xfm_normalize.pl

normalize an XFM or grid transform to a standard uniform axis-aligned format

xfm_normalize.pl <input.xfm|input.mnc> <output.xfm> [options]

DESCRIPTION

xfm_normalize.pl normalizes an XFM transformation file or a MINC grid volume to a standard representation on a uniform, axis-aligned grid. This is useful for converting grid transforms with irregular sampling or oblique axes into a canonical form that is compatible with tools that expect regular grids.

The input can be either an .xfm file containing a grid transform or a .mnc file representing a deformation field directly. The output is always an .xfm file with an associated grid volume resampled to uniform spacing. A reference volume can be specified with --like to define the output sampling grid.

OPTIONS

--verbose

Print progress information during processing.

--clobber

Overwrite existing output files.

--like <mnc>

Specify a reference MINC volume whose sampling grid defines the output grid geometry (extent, step, and start values).

--step <f>

Isotropic step size in millimetres for the output grid.

--exact

Preserve exact grid values without smoothing or interpolation artifacts.

--invert

Invert the transformation before writing the output.

EXAMPLES

Normalize an XFM to a uniform grid:

xfm_normalize.pl input.xfm output.xfm

Normalize with a specific step size and reference volume:

xfm_normalize.pl input.xfm output.xfm --step 1.0 --like reference.mnc

Normalize and invert a grid transform:

xfm_normalize.pl input.xfm output.xfm --invert --clobber --verbose

AUTHOR

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

xfm2def(1), xfmconcat(1)