phantomfit_elastix.pl

hierarchical nonlinear fitting constrained by spherical harmonics using Elastix

phantomfit_elastix.pl [options] source.mnc target.mnc source_mask.mnc target_mask.mnc bricks.mnc [...] output.xfm

DESCRIPTION

phantomfit_elastix.pl is a variant of phantomfit.pl that uses Elastix for the nonlinear registration step. This variant accepts five positional inputs: the source and target volumes, corresponding source and target masks, and a bricks volume that identifies the internal marker structure of the phantom. The deformation field is constrained by a spherical-harmonic basis to produce a smooth parametric distortion model.

The fitting proceeds through multiple resolution levels. The bricks volume provides additional structural constraints specific to phantoms with a regular grid of internal markers. An output directory can be specified for Elastix intermediate results.

OPTIONS

-verbose: Print progress information during processing.
-debug: Enable debug mode with additional diagnostic output.
-clobber: Overwrite existing output files.
-fake: Print the commands that would be executed without running them.
-init_xfm <xfm>: Use the specified transformation as the initial starting estimate.
-order <n>: Maximum order of the spherical-harmonic expansion. Default: 5.
-par <file>: Write the spherical-harmonic parameter file to the specified path.
-measure: Only measure the distortion without iterative fitting.
-step_iterations <n>: Number of iterations at each step of the hierarchical registration.
-min_step <f>: Minimum step size in millimetres for the finest level of the hierarchy. Default: 1.
-limit: Limit the magnitude of the estimated distortion field.
-keep <f>: Fraction of the distortion field to retain after filtering. Default: 1.0.
-cylindric: Use cylindrical coordinate representation for the distortion model.
-init <xfm>: Provide an initial linear transformation for the registration.
-work_dir <dir>: Specify a working directory for intermediate files.
-outdir <dir>: Specify an output directory for Elastix intermediate results.
-pca: Use PCA regularization for the distortion model.
-pcs <n>: Number of principal components to retain when using PCA regularization.

EXAMPLES

Fit a distortion model using Elastix with brick markers:

phantomfit_elastix.pl phantom_scan.mnc phantom_model.mnc \
    source_mask.mnc target_mask.mnc bricks.mnc output.xfm

Fit with higher-order harmonics and a custom output directory:

phantomfit_elastix.pl -order 7 -min_step 0.5 -outdir /tmp/elastix_work \
    -verbose phantom_scan.mnc phantom_model.mnc \
    source_mask.mnc target_mask.mnc bricks.mnc output.xfm

Fit with parameter output and PCA regularization:

phantomfit_elastix.pl -par distortion.par -pca -pcs 10 -clobber \
    phantom_scan.mnc phantom_model.mnc \
    source_mask.mnc target_mask.mnc bricks.mnc output.xfm

AUTHOR

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

COPYRIGHTS