Man page - cmtk-mrbias(1)

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Manual

mrbias

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
Global Toolkit Options (these are shared by all CMTK tools)
Bias Field Parameterization
Input Image Preprocessing
Entropy Estimation Settings
Optimization Algorithm Settings
Input and Output Options
Image/Transformation Database
AUTHORS
LICENSE
BUGS
ACKNOWLEDGMENTS

NAME

mrbias - MR Image Intensity Bias Field Correction

SYNOPSIS

mrbias InputImage OutputImage

DESCRIPTION

This program corrects intensity inhomogeneity artifacts in MR images using a bias field estimated via entropy minimization.

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.

--xml

Write command line syntax specification in XML markup (for Slicer integration).

--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).

Bias Field Parameterization

--degree-add <integer> , -A <integer>

Polynomial degree for additive correction. [Default: 0]

--degree-mul <integer> , -M <integer>

Polynomial degree for multiplicative correction. [Default: 2]

--incremental , -I

Incrementally increase polynomial degrees.

Input Image Preprocessing

--set-padding-value <double>

Set padding value for input intensity image. Pixels with this value will be ignored. [Default: disabled]

--mask <labelmap-path> , -m <labelmap-path>

Binary mask image filename. [Default: NONE]

--thresh-min <float> , -t <float>

Minimum intensity threshold for image foreground. [Default: disabled]

--thresh-max <float> , -T <float>

Minimum intensity threshold for image foreground. [Default: disabled]

--thresh-auto

Automatic minimum intensity threshold selection for image foreground using an estimate of image noise level.

--thresh-otsu-nbins <integer>

If this is a positive integer, use automatic minimum intensity threshold selection for image foreground by Otsu thresholding with given number of histogram bins. [Default: 0]

Entropy Estimation Settings

--log-intensities , -L

Use log intensities for entropy estimation.

--sampling-density <float> , -s <float>

Image sampling density to use only subset of image pixels [Default: disabled]

--num-bins <integer> , -n <integer>

Number of histogram bins for entropy estimation [Default: 256]

Optimization Algorithm Settings

--step-max <double>

Maximum (initial) search step size. [Default: 1]

--step-min <double>

Minimum (final) search step size. [Default: 0.1]

Input and Output Options

--import-bias-add <image-path>

Import additive bias field (disables optimization). [Default: NONE]

--import-bias-mul <image-path>

Import multiplicative bias field (disables optimization). [Default: NONE]

--write-bias-add <image-path>

File name for output of additive bias field. [Default: NONE]

--write-bias-mul <image-path>

File name for output of multiplicative bias field. [Default: NONE]

--write-float , -F

Write output image with floating point pixel data. If this is not given, the input data type is used.

Image/Transformation Database

--db <string>

Path to image/transformation database that should be updated with the newly created image. [Default: NONE]

AUTHORS

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

LICENSE

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

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.