TITLE:

     Fix interleaved motion using inverse interpolation


DESCRIPTION:

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


SYNTAX:

     [options] InputImage OutputImage 

  where

     InputImage =        Input image path

     OutputImage =       Output image path


LIST OF SUPPORTED 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.

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]

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)

  --num-iterations <integer>, -n <integer>
            Maximum number of inverse interpolation iterations
            [Default: 20]

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]


