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jidb(1) The Computational Morphometry Toolkit jidb(1)


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).

Interleaving Options

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
Number of interleaved passes [Default: 2]
Set contribution weight for a pass in the form 'pass:weight'

Motion Correction / Registration Options

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 following:
Use Normalized Mutual Information for pass-to-refereence registration
Use standard Mutual Information for pass-to-refereence registration
Use Correlation Ratio for pass-to-refereence registration
Use Mean Squared Differences for pass-to-refereence registration [This is the default]
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

Standard deviation of Gaussian kernel for volume injection [Default: 1]
Truncation radius of injection kernel [Default: 4]

Deblurring Options

Kernel for the inverse interpolation reconstruction Supported values: "box", "gaussian", or use one of the following:
Box-shaped PSF
Gaussian-shaped PSF
Set global scale factor for point spread function size, which itself is derived from the input image. [Default: 1]

Optimization Options

Use fourth-order (rather than second-order) error for optimization.
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) [Default: 0]

Output Options

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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CMTK is developed with support from the NIAAA under Grant AA021697, National Consortium on Alcohol and Neurodevelopment in Adolescence (N-CANDA): Data Integration Component. From April 2009 through September 2011, CMTK development and maintenance was supported by the NIBIB under Grant EB008381.

Jun 6 2022 CMTK 3.3.1p2