Getting started

A standard QSM data processing pipeline usually consists of the following procedures:

• convert DICOM phase values (usually between -4096 and 4095) to wrapped phase values [-pi,pi)
• unwrap phase values and recover the total field shifted
• remove field contributions which are not generated by brain tissue (i.e. the background field)
• map susceptibility sources from the local (or tissue) field

Sepia provides 4 standalone applications for the above procedures:

1. Sepia (One-stop QSM processing)
   one-stop processing platform for processes from loading the multi-echo GRE data(either NIfTI or DICOM) to generate a magnetic susceptibility map
2. Phase unwrapping standalone
   standalone that converts complex-valued mGRE data (DICOM or NIfTI) to an unwrapped total field map
3. Background field removal standalone
   standalone that removes background field contributions from a total field map to produce a local field map
4. QSM standalone
   standalone that maps magnetic susceptibility sources from a local field map