jidb - Fix interleaved motion using joint iterative deblurring

       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)

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

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

       This  tool  splits an interleaved input image into the pass images, co-registers them, and reconstructs a
       motion-corrected image

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

       jidb - Fix interleaved motion using joint iterative deblurring

GlobalToolkitOptions(thesearesharedbyallCMTKtools)--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).

   InterleavingOptions--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 [Thisisthedefault]--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'

   MotionCorrection/RegistrationOptions--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 [Thisisthedefault]--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]VolumeInjectionOptions--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]DeblurringOptions--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]OptimizationOptions--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]OutputOptions--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]

       jidb [options] inImage outImage