Sepia QSM
Pipeline for processing Quantitative Susceptibility Mapping (QSM) data using the SEPIA toolbox.
__init__
Sepia 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
|
sepia_toolbox_path
|
str
|
Path to the SEPIA toolbox. If None, assumes SEPIA is in MATLAB path. |
None
|
reverse_phase
|
int
|
Set to 1 to reverse phase polarity (for GE scanners). |
0
|