avg_adm(1)					       The Computational Morphometry Toolkit						avg_adm(1)

NAME

       avg_adm - Average using ADM

SYNOPSIS

       avg_adm [options] list0 [list1 ...]

DESCRIPTION

       Compute average-shape average-intensity images and deformation maps using an active deformation model.

OPTIONS

   Global Toolkit Options (these are shared by all CMTK tools)
       --help
	    Write list of basic command line options to standard output.

       --help-all
	    Write complete list of basic and advanced command line options to standard output.

       --wiki
	    Write list of command line options to standard output in MediaWiki markup.

       --man
	    Write man page source in 'nroff' markup to standard output.

       --version
	    Write toolkit version to standard output.

       --echo
	    Write the current command line to standard output.

       --verbose-level <integer>
	    Set verbosity level.

       --verbose, -v
	    Increment verbosity level by 1 (deprecated; supported for backward compatibility).

       --threads <integer>
	    Set maximum number of parallel threads (for POSIX threads and OpenMP).

   Main Options
       --label, -l
	    Label mode (as opposed to grey)

       --set-padding <float>
	    Set padding value in input files [Default: disabled]

       --replace-padding <float>
	    Replace padding value in input files [Default: disabled]

       --pad-out <double>, -p <double>
	    Padding value for output file [Default: disabled]

       --jacobian, -j
	    Average Jacobian determinants of deformations.

       --auto-scale, -a
	    Auto-scale image intensities

       --char
	    Output is 8 bits, signed [default: automatic]

       --byte
	    Output is 8 bits, unsigned

       --short
	    Output is 16 bits, signed

       --ushort
	    Output is 16 bits, unsigned

       --int
	    Output is 32 bits signed

       --float
	    Output is 32 bits floating point

       --double
	    Output is 64 bits floating point

       --no-scale-model, -S
	    Exclude scale from statistical deformation model

       --no-ref-model, -R
	    Exclude reference coordinate frame from deformation model

       --no-ref-data, -r
	    Exclude reference data from averaging

       --output <string>, -o <string>
	    Output file name [FORMAT:]path [Default: NONE]

       --input-warp <string>, -I <string>
	    Input file name for average warp [Default: NONE]

       --output-warp <string>, -O <string>
	    Output file name for average warp [Default: NONE]

       --with-affine, -A
	    Include affine component of first warp in output

       --nn Use nearest neigbor interpolation

       --cubic
	    Use tri-cubic interpolation

       --replace-from <string>
	    Replace from pattern

       --replace-to <string>
	    Replace to pattern

AUTHORS

       Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, and Daniel B. Russakoff

LICENSE

       http://www.fsf.org/licensing/licenses/gpl.html

BUGS

       Report bugs at http://nitrc.org/projects/cmtk/

ACKNOWLEDGMENTS

       From  April 2009 through September 2011, CMTK Development and Maintenance was supported by the National Institute of Biomedical Imaging and
       Bioengineering under Grant No.R01 EB008381 (PI: Torsten Rohlfing).

CMTK 2.2.2							    Jul 20 2012 							avg_adm(1)