par2xfm.pl

convert distortion parameters to an XFM grid transform

par2xfm.pl <par_in> <xfm_out> [options]

DESCRIPTION

par2xfm.pl converts a spherical-harmonic distortion parameter file into an XFM transformation file containing a nonlinear grid transform. The parameter file typically comes from a phantom distortion fitting procedure (e.g. phantomfit.pl). The script evaluates the parametric distortion model on a regular grid and writes the result as a MINC .xfm file that can be applied with standard tools such as mincresample.

Options control the grid spacing, the maximum distortion magnitude, the spatial extent of the grid, and whether the transform should be inverted. A cylindric coordinate mode is available for use with cylindrical phantoms.

OPTIONS

--verbose: Print progress information during processing.
--clobber: Overwrite existing output files.
--spacing <f>: Grid spacing in millimetres for the output deformation field. Default: 2.
--max <f>: Maximum allowed distortion magnitude in millimetres. Values exceeding this are clipped. Default: 5.0.
--noinvert: Do not invert the transformation. By default the transform is inverted so that it can be used to correct the distortion.
--extent <f>: Spatial extent (half-width) of the output grid in millimetres. Default: 300.
--step <f>: Evaluation step size used when sampling the parametric model onto the grid.
--scaling <f>: Apply a global scaling factor to the distortion field.
--cylindric: Use cylindrical coordinate representation for the distortion model. This is appropriate when the distortion was fit using a cylindrical phantom.

EXAMPLES

Convert a parameter file to an XFM with default settings:

par2xfm.pl distortion.par correction.xfm

Create a grid transform with finer spacing and larger extent:

par2xfm.pl distortion.par correction.xfm --spacing 1 --extent 400

Convert without inverting and using cylindrical coordinates:

par2xfm.pl distortion.par correction.xfm --noinvert --cylindric --clobber

AUTHOR

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

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