table of contents
| 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, Daniel B. Russakoff, and Yaroslav Halchenko
LICENSE¶
BUGS¶
Report bugs at http://nitrc.org/projects/cmtk/
ACKNOWLEDGMENTS¶
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.
| Mar 20 2024 | CMTK 3.3.1p2 |