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)