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`_ * `qi unwrap_path`_ * `qi unwrap_laplace`_ qi fieldmap ----------- Calculates a B0 fieldmap from multi-echo GRE complex data by computing the phase difference between consecutive echoes. **Example Command Line** .. code-block:: bash 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 ``$QUIT_THREADS``). * ``--out, -o`` Add a prefix to output filenames. **Outputs** * ``Fieldmap.nii.gz`` - The fieldmap in Hertz (or PPM if ``--B0`` is specified). qi unwrap_path -------------- An implementation of the quality-guided path-based unwrapping of Abdul-Rahman et al. This is the recommended method to use (preferable over Laplacian). **Example Command Line** .. code-block:: bash qi unwrap_path phase_file.nii.gz The phase file must be specified in radians (i.e. between :math:`-\pi` and :math:`+\pi`). Does not read input from ``stdin``. **Outputs** * ``{input}_unwrapped.nii.gz`` - The unwrapped phase value, in radians. *Important Options* * ``--out, -o`` Change the output filename prefix. * ``--threads, -T`` Use N threads (default is hardware limit or ``$QUIT_THREADS``). **References** - `Abdul-Rahman et al 1 `_ - `Abdul-Rahman et al 2 `_ 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** .. code-block:: bash 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** - `Bakker et al `_