phantom_distortion_measure.pl

calculate geometric distortion from phantom scans via hierarchical nonlinear registration

phantom_distortion_measure.pl <scan_1> [scan_2 ...] <output.par> <output.xfm> [options]

DESCRIPTION

phantom_distortion_measure.pl measures geometric distortion in MRI scanner acquisitions by performing hierarchical nonlinear registration between one or more phantom scans and a known distortion-free phantom model. The registration is constrained by a spherical-harmonic basis to produce a smooth parametric distortion field. The output consists of a parameter file (.par) describing the distortion in spherical-harmonic coefficients and an XFM grid transform file.

Multiple phantom scans can be provided to improve robustness by averaging the distortion estimates. The phantom model must be specified with the --model option. The order of the spherical-harmonic expansion, the minimum registration step size, and various other parameters can be tuned.

OPTIONS

--verbose: Print progress information during processing.
--debug: Enable debug mode with additional diagnostic output.
--clobber: Overwrite existing output files.
--order <n>: Order of the spherical-harmonic expansion used to model the distortion field. Default: 5.
--work_dir <dir>: Specify a working directory for intermediate files. A temporary directory is used if not specified.
--model <dir>: Path to the phantom model directory. This option is required.
--min_step <f>: Minimum step size in millimetres for the hierarchical registration. Default: 2.
--no_core_extract: Skip the core extraction step that isolates the phantom interior from the background.
--measure: Only measure the distortion without fitting the parametric model.
--mask <mask.mnc>: Specify a mask to restrict the region used for distortion measurement.
--exclude <file>: Specify a file listing regions to exclude from the distortion fit.
--limit_linear: Limit the linear component of the registration.
--keep <f>: Fraction of the distortion field to retain after filtering. Default: 1.0.
--cylindric: Use cylindrical coordinate representation for the distortion model.
--acr: Use ACR (American College of Radiology) phantom geometry.
--init <xfm>: Provide an initial transformation for the registration.
--step_iterations <n>: Number of iterations at each step of the hierarchical registration.
--adni: Use ADNI (Alzheimer’s Disease Neuroimaging Initiative) phantom geometry.
--out-roi <file>: Write a region-of-interest mask to the specified file.
--only-roi: Only compute the distortion within the specified region of interest.
--dilate-roi <n>: Dilate the region-of-interest mask by the given number of voxels.
--pca: Use PCA (Principal Component Analysis) regularization for the distortion model.
--pcs <n>: Number of principal components to retain when using PCA regularization.
--dd: Use Diffeomorphic Demons for the nonlinear registration step.
--ants: Use ANTs (mincANTS) for the nonlinear registration step.
--keep-tmp: Do not remove temporary working files after processing.

EXAMPLES

Measure distortion from a single phantom scan:

phantom_distortion_measure.pl phantom_scan.mnc distortion.par distortion.xfm \
    --model /path/to/phantom_model --verbose

Measure distortion from multiple scans with higher-order harmonics:

phantom_distortion_measure.pl scan1.mnc scan2.mnc scan3.mnc \
    distortion.par distortion.xfm \
    --model /path/to/phantom_model --order 7 --min_step 1

Use cylindrical coordinates with ANTs registration:

phantom_distortion_measure.pl phantom.mnc distortion.par distortion.xfm \
    --model /path/to/phantom_model --cylindric --ants --clobber

AUTHOR

Vladimir S. Fonov. McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.

COPYRIGHTS