make_random_grid.pl

generate a random deformation grid for testing

make_random_grid.pl <sample.mnc> <output_grid> [options]

DESCRIPTION

make_random_grid.pl generates a pseudo-random deformation grid in MINC format. The grid has the same sampling geometry as the input sample volume. The deformation vectors at each voxel are drawn from a random distribution and then smoothed with a Gaussian kernel. This tool is primarily used for generating deformation fields for defacing (see deface_volume.pl) or for testing nonlinear registration pipelines.

The amplitude and smoothness of the deformation field can be controlled via command-line options. An optional mask can restrict the non-zero deformation region.

OPTIONS

--verbose: Print progress information during processing.
--clobber: Overwrite existing output files.
--amplitude <f>: Peak amplitude (in mm) of the random deformation vectors. Default: 1.0.
--fwhm <f>: Full-width at half-maximum (in mm) of the Gaussian smoothing kernel applied to the random field. Default: 10.
--keep_tmp: Do not delete temporary working files after completion.
--mask <mask.mnc>: Restrict non-zero deformation to the region defined by the given binary mask.
--byte: Store the output grid with byte (8-bit) precision instead of the default floating-point precision.
--edge_smooth <f>: FWHM (in mm) of the smoothing kernel applied at the boundary between the deformed and undeformed regions when a mask is used.

EXAMPLES

Generate a random deformation grid matching the geometry of a sample volume:

make_random_grid.pl sample.mnc random_grid.mnc

Generate a high-amplitude grid for defacing:

make_random_grid.pl --amplitude 12 --fwhm 6 \
    sample.mnc deface_grid.mnc

Generate a masked deformation field:

make_random_grid.pl --mask face_mask.mnc --amplitude 10 \
    --edge_smooth 3 --clobber sample.mnc masked_grid.mnc

AUTHOR

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

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