bestlinreg_s2

perform best linear registration (symmetric variant 2)

bestlinreg_s2 [options] source.mnc target.mnc output.xfm [output.mnc]

DESCRIPTION

bestlinreg_s2 is a variant of the bestlinreg family that uses a blur+dxyz configuration for its internal multi-scale fitting stages. The stage schedule differs from both bestlinreg_s and bestlinreg_g, providing an alternative convergence profile. It accepts most of the same options as bestlinreg_g (excluding -notrans) and produces a linear .xfm transformation with an optional resampled output volume.

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.
-close: Assume the source and target are already roughly aligned.

EXAMPLES

bestlinreg_s2 -xcorr subject.mnc model.mnc output.xfm

Rigid-body registration with masks:

bestlinreg_s2 -lsq6 -source_mask src_mask.mnc -target_mask tgt_mask.mnc \
    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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