---
name: "cmtk-mrbias"
section: "1"
platform: "linux"
package: "cmtk"
version: "3.3.1p2+dfsg-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cmtk-mrbias"
---

# cmtk-mrbias(1)

MR Image Intensity Bias Field Correction

## 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.