a right phase unwrapping method for your data

Tutorial

• SEPIA 101 - First QSM with SEPIA
• Integration of New Phase unwrapping/BFR/QSM Method in SEPIA: Part 1
• Integration of New Phase unwrapping/BFR/QSM Method in SEPIA: Part 2
• (f)MRI Toolkit 2019

Acknowledgements and References

• Acknowledgments
• References

Indices and tables

• Index
• Module Index
• Search Page