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
|
A more detailed description:
This pipeline is deprecated. Please use the new QSM pipeline instead.
This pipeline contains the processing steps to compute Quantitative Susceptibility Mapping (QSM) from multi-echo gradient echo (GRE) data using the SEPIA toolbox. It is used in our paper:
[1] Wang Y, Ye C, Pan R, Tang B, Li C, Liu J, Tao W, Zhang X, Yang T, Yan Y, Jiang S, Lui S, Wu B. Cognitive implications and associated transcriptomic signatures of distinct regional iron depositions in cerebral small vessel disease. Alzheimers Dement. 2025 Apr;21(4):e70196. doi: 10.1002/alz.70196. PMID: 40257048; PMCID: PMC12010275.