<?xml version="1.0" encoding="utf-8"?>
<executable>
<category>
CMTK.Registration
</category>
<title>
Rigid and affine registration
</title>
<description>
This program performs rigid and affine image registration using multi-resolution optimization of voxel-based image similarity measures.
</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>
Automation
</label>
<description>
Automation Options
</description>
<integer>
<default>
0
</default>
<description>
Automatic optimization and resolution parameter generation for &lt;n&gt; levels
</description>
<name>
auto_multi_levels
</name>
<label>
auto_multi_levels
</label>
<longflag>
--auto_multi_levels
</longflag>

</integer>

</parameters>
<parameters>
<label>
Optimization
</label>
<description>
Optimization settings
</description>
<double>
<default>
8
</default>
<description>
Exploration [initial optimizer step size]
</description>
<name>
exploration
</name>
<label>
exploration
</label>
<flag>
-e
</flag>
<longflag>
--exploration
</longflag>

</double>
<double>
<default>
0.1
</default>
<description>
Accuracy [final optimizer step size]
</description>
<name>
accuracy
</name>
<label>
accuracy
</label>
<flag>
-a
</flag>
<longflag>
--accuracy
</longflag>

</double>
<double>
<default>
0.5
</default>
<description>
Factor for search step size reduction. Must be &gt; 0.0 and &lt; 1.0
</description>
<name>
stepfactor
</name>
<label>
stepfactor
</label>
<flag>
-f
</flag>
<longflag>
--stepfactor
</longflag>

</double>
<double>
<default>
0
</default>
<description>
Optional threshold to terminate optimization (level) if relative change of target function drops below this value.
</description>
<name>
delta_f_threshold
</name>
<label>
delta_f_threshold
</label>
<longflag>
--delta_f_threshold
</longflag>

</double>

</parameters>
<parameters>
<label>
Resolution
</label>
<description>
Image resolution parameters
</description>
<double>
<default>
1
</default>
<description>
Image sampling (finest resampled image resolution)
</description>
<name>
sampling
</name>
<label>
sampling
</label>
<flag>
-s
</flag>
<longflag>
--sampling
</longflag>

</double>
<double>
<default>
-1
</default>
<description>
Upper limit for image sampling in multiresolution hierarchy
</description>
<name>
coarsest
</name>
<label>
coarsest
</label>
<longflag>
--coarsest
</longflag>

</double>
<boolean>
<description>
Do not use original data in full resolution, omit final stage in multiresolution hierarchy, thus reducing computation time.
</description>
<name>
omit_original_data
</name>
<label>
omit_original_data
</label>
<longflag>
--omit_original_data
</longflag>

</boolean>

</parameters>
<parameters>
<label>
Transformation
</label>
<description>
Transformation parameters
</description>
<integer-vector multiple="true">
<description>
Add number of degrees of freedom [can be repeated]
</description>
<name>
dofs
</name>
<label>
dofs
</label>
<longflag>
--dofs
</longflag>

</integer-vector>
<integer-vector multiple="true">
<description>
Add number of degrees of freedom for final level only [can be repeated]
</description>
<name>
dofs_final
</name>
<label>
dofs_final
</label>
<longflag>
--dofs_final
</longflag>

</integer-vector>
<boolean>
<description>
Do not auto-switch reference and floating image for improved computational performance
</description>
<name>
no_switch
</name>
<label>
no_switch
</label>
<flag>
-n
</flag>
<longflag>
--no_switch
</longflag>

</boolean>
<boolean>
<description>
Initialized transformation by translating floating image FOV center onto reference image FOV center
</description>
<name>
initxlate
</name>
<label>
initxlate
</label>
<flag>
-i
</flag>
<longflag>
--initxlate
</longflag>

</boolean>
<transform fileExtensions=".txt">
<channel>
input
</channel>
<default>

</default>
<description>
Initialize transformation from given path
</description>
<name>
initial
</name>
<label>
initial
</label>
<longflag>
--initial
</longflag>

</transform>
<boolean>
<description>
Invert initial transformation before initializing registration
</description>
<name>
initial_is_inverse
</name>
<label>
initial_is_inverse
</label>
<longflag>
--initial_is_inverse
</longflag>

</boolean>

</parameters>
<parameters>
<label>
Image data
</label>
<description>
Image data
</description>
<string-enumeration>
<default>
nmi
</default>
<element>
nmi
</element>
<element>
mi
</element>
<element>
cr
</element>
<element>
msd
</element>
<element>
ncc
</element>
<description>
Registration metric for motion estimation by image-to-image registration.
</description>
<name>
registration_metric
</name>
<label>
registration_metric
</label>
<longflag>
--registration_metric
</longflag>

</string-enumeration>
<boolean>
<description>
Match floating image histogram to reference image histogram.
</description>
<name>
match_histograms
</name>
<label>
match_histograms
</label>
<longflag>
--match_histograms
</longflag>

</boolean>

</parameters>
<parameters>
<label>
SlicerImport
</label>
<description>
Import Results into Slicer
</description>
<transform fileExtensions=".txt" reference="FloatingImage">
<channel>
output
</channel>
<default>

</default>
<description>
Output path for final transformation in ITK format
</description>
<name>
out_itk
</name>
<label>
out_itk
</label>
<longflag>
--out_itk
</longflag>

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

</default>
<description>
Write reformatted floating image.
</description>
<name>
write_reformatted
</name>
<label>
write_reformatted
</label>
<longflag>
--write_reformatted
</longflag>

</image>

</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 new registration and/or reformatted image.
</description>
<name>
db
</name>
<label>
db
</label>
<longflag>
--db
</longflag>

</string>

</parameters>

</executable>

