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mrbias - MR Image Intensity Bias Field Correction

mrbias(1) The Computational Morphometry Toolkit mrbias(1)

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.
Sep 11 2017 CMTK 3.3.1