c_fit_harmonics_grids

Fit cylindrical harmonic coefficients to deformation grids for distortion correction.

c_fit_harmonics_grids <grid1> <mask1> [<grid2> <mask2> ...] <output.par> [options]

DESCRIPTION

c_fit_harmonics_grids fits cylindrical harmonic basis functions to one or more deformation grid files to estimate a parametric model of geometric distortion. Each deformation grid is paired with a mask that defines the region over which the fitting is performed.

The cylindrical harmonic model is particularly suited for correcting gradient-coil-induced distortions in MRI, where the distortion pattern has cylindrical symmetry. The fitted coefficients are written to a parameter file that can be converted to a correction grid using c_param2grid.

Multiple grid/mask pairs can be provided to perform a joint fit across several acquisitions, improving robustness.

OPTIONS

--verbose

Print progress information during processing.

--clobber

Overwrite the output file if it already exists.

--order n

Maximum order of the cylindrical harmonic expansion.

--skip n

Skip every n-th voxel during fitting to reduce computation time.

--cylindrical

Use cylindrical harmonic basis functions (default behaviour).

--limit val

Exclude voxels with displacement magnitude above this threshold.

--par file

Initialize fitting from an existing parameter file.

EXAMPLES

# Fit cylindrical harmonics to a single grid/mask pair
c_fit_harmonics_grids grid.mnc mask.mnc output.par --order 10

# Fit using multiple grid/mask pairs with outlier rejection
c_fit_harmonics_grids grid1.mnc mask1.mnc grid2.mnc mask2.mnc \
    output.par --order 12 --limit 5.0

# Use voxel skipping for faster fitting
c_fit_harmonics_grids grid.mnc mask.mnc output.par --order 8 --skip 2

AUTHOR

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

COPYRIGHTS

Copyright © 2009-2024 by Vladimir S. Fonov

SEE ALSO

c_param2grid , fit_harmonics_grids , phantomfit.pl