.TH mrbias "1" "Jan 25 2019" "CMTK 3.3.1p1" "The Computational Morphometry Toolkit"
.SH NAME
mrbias \- MR Image Intensity Bias Field Correction
.SH SYNOPSIS
\fBmrbias\fR InputImage OutputImage 
.SH DESCRIPTION
This program corrects intensity inhomogeneity artifacts in MR images using a bias field estimated via entropy minimization.
.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\-\-xml\fR
Write command line syntax specification in XML markup (for Slicer integration).
.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 Bias Field Parameterization
.TP 5
\fB\-\-degree-add\fR \fI<integer>\fR, \fB\-A\fR \fI<integer>\fR
Polynomial degree for additive correction.
.B [Default: 0]
.TP 5
\fB\-\-degree-mul\fR \fI<integer>\fR, \fB\-M\fR \fI<integer>\fR
Polynomial degree for multiplicative correction.
.B [Default: 2]
.TP 5
\fB\-\-incremental\fR, \fB\-I\fR
Incrementally increase polynomial degrees.
.SS Input Image Preprocessing
.TP 5
\fB\-\-set-padding-value\fR \fI<double>\fR
Set padding value for input intensity image. Pixels with this value will be ignored.
.B [Default: disabled]
.TP 5
\fB\-\-mask\fR \fI<labelmap-path>\fR, \fB\-m\fR \fI<labelmap-path>\fR
Binary mask image filename.
.B [Default: NONE]
.TP 5
\fB\-\-thresh-min\fR \fI<float>\fR, \fB\-t\fR \fI<float>\fR
Minimum intensity threshold for image foreground.
.B [Default: disabled]
.TP 5
\fB\-\-thresh-max\fR \fI<float>\fR, \fB\-T\fR \fI<float>\fR
Minimum intensity threshold for image foreground.
.B [Default: disabled]
.TP 5
\fB\-\-thresh-auto\fR
Automatic minimum intensity threshold selection for image foreground using an estimate of image noise level.
.TP 5
\fB\-\-thresh-otsu-nbins\fR \fI<integer>\fR
If this is a positive integer, use automatic minimum intensity threshold selection for image foreground by Otsu thresholding with given number of histogram bins.
.B [Default: 0]
.SS Entropy Estimation Settings
.TP 5
\fB\-\-log-intensities\fR, \fB\-L\fR
Use log intensities for entropy estimation.
.TP 5
\fB\-\-sampling-density\fR \fI<float>\fR, \fB\-s\fR \fI<float>\fR
Image sampling density to use only subset of image pixels
.B [Default: disabled]
.TP 5
\fB\-\-num-bins\fR \fI<integer>\fR, \fB\-n\fR \fI<integer>\fR
Number of histogram bins for entropy estimation
.B [Default: 256]
.SS Optimization Algorithm Settings
.TP 5
\fB\-\-step-max\fR \fI<double>\fR
Maximum (initial) search step size.
.B [Default: 1]
.TP 5
\fB\-\-step-min\fR \fI<double>\fR
Minimum (final) search step size.
.B [Default: 0.1]
.SS Input and Output Options
.TP 5
\fB\-\-import-bias-add\fR \fI<image-path>\fR
Import additive bias field (disables optimization).
.B [Default: NONE]
.TP 5
\fB\-\-import-bias-mul\fR \fI<image-path>\fR
Import multiplicative bias field (disables optimization).
.B [Default: NONE]
.TP 5
\fB\-\-write-bias-add\fR \fI<image-path>\fR
File name for output of additive bias field.
.B [Default: NONE]
.TP 5
\fB\-\-write-bias-mul\fR \fI<image-path>\fR
File name for output of multiplicative bias field.
.B [Default: NONE]
.TP 5
\fB\-\-write-float\fR, \fB\-F\fR
Write output image with floating point pixel data. If this is not given, the input data type is used.
.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.