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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

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