<?xml version="1.0" encoding="utf-8"?>
<executable>
<category>
CMTK.Artifact Correction
</category>
<title>
Fix interleaved motion using inverse interpolation
</title>
<description>
This tool splits an interleaved input image into the pass images, co-registers them, and reconstructs a motion-corrected image
</description>
<license>
http://www.fsf.org/licensing/licenses/gpl.html
</license>
<contributor>
Torsten Rohlfing
</contributor>
<acknowledgements>
CMTK is supported by the National Institute of Biomedical Imaging and BioEngineering under Grant EB008381
</acknowledgements>
<documentation-url>
https://neuro.sri.com/cmtk/wiki/
</documentation-url>
<version>
1.1.3-svn
</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="scalar">
<channel>
output
</channel>
<name>
OutputImage
</name>
<label>
OutputImage
</label>
<description>
Output image path
</description>
<index>
1
</index>

</image>

</parameters>
<parameters>
<label>
interleave
</label>
<description>
Interleaving Options
</description>
<string-enumeration>
<default>
guess-from-input
</default>
<element>
guess-from-input
</element>
<element>
axial
</element>
<element>
sagittal
</element>
<element>
coronal
</element>
<element>
interleave-x
</element>
<element>
interleave-y
</element>
<element>
interleave-z
</element>
<description>
Define interleave axis: this is the through-slice direction of the acquisition.
</description>
<name>
interleave_axis
</name>
<label>
interleave_axis
</label>
<longflag>
--interleave_axis
</longflag>

</string-enumeration>
<integer>
<default>
2
</default>
<description>
Number of interleaved passes
</description>
<name>
passes
</name>
<label>
passes
</label>
<flag>
-p
</flag>
<longflag>
--passes
</longflag>

</integer>
<boolean multiple="true">
<default>
false
</default>
<description>
Set contribution weight for a pass in the form 'pass:weight'
</description>
<name>
pass_weight
</name>
<label>
pass_weight
</label>
<flag>
-W
</flag>
<longflag>
--pass_weight
</longflag>

</boolean>

</parameters>
<parameters>
<label>
motion
</label>
<description>
Motion Correction / Registration Options
</description>
<image type="scalar">
<channel>
input
</channel>
<default>

</default>
<description>
Use a separate high-resolution reference image for registration
</description>
<name>
reference_image
</name>
<label>
reference_image
</label>
<flag>
-R
</flag>
<longflag>
--reference_image
</longflag>

</image>
<string-enumeration>
<default>
msd
</default>
<element>
nmi
</element>
<element>
mi
</element>
<element>
cr
</element>
<element>
msd
</element>
<element>
cc
</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>
<file>
<channel>
input
</channel>
<default>

</default>
<description>
Path of file from which to import transformations between passes.
</description>
<name>
import_xforms_path
</name>
<label>
import_xforms_path
</label>
<longflag>
--import_xforms_path
</longflag>

</file>
<file>
<channel>
output
</channel>
<default>

</default>
<description>
Path of file to which to export transformations between passes.
</description>
<name>
export_xforms_path
</name>
<label>
export_xforms_path
</label>
<longflag>
--export_xforms_path
</longflag>

</file>
<double>
<default>
0.5
</default>
<description>
Standard deviation of Gaussian kernel for volume injection in multiples of pixel size in each direction.
</description>
<name>
injection_kernel_sigma
</name>
<label>
injection_kernel_sigma
</label>
<flag>
-S
</flag>
<longflag>
--injection_kernel_sigma
</longflag>

</double>
<double>
<default>
2
</default>
<description>
Truncation radius factor of injection kernel. The kernel is truncated at sigma*radius, where sigma is the kernel standard deviation.
</description>
<name>
injection_kernel_radius
</name>
<label>
injection_kernel_radius
</label>
<flag>
-r
</flag>
<longflag>
--injection_kernel_radius
</longflag>

</double>

</parameters>
<parameters>
<label>
invint
</label>
<description>
Inverse Interpolation Options
</description>
<string-enumeration>
<default>
cubic
</default>
<element>
cubic
</element>
<element>
linear
</element>
<element>
hamming-sinc
</element>
<element>
cosine-sinc
</element>
<description>
Kernel for the inverse interpolation reconstruction
</description>
<name>
inverse_interpolation_kernel
</name>
<label>
inverse_interpolation_kernel
</label>
<longflag>
--inverse_interpolation_kernel
</longflag>

</string-enumeration>
<boolean>
<description>
Use fourth-order (rather than second-order) error for optimization.
</description>
<name>
fourth_order_error
</name>
<label>
fourth_order_error
</label>
<flag>
-f
</flag>
<longflag>
--fourth_order_error
</longflag>

</boolean>
<integer>
<default>
20
</default>
<description>
Maximum number of inverse interpolation iterations
</description>
<name>
num_iterations
</name>
<label>
num_iterations
</label>
<flag>
-n
</flag>
<longflag>
--num_iterations
</longflag>

</integer>
<boolean>
<description>
Turn off regional intensity truncatrion
</description>
<name>
no_truncation
</name>
<label>
no_truncation
</label>
<flag>
-T
</flag>
<longflag>
--no_truncation
</longflag>

</boolean>

</parameters>
<parameters>
<label>
output
</label>
<description>
Output Options
</description>
<image type="scalar">
<channel>
output
</channel>
<default>

</default>
<description>
Write initial volume injection image to path
</description>
<name>
write_injected_image
</name>
<label>
write_injected_image
</label>
<longflag>
--write_injected_image
</longflag>

</image>
<boolean>
<description>
Write output images as floating point [default: same as input]
</description>
<name>
write_images_as_float
</name>
<label>
write_images_as_float
</label>
<flag>
-F
</flag>
<longflag>
--write_images_as_float
</longflag>

</boolean>

</parameters>

</executable>

