.TH filter "1" "Jan 25 2019" "CMTK 3.3.1p1" "The Computational Morphometry Toolkit"
.SH NAME
filter \- Filter a volume image
.SH SYNOPSIS
filter [options] input output
filter [options] [-s,--studholme] input output average subject img0 [img1...]
filter [options] [-R,--rohlfing] input output subject
.SH DESCRIPTION
This tool applies spatial filtering operators, including cnotent-sensitive opersators, based on selective Gaussian kernels.
.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\-\-gaussian\fR \fI<float>\fR, \fB\-g\fR \fI<float>\fR
Gaussian filter width (sigma)
.B [Default: disabled]
.TP 5
\fB\-\-radius\fR \fI<float>\fR, \fB\-r\fR \fI<float>\fR
Filter radius (truncated outside)
.B [Default: 2]
.TP 5
\fB\-\-mask\fR \fI<string>\fR, \fB\-m\fR \fI<string>\fR
Binary mask file name
.B [Default: NONE]
.TP 5
\fB\-\-studholme\fR, \fB\-s\fR
Use Studholme's consistent filtering
.TP 5
\fB\-\-bin-width\fR \fI<float>\fR, \fB\-b\fR \fI<float>\fR
Intensity bin width for consistent filtering
.B [Default: 10]
.TP 5
\fB\-\-rohlfing\fR, \fB\-R\fR
Use Rohlfing's single-image consistent filtering
.TP 5
\fB\-\-intensity-gaussian\fR \fI<float>\fR, \fB\-G\fR \fI<float>\fR
Intensity gaussian sigma for consistent filtering
.B [Default: 0]
.SS Image/Transformation Database
.TP 5
\fB\-\-db\fR \fI<string>\fR
Path to image/transformation database that should be updated with the newly created image.
.B [Default: NONE]
.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.