This is the command cmtk-jidb that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
jidb - Fix interleaved motion using joint iterative deblurring
jidb [options] inImage outImage
This tool splits an interleaved input image into the pass images, co-registers them, and
reconstructs a motion-corrected image
Global Toolkit Options (these are shared by all CMTK tools)
Write list of basic command line options to standard output.
Write complete list of basic and advanced command line options to standard output.
Write list of command line options to standard output in MediaWiki markup.
Write man page source in 'nroff' markup to standard output.
Write toolkit version to standard output.
Write the current command line to standard output.
Set verbosity level.
Increment verbosity level by 1 (deprecated; supported for backward compatibility).
Set maximum number of parallel threads (for POSIX threads and OpenMP).
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 image [This is the default]
Interleaved axial images
Interleaved sagittal images
Interleaved coronal images
Interleaved along x axis
Interleaved along y axis
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 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
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
Use Mean Squared Differences for pass-to-refereence registration [This is the
--cc Use Cross-Correlation for pass-to-refereence registration
Path of file from which to import transformations between passes. [Default: NONE]
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]
Kernel for the inverse interpolation reconstruction Supported values: "box",
"gaussian", or use one of the following:
Set global scale factor for point spread function size, which itself is derived from
the input image. [Default: 1]
Use fourth-order (rather than second-order) error for optimization.
--num-iterations <integer>, -n <integer>
Maximum number of inverse interpolation iterations [Default: 20]
Turn off regional intensity truncatrion
Set constraint weight for Tikhonov-type L-Norm regularization (0 disables constraint)
Write initial volume injection image to path [Default: NONE]
Write output images as floating point [default: same as input]
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R.
Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
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