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.
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, and Daniel B. Russakoff
LICENSE
http://www.fsf.org/licensing/licenses/gpl.html
BUGS
Report bugs at http://nitrc.org/projects/cmtk/
ACKNOWLEDGMENTS
From April 2009 through September 2011, CMTK Development and Maintenance was supported by the National Institute of Biomedical Imaging and
Bioengineering under Grant No.R01 EB008381 (PI: Torsten Rohlfing).
CMTK 2.2.2 Jul 20 2012 mrbias(1)