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

LICENSE

       http://www.fsf.org/licensing/licenses/gpl.html

BUGS

       Report bugs at http://nitrc.org/projects/cmtk/

ACKNOWLEDGMENTS

       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.

CMTK 3.3.1p2                                       Feb 26 2025                                           jidb(1)