cmtk-avg_adm (1)

avg_adm [options] list0 [list1 ...]

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

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

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

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

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

CMTK is developed with support from the NIAAA under Grant AA021697, National Consortium on Alcohol and Neurodevelopment in Adolescence (N-CANDA): Data Integration Component. From April 2009 through September 2011, CMTK development and maintenance was supported by the NIBIB under Grant EB008381.