bestlinreg.pl

perform best linear registration between two MINC volumes

bestlinreg.pl [options] source.mnc target.mnc output.xfm [output.mnc]

DESCRIPTION

bestlinreg.pl performs hierarchical linear registration between a source and target MINC volume using minctracc. The fitting proceeds through a series of blur levels and step sizes with parameters optimised by Claude Lepage for robust convergence. The result is a linear transformation (.xfm) that maps the source volume into the space of the target volume. An optional resampled output volume can also be produced.

The script supports 6-, 7-, 9-, and 12-parameter affine models, defaulting to 9-parameter (rigid body plus independent scaling). Source and target masks can be supplied to restrict the region used for fitting.

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 even if an output filename is given.

-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 (3 rotations, 3 translations).

-lsq7

Use a 7-parameter similarity model (rigid body plus one global scale).

-lsq9

Use a 9-parameter model (rigid body plus three independent scales). This is the default.

-lsq12

Use a full 12-parameter affine model (rigid body, scales, and shears).

-quaternions

Use quaternion-based rotation parametrisation in minctracc.

EXAMPLES

Register a subject to an MNI model with the default 9-parameter model:

bestlinreg.pl subject.mnc mni_icbm152_t1_tal_nlin_sym_09c.mnc subject_to_mni.xfm

Perform a rigid-body registration with an initial transform:

bestlinreg.pl -lsq6 -init_xfm rough.xfm -clobber \
    subject.mnc target.mnc refined.xfm resampled.mnc

Register with masks on both source and target:

bestlinreg.pl -source_mask src_mask.mnc -target_mask tgt_mask.mnc \
    src.mnc tgt.mnc output.xfm

AUTHOR

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

COPYRIGHTS

Copyright (C) Vladimir S. Fonov and McGill University. Licensed under the terms of the GNU General Public License version 3 or later.

SEE ALSO

bestlinreg_g(1), bestlinreg_s(1), minctracc(1), mritotal(1)