.TH avg_adm "1" "Jan 25 2019" "CMTK 3.3.1p1" "The Computational Morphometry Toolkit"
.SH NAME
avg_adm \- Average using ADM
.SH SYNOPSIS
avg_adm [options] list0 [list1 ...]
.SH DESCRIPTION
Compute average-shape average-intensity images and deformation maps using an active deformation model.
.SH OPTIONS
.SS Global Toolkit Options (these are shared by all CMTK tools)
.TP 5
\fB\-\-help\fR
Write list of basic command line options to standard output.
.TP 5
\fB\-\-help-all\fR
Write complete list of basic and advanced command line options to standard output.
.TP 5
\fB\-\-wiki\fR
Write list of command line options to standard output in MediaWiki markup.
.TP 5
\fB\-\-man\fR
Write man page source in 'nroff' markup to standard output.
.TP 5
\fB\-\-version\fR
Write toolkit version to standard output.
.TP 5
\fB\-\-echo\fR
Write the current command line to standard output.
.TP 5
\fB\-\-verbose-level\fR \fI<integer>\fR
Set verbosity level.
.TP 5
\fB\-\-verbose\fR, \fB\-v\fR
Increment verbosity level by 1 (deprecated; supported for backward compatibility).
.TP 5
\fB\-\-threads\fR \fI<integer>\fR
Set maximum number of parallel threads (for POSIX threads and OpenMP).
.SS Main Options
.TP 5
\fB\-\-label\fR, \fB\-l\fR
Label mode (as opposed to grey)
.TP 5
\fB\-\-set-padding\fR \fI<float>\fR
Set padding value in input files
.B [Default: disabled]
.TP 5
\fB\-\-replace-padding\fR \fI<float>\fR
Replace padding value in input files
.B [Default: disabled]
.TP 5
\fB\-\-pad-out\fR \fI<double>\fR, \fB\-p\fR \fI<double>\fR
Padding value for output file
.B [Default: disabled]
.TP 5
\fB\-\-jacobian\fR, \fB\-j\fR
Average Jacobian determinants of deformations.
.TP 5
\fB\-\-auto-scale\fR, \fB\-a\fR
Auto-scale image intensities
.TP 5
\fB\-\-char\fR
Output is 8 bits, signed [default: automatic]
.TP 5
\fB\-\-byte\fR
Output is 8 bits, unsigned
.TP 5
\fB\-\-short\fR
Output is 16 bits, signed
.TP 5
\fB\-\-ushort\fR
Output is 16 bits, unsigned
.TP 5
\fB\-\-int\fR
Output is 32 bits signed
.TP 5
\fB\-\-float\fR
Output is 32 bits floating point
.TP 5
\fB\-\-double\fR
Output is 64 bits floating point

.TP 5
\fB\-\-no-scale-model\fR, \fB\-S\fR
Exclude scale from statistical deformation model
.TP 5
\fB\-\-no-ref-model\fR, \fB\-R\fR
Exclude reference coordinate frame from deformation model
.TP 5
\fB\-\-no-ref-data\fR, \fB\-r\fR
Exclude reference data from averaging
.TP 5
\fB\-\-output\fR \fI<string>\fR, \fB\-o\fR \fI<string>\fR
Output file name [FORMAT:]path
.B [Default: NONE]
.TP 5
\fB\-\-input-warp\fR \fI<string>\fR, \fB\-I\fR \fI<string>\fR
Input file name for average warp
.B [Default: NONE]
.TP 5
\fB\-\-output-warp\fR \fI<string>\fR, \fB\-O\fR \fI<string>\fR
Output file name for average warp
.B [Default: NONE]
.TP 5
\fB\-\-with-affine\fR, \fB\-A\fR
Include affine component of first warp in output
.TP 5
\fB\-\-nn\fR
Use nearest neigbor interpolation
.TP 5
\fB\-\-cubic\fR
Use tri-cubic interpolation
.TP 5
\fB\-\-replace-from\fR \fI<string>\fR
Replace from pattern
.TP 5
\fB\-\-replace-to\fR \fI<string>\fR
Replace to pattern
.SH AUTHORS
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
.SH LICENSE
http://www.fsf.org/licensing/licenses/gpl.html
.SH BUGS
Report bugs at http://nitrc.org/projects/cmtk/
.SH 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.