bestlinreg_s

perform best linear registration (symmetric variant)

bestlinreg_s [options] source.mnc target.mnc output.xfm [output.mnc]

DESCRIPTION

bestlinreg_s is a variant of bestlinreg_g that uses a different internal blur and tolerance schedule during the hierarchical multi-scale fitting stages. The altered schedule is designed to provide improved convergence behaviour for certain registration scenarios. It accepts the same options as bestlinreg_g and produces the same output: a linear .xfm transformation and an optional resampled volume.

Like bestlinreg_g, it supports selectable cost functions (mutual information, normalised mutual information, cross-correlation), secondary source/target channels, and individual constraints on affine transformation components.

OPTIONS

-verbose: Print progress information during processing.
-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.
-noresample: Do not produce a resampled output volume.
-source_mask <mask.mnc>: Apply the given binary mask to the source volume during registration.
-target_mask <mask.mnc>: Apply the given binary mask to the target volume during registration.
-lsq6: Use a 6-parameter rigid-body model.
-lsq7: Use a 7-parameter similarity model.
-lsq9: Use a 9-parameter model. This is the default.
-lsq12: Use a full 12-parameter affine model.
-quaternions: Use quaternion-based rotation parametrisation.
-mi: Use mutual information as the cost function.
-nmi: Use normalised mutual information as the cost function.
-xcorr: Use cross-correlation as the cost function.
-work_dir <dir>: Use the specified directory for intermediate files.
-sec_source <source2.mnc>: Supply a secondary source volume for multi-channel registration.
-sec_target <target2.mnc>: Supply a secondary target volume for multi-channel registration.
-noshear: Disable shear parameters in the affine model.
-noscale: Disable scale parameters in the affine model.
-norot: Disable rotation parameters in the affine model.
-noshift: Disable shift (translation) parameters in the affine model.
-notrans: Equivalent to disabling all translation parameters.
-close: Assume the source and target are already roughly aligned.

EXAMPLES

Standard registration with the symmetric schedule:

bestlinreg_s subject.mnc model.mnc subject_to_model.xfm

Registration with NMI cost function and a resampled output:

bestlinreg_s -nmi -clobber subject.mnc model.mnc output.xfm output.mnc

AUTHOR

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

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