NAME¶
jidb - Fix interleaved motion using joint iterative deblurring
SYNOPSIS¶
jidb [options] inImage outImage
DESCRIPTION¶
This tool splits an interleaved input image into the pass images, co-registers
them, and reconstructs a motion-corrected image
OPTIONS¶
- --help
- Write list of basic command line options to standard
output.
- --help-all
- Write complete list of basic and advanced command line
options to standard output.
- --wiki
- Write list of command line options to standard output in
MediaWiki markup.
- --man
- Write man page source in 'nroff' markup to standard
output.
- --version
- Write toolkit version to standard output.
- --echo
- 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).
Interleaving Options¶
- --interleave-axis
- Define interleave axis: this is the through-slice direction
of the acquisition. Supported values: "guess-from-input",
"axial", "sagittal", "coronal",
"interleave-x", "interleave-y",
"interleave-z", where the default is
"guess-from-input", or use one of the following:
- --guess-from-input
- Guess from input image [This is the default]
- --axial, -a
- Interleaved axial images
- --sagittal, -s
- Interleaved sagittal images
- --coronal, -c
- Interleaved coronal images
- --interleave-x, -x
- Interleaved along x axis
- --interleave-y, -y
- Interleaved along y axis
- --interleave-z, -z
- Interleaved along z axis
- --passes <integer>, -p
<integer>
- Number of interleaved passes [Default: 2]
- --pass-weight <string>, -W
<string>
- Set contribution weight for a pass in the form
'pass:weight'
Motion Correction / Registration Options¶
- --reference-image <image-path>,
-R <image-path>
- Use a separate high-resolution reference image for
registration [Default: NONE]
- --registration-metric
- Registration metric for motion estimation by image-to-image
registration. Supported values: "nmi", "mi",
"cr", "msd", "cc", where the default is
"msd", or use one of the following:
- --nmi
- Use Normalized Mutual Information for pass-to-refereence
registration
- --mi
- Use standard Mutual Information for pass-to-refereence
registration
- --cr
- Use Correlation Ratio for pass-to-refereence
registration
- --msd
- Use Mean Squared Differences for pass-to-refereence
registration [This is the default]
- --cc
- Use Cross-Correlation for pass-to-refereence
registration
- --import-xforms-path <path>
- Path of file from which to import transformations between
passes. [Default: NONE]
- --export-xforms-path <path>
- Path of file to which to export transformations between
passes. [Default: NONE]
Volume Injection Options¶
- --injection-kernel-sigma <double>,
-S <double>
- Standard deviation of Gaussian kernel for volume injection
[Default: 1]
- --injection-kernel-radius <integer>,
-r <integer>
- Truncation radius of injection kernel [Default:
4]
Deblurring Options¶
- --psf
- Kernel for the inverse interpolation reconstruction
Supported values: "box", "gaussian", or use one of the
following:
- --box
- Box-shaped PSF
- --gaussian
- Gaussian-shaped PSF
- --psf-scale <double>
- Set global scale factor for point spread function size,
which itself is derived from the input image. [Default: 1]
Optimization Options¶
- --fourth-order-error, -f
- Use fourth-order (rather than second-order) error for
optimization.
- --num-iterations <integer>, -n
<integer>
- Maximum number of inverse interpolation iterations
[Default: 20]
- --no-truncation, -T
- Turn off regional intensity truncatrion
- --l-norm-weight <double>
- Set constraint weight for Tikhonov-type L-Norm
regularization (0 disables constraint) [Default: 0]
Output Options¶
- --write-injected-image
<image-path>
- Write initial volume injection image to path [Default:
NONE]
- --write-images-as-float, -F
- Write output images as floating point [default: same as
input]
AUTHORS¶
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis,
Calvin R. Maurer, and Daniel B. Russakoff
LICENSE¶
http://www.fsf.org/licensing/licenses/gpl.html
BUGS¶
Report bugs at
http://nitrc.org/projects/cmtk/
ACKNOWLEDGMENTS¶
From April 2009 through September 2011, CMTK Development and Maintenance was
supported by the National Institute of Biomedical Imaging and Bioengineering
under Grant No.R01 EB008381 (PI: Torsten Rohlfing).