Provided by: cmtk_3.3.1-1.2build1_amd64 bug


       mrbias - MR Image Intensity Bias Field Correction


       mrbias InputImage OutputImage


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


   Global Toolkit Options (these are shared by all CMTK tools)
            Write list of basic command line options to standard output.

            Write complete list of basic and advanced command line options to standard output.

            Write list of command line options to standard output in MediaWiki markup.

            Write man page source in 'nroff' markup to standard output.

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

            Write toolkit version to standard output.

            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]

            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]


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



       Report bugs at


       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.