NAME

       film - Fix interleaved motion using inverse interpolation

SYNOPSIS

       film InputImage OutputImage

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.

       --xml
            Write command line syntax specification in XML markup (for Slicer integration).

       --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).

   Input Options
       --padding-value <double>
            Set padding value for input image. Pixels with this value will be ignored.  [Default:
            disabled]

   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]

   Initial Volume Injection Options
       --injection-kernel-sigma <double>, -S <double>
            Standard deviation of Gaussian kernel for volume injection in multiples of pixel size
            in each direction.  [Default: 0.5]

       --injection-kernel-radius <double>, -r <double>
            Truncation  radius  factor  of  injection  kernel.  The  kernel   is   truncated   at
            sigma*radius, where sigma is the kernel standard deviation.  [Default: 2]

   Inverse Interpolation Options
       --inverse-interpolation-kernel
            Kernel  for  the  inverse  interpolation  reconstruction  Supported  values: "cubic",
            "linear", "hamming-sinc", "cosine-sinc", where the default is "cubic", or use one  of
            the following:

            --cubic, -C
                 Tricubic interpolation [This is the default]

            --linear, -L
                 Trilinear interpolation (faster but less accurate)

            --hamming-sinc, -H
                 Hamming-windowed sinc interpolation

            --cosine-sinc, -O
                 Cosine-windowed sinc interpolation (most accurate but slowest)

       --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]

   Reconstruction Regularization Options
       --l-norm-weight <double>
            Set constraint weight for Tikhonov-type L-Norm regularization (0 disables constraint)
            [Default: 0]

       --no-truncation, -T
            Turn off regional intensity truncatrion

   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.