film(1) 					       The Computational Morphometry Toolkit						   film(1)

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 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]

   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, 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 							   film(1)