Provided by: cmtk_3.0.0-1ubuntu1_amd64 bug


       epiunwarp - Unwarp Echo Planar Images


       epiunwarp InputImage1 InputImage2 OutputImage1 OutputImage2 OutputDField


       Correct  B0 field inhomogeneity-induced distortion in Echo Planar Images (e.g., diffusion-
       weighted images) using two images acquired with opposing phase encoding directions.


   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).

   Input Image Parameters
            Define the phase-encoded  image  coordinate  direction.   Supported  values:  "phase-
            encode-ap", "phase-encode-is", "phase-encode-lr", where the default is "phase-encode-
            ap", or use one of the following:

            --phase-encode-ap, -y
                 Anterior/posterior phase encoding (this is the most common case)  [This  is  the

            --phase-encode-is, -z
                 Top/bottom phase encoding (this is rare)

            --phase-encode-lr, -x
                 Lateral, left/right phase encoding (this is extremely rare)

            Use  this switch is the reverse phase-encoded image does not need to be flipped prior
            to unwarping. If normal and reverse phase-encoded image display  in  the  same  gross
            orientation  in  'triplanar',  then  flipping is not necessary and must be turned off
            using this switch.

   Optimization Parameters
            Disable initialization of unwarping by shifting each row to align the centers of mass
            of forward and reverse acquisition. Instead, use all-zero initial deformation field.

       --smooth-sigma-max <double>
            Maximum  image  smoothing kernel width for coarsest level of multi-scale computation.
            [Default: 8]

       --smooth-sigma-min <double>
            Minimum image smoothing kernel width for finest level of multi-scale computation (0 =
            no smoothing; original image scale).  [Default: 0]

       --smooth-sigma-diff <double>
            Difference between image smoothing kernel widths between two successive levels of the
            multi-scale computation.  [Default: 0.25]

       --smoothness-constraint-weight <double>
            Weight factor for the second-order smoothness constraint term in the  unwarping  cost
            function.  [Default: 0]

       --folding-constraint-weight <double>
            Weight  factor  for  the  folding-prevention  constraint  term  in the unwarping cost
            function.  [Default: 0]

       --iterations <integer>, -i <integer>
            Number of L-BFGS optimization iterations (per multi-scale level).  [Default: 10]

   Output Options
       --write-jacobian-fwd <string>
            Write Jacobian intensity correction map for forward image.  [Default: NONE]

       --write-jacobian-rev <string>
            Write Jacobian intensity correction map for reverse-encoded image.  [Default: NONE]


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



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       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.