<?xml version="1.0" encoding="utf-8"?>
<executable>
<category>
CMTK.Artifact Correction
</category>
<title>
MR Image Intensity Bias Field Correction
</title>
<description>
This program corrects intensity inhomogeneity artifacts in MR images using a bias field estimated via entropy minimization.
</description>
<license>
http://www.fsf.org/licensing/licenses/gpl.html
</license>
<contributor>
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
</contributor>
<acknowledgements>
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.
</acknowledgements>
<documentation-url>
https://neuro.sri.com/cmtk/wiki/
</documentation-url>
<version>
</version>
<parameters>
<label>
Bias Field
</label>
<description>
Bias Field Parameterization
</description>
<integer>
<default>
0
</default>
<description>
Polynomial degree for additive correction.
</description>
<name>
degree_add
</name>
<label>
degree_add
</label>
<flag>
-A
</flag>
<longflag>
--degree_add
</longflag>

</integer>
<integer>
<default>
2
</default>
<description>
Polynomial degree for multiplicative correction.
</description>
<name>
degree_mul
</name>
<label>
degree_mul
</label>
<flag>
-M
</flag>
<longflag>
--degree_mul
</longflag>

</integer>
<boolean>
<description>
Incrementally increase polynomial degrees.
</description>
<name>
incremental
</name>
<label>
incremental
</label>
<flag>
-I
</flag>
<longflag>
--incremental
</longflag>

</boolean>

</parameters>
<parameters>
<label>
Preprocessing
</label>
<description>
Input Image Preprocessing
</description>
<double>
<description>
Set padding value for input intensity image. Pixels with this value will be ignored.
</description>
<name>
set_padding_value
</name>
<label>
set_padding_value
</label>
<longflag>
--set_padding_value
</longflag>

</double>
<image type="label">
<channel>
input
</channel>
<default>

</default>
<description>
Binary mask image filename.
</description>
<name>
mask
</name>
<label>
mask
</label>
<flag>
-m
</flag>
<longflag>
--mask
</longflag>

</image>
<float>
<description>
Minimum intensity threshold for image foreground.
</description>
<name>
thresh_min
</name>
<label>
thresh_min
</label>
<flag>
-t
</flag>
<longflag>
--thresh_min
</longflag>

</float>
<float>
<description>
Minimum intensity threshold for image foreground.
</description>
<name>
thresh_max
</name>
<label>
thresh_max
</label>
<flag>
-T
</flag>
<longflag>
--thresh_max
</longflag>

</float>
<boolean>
<description>
Automatic minimum intensity threshold selection for image foreground using an estimate of image noise level.
</description>
<name>
thresh_auto
</name>
<label>
thresh_auto
</label>
<longflag>
--thresh_auto
</longflag>

</boolean>
<integer>
<default>
0
</default>
<description>
If this is a positive integer, use automatic minimum intensity threshold selection for image foreground by Otsu thresholding with given number of histogram bins.
</description>
<name>
thresh_otsu_nbins
</name>
<label>
thresh_otsu_nbins
</label>
<longflag>
--thresh_otsu_nbins
</longflag>

</integer>

</parameters>
<parameters advanced="true">
<label>
Entropy Estimation
</label>
<description>
Entropy Estimation Settings
</description>
<boolean>
<description>
Use log intensities for entropy estimation.
</description>
<name>
log_intensities
</name>
<label>
log_intensities
</label>
<flag>
-L
</flag>
<longflag>
--log_intensities
</longflag>

</boolean>
<float>
<description>
Image sampling density to use only subset of image pixels
</description>
<name>
sampling_density
</name>
<label>
sampling_density
</label>
<flag>
-s
</flag>
<longflag>
--sampling_density
</longflag>

</float>
<integer>
<default>
256
</default>
<description>
Number of histogram bins for entropy estimation
</description>
<name>
num_bins
</name>
<label>
num_bins
</label>
<flag>
-n
</flag>
<longflag>
--num_bins
</longflag>

</integer>

</parameters>
<parameters advanced="true">
<label>
Optimization
</label>
<description>
Optimization Algorithm Settings
</description>
<double>
<default>
1
</default>
<description>
Maximum (initial) search step size.
</description>
<name>
step_max
</name>
<label>
step_max
</label>
<longflag>
--step_max
</longflag>

</double>
<double>
<default>
0.1
</default>
<description>
Minimum (final) search step size.
</description>
<name>
step_min
</name>
<label>
step_min
</label>
<longflag>
--step_min
</longflag>

</double>

</parameters>
<parameters advanced="true">
<label>
I/O
</label>
<description>
Input and Output Options
</description>
<image type="scalar">
<channel>
input
</channel>
<default>

</default>
<description>
Import additive bias field (disables optimization).
</description>
<name>
import_bias_add
</name>
<label>
import_bias_add
</label>
<longflag>
--import_bias_add
</longflag>

</image>
<image type="scalar">
<channel>
input
</channel>
<default>

</default>
<description>
Import multiplicative bias field (disables optimization).
</description>
<name>
import_bias_mul
</name>
<label>
import_bias_mul
</label>
<longflag>
--import_bias_mul
</longflag>

</image>
<image type="scalar">
<channel>
output
</channel>
<default>

</default>
<description>
File name for output of additive bias field.
</description>
<name>
write_bias_add
</name>
<label>
write_bias_add
</label>
<longflag>
--write_bias_add
</longflag>

</image>
<image type="scalar">
<channel>
output
</channel>
<default>

</default>
<description>
File name for output of multiplicative bias field.
</description>
<name>
write_bias_mul
</name>
<label>
write_bias_mul
</label>
<longflag>
--write_bias_mul
</longflag>

</image>
<boolean>
<description>
Write output image with floating point pixel data. If this is not given, the input data type is used.
</description>
<name>
write_float
</name>
<label>
write_float
</label>
<flag>
-F
</flag>
<longflag>
--write_float
</longflag>

</boolean>

</parameters>
<parameters>
<label>
Database
</label>
<description>
Image/Transformation Database
</description>
<string>
<channel>
input
</channel>
<default>

</default>
<description>
Path to image/transformation database that should be updated with the newly created image.
</description>
<name>
db
</name>
<label>
db
</label>
<longflag>
--db
</longflag>

</string>

</parameters>

</executable>

