NAME

       epiunwarp - Unwarp Echo Planar Images

SYNOPSIS

       epiunwarp InputImage1 InputImage2 OutputImage1 OutputImage2 OutputDField OutputDFieldRev

DESCRIPTION

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

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.

       --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 Image Parameters
       --phase-encode
            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
                 default]

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

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

       --no-flip
            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
       --no-init-shift-com
            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]

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.