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.