Provided by: cmtk_3.3.1-1.2build1_amd64 bug


       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.

       --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
            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]

            --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 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

       --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
            Kernel  for  the  inverse  interpolation  reconstruction  Supported  values:   "box",
            "gaussian", or use one of the following:

                 Box-shaped PSF

                 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]


       Torsten  Rohlfing,  with  contributions  from  Michael  P. Hasak, Greg Jefferis, Calvin R.
       Maurer, Daniel B. Russakoff, and Yaroslav Halchenko



       Report bugs at


       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.