jidb(1) The Computational Morphometry Toolkit jidb(1)
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
Global Toolkit Options (these are shared by all CMTK tools)
--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 fol-
lowing:
--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).
CMTK 2.2.2 Jul 20 2012 jidb(1)