cmtk-jidb - Online in the Cloud

PROGRAM:

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 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, Daniel B. Russakoff, and Yaroslav Halchenko

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