Susceptibility¶
Susceptibility is a fundamental magnetic property of a material, and determines whether materials are paramagnetic (positive susceptibility) or diamagnetic (negative susceptibility). Quantitative Susceptibility Mapping (QSM) is a branch of MRI that aims to measure the susceptiblity of objects from the phase of the MR data. QUIT currently does not contain a full QSM processing pipeline, but does contain some phase unwrapping tools.
qi unwrap_path¶
An implementation of the quality-guided path-based unwrapping of Abdul-Rahman et al. This is the recommended method to use (preferable over Laplacian).
Example Command Line
qi unwrap_path phase_file.nii.gz
The phase file must be specified in radians (i.e. between \(-\pi\) and \(+\pi\)). Does not read input from stdin
, and currently there are no arguments to control the algorithms behaviour.
Outputs
input_unwrapped.nii.gz
- The unwrapped phase value, in radians.
References
qi unwrap_laplace¶
Implements Laplacian-based phase-unwrapping. Along with phase-unwrapping, the Laplacian method implicitly removes background fields. This means it can alter phase values in undesirable ways and hence is not the preferred method.
Example Command Line
qi unwrap_laplace phase_file.nii.gz
The phase file must be specified in radians (i.e. between -pi and +pi). Does not read input from stdin.
Outputs
input_unwrapped.nii.gz
The unwrapped phase, in radians.
Important Options
--mask, -m
Specify a mask, the phase will only be unwrapped inside this.
--erode, -e
Radius to erode the input mask by (default 1 mm).
References