QSM Pipeline
QSM Processing Pipeline using Sepia and QQNet.
__init__
QSM processing pipeline.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
subject
|
BIDSSubject
|
A BIDS subject object. |
required |
session
|
BIDSSession
|
A BIDS session object. |
required |
output_path
|
str
|
Output directory to save results. |
required |
use_which_t1w
|
str
|
Keyword to select the desired T1w image. |
None
|
normalize
|
bool
|
If True, normalize QSM (and other scalar maps) to MNI space via T1w. |
False
|
phase_image_correction
|
bool
|
If True, apply phase image correction for inter-slice phase polarity differences in the GE data. (https://github.com/kschan0214/sepia/discussions/93) |
False
|
reverse_phase
|
int
|
Set to 1 to inverse phase polarity (for GE scanners). |
0
|
A more detailed description:
This pipeline contains the processing steps to compute Quantitative Susceptibility Mapping (QSM) and other scalar maps from multi-echo gradient echo (GRE) data by the following steps:
- QSM reconstruction using a combined approach from the SEPIA toolbox and Chisep toolbox, including:
- Phase unwrapping (SEPIA: ROMEO total field calculation)
- Background field removal using V-SHARP (SEPIA)
- Dipole inversion using iLSQR (Chisep)