APART-QSM is a new proposed QSM separation method using an iterative data fitting scheme.
APART-QSM can separate paramagnetic and diamagnetic susceptibility components on in vivo and ex vivo data.
APART-QSM can handle an arbitrary number of complex GRE data input measurements to provide high-quality QSM separation maps with more faithful tissue delineation of the small brain sub-regions.
This repository contains two implementations of APART-QSM method based on single-orientation and multiple orientation data.
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preprocessing on phase data and QSM initialization
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Nifti toolbox
saving reconstruction results
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brain mask generation and registration for multi-orientation data
Recommended MATLAB version: MATLAB 9.7 (R2019a)
APART_QSM_single_ori_demo.m is a demo for susceptibility separation using single orientation data.
APART_QSM_multi_ori_demo.m is a demo for susceptibility separation using multiple orientation data.
For data acquired with 3D multi-echo GRE sequences, you should do the following preprocessing steps before running STI reconstruction codes in this repository:
(1) Extract the tissue mask from magnitude images using FSL Bet.
(2) Unwrap the raw phase data using Laplacian-based phase unwrapping in STI_Suite V3.0 toolbox.
(3) Divide the background and local phase using VSHARP in STI_Suite V3.0 toolbox.
(4) Co-register the magnitude images at different orientations to a reference orientation (supine position) using FSL FLIRT.
(5) Apply the transform matrix to the corresponding local phase and calculate magnetic field direction (obtain B0_dirs).
(6) Once the above steps are completed, you can run demos successfully as long as Nifti toolbox is installed and added to the path.