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. For SEPIA v1.1.1, it provides interfaces to use the following toolboxes freely available online for academic purposes, i.e.

  1. MEDI toolbox (updated Jan 15, 2020)

  2. STI Suite (v3.0)

  3. FANSI toolbox (v3.0, released on 2021.10.15, i.e., commit b6ac1c9e)

  4. SEGUE (accessed 12 September 2019)

  5. MRI susceptibility calculation methods (accessed 12 September 2019)

  6. MRITOOLS (v3.5.5) (2022-Oct-11: v3.5.6 passed)

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.


We recommand to use only one specific SEPIA version throughtout a single study (i.e., re-run all the processing with the latest version or do not update SEPIA in the middle of your study) to ensure all data undergoing a consistient processing pipeline.

If you encounter a bug in SEPIA, please report to this GitHub issue page

If you have a more general question reagrding the usgae of SEPIA and/or other QSM questions, please make use of the GitHub Discussion page

Indices and tables