mrbias - MR Image Intensity Bias Field Correction

       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.

CMTK 3.3.1p2                                       Feb 26 2025                                         mrbias(1)

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

       Report bugs at http://nitrc.org/projects/cmtk/

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

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

       mrbias - MR Image Intensity Bias Field Correction

GlobalToolkitOptions(thesearesharedbyallCMTKtools)--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).

   BiasFieldParameterization--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.

   InputImagePreprocessing--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]EntropyEstimationSettings--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]OptimizationAlgorithmSettings--step-max<double>
            Maximum (initial) search step size.  [Default:1]--step-min<double>
            Minimum (final) search step size.  [Default:0.1]InputandOutputOptions--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/TransformationDatabase--db<string>
            Path to image/transformation  database  that  should  be  updated  with  the  newly  created  image.
            [Default:NONE]

mrbias InputImage OutputImage