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 tools for calculating fieldmaps and phase unwrapping.

qi fieldmap

Calculates a B0 fieldmap from multi-echo GRE complex data by computing the phase difference between consecutive echoes.

Example Command Line

qi fieldmap multi_echo_gre.nii.gz --delta_te=2.0 --out=my_fieldmap < input.json

The input file should be complex-valued multi-echo GRE data. Does not read input from stdin.

Important Options

  • --delta_te

    The echo time difference between consecutive echoes, in milliseconds. Required.

  • --B0

    Field-strength in Tesla. If specified, the output will be in PPM instead of Hertz.

  • --threads, -T

    Use N threads (default is hardware limit or $QUIT_THREADS).

  • --out, -o

    Add a prefix to output filenames.

Outputs

  • Fieldmap.nii.gz - The fieldmap in Hertz (or PPM if --B0 is specified).

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.

Outputs

  • {input}_unwrapped.nii.gz - The unwrapped phase value, in radians.

Important Options

  • --out, -o

    Change the output filename prefix.

  • --threads, -T

    Use N threads (default is hardware limit or $QUIT_THREADS).

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}_unwrap.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).

  • --debug, -d

    Output intermediate debugging images showing the unwrapping steps.

  • --threads, -T

    Use N threads (default is hardware limit or $QUIT_THREADS).

  • --out, -o

    Add a prefix to output filenames.

References