<?xml version="1.0" encoding="utf-8"?>
<executable>
<category>
CMTK.Segmentation
</category>
<title>
Levelset segmentation
</title>
<description>
Levelset-type segmentation of foreground/background using minimum regional variance energy
</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>
General
</label>
<description>
General Parameters
</description>
<image type="scalar">
<channel>
input
</channel>
<name>
InputImage
</name>
<label>
InputImage
</label>
<description>
Input image path
</description>
<index>
0
</index>

</image>
<image type="label">
<channel>
output
</channel>
<name>
OutputImage
</name>
<label>
OutputImage
</label>
<description>
Output image path
</description>
<index>
1
</index>

</image>
<boolean>
<description>
Binarize levelset and write as byte mask, rather than write floating-point levelset function itself.
</description>
<name>
binarize
</name>
<label>
binarize
</label>
<flag>
-b
</flag>
<longflag>
--binarize
</longflag>

</boolean>

</parameters>
<parameters advanced="true">
<label>
Levelset Initialization
</label>
<description>
These parameters control the initialization of the levelset function
</description>
<double>
<default>
1
</default>
<description>
Scale factor to reduce or increase the size of the initial foreground region sphere.
</description>
<name>
scale_initial_sphere
</name>
<label>
scale_initial_sphere
</label>
<longflag>
--scale_initial_sphere
</longflag>

</double>

</parameters>
<parameters advanced="true">
<label>
Levelset Evolution Parameters
</label>
<description>
These parameters control the evolution of the levelset function
</description>
<integer>
<default>
100
</default>
<description>
Maximum number of iterations
</description>
<name>
iterations
</name>
<label>
iterations
</label>
<flag>
-n
</flag>
<longflag>
--iterations
</longflag>

</integer>
<boolean>
<description>
Force given number of iterations, even when convergence has been detected
</description>
<name>
force_iterations
</name>
<label>
force_iterations
</label>
<flag>
-f
</flag>
<longflag>
--force_iterations
</longflag>

</boolean>
<double>
<default>
2
</default>
<description>
Gaussian filter sigma in world coordinate units (e.g., mm)
</description>
<name>
filter_sigma
</name>
<label>
filter_sigma
</label>
<flag>
-s
</flag>
<longflag>
--filter_sigma
</longflag>

</double>
<double>
<default>
0.1
</default>
<description>
Time constant for levelset evolution; must be &gt; 0; larger is faster
</description>
<name>
delta
</name>
<label>
delta
</label>
<flag>
-d
</flag>
<longflag>
--delta
</longflag>

</double>
<double>
<default>
1
</default>
<description>
Levelset threshold: levelset function is truncated at +/- this value
</description>
<name>
levelset_threshold
</name>
<label>
levelset_threshold
</label>
<flag>
-t
</flag>
<longflag>
--levelset_threshold
</longflag>

</double>

</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>

