epiunwarp - Unwarp Echo Planar Images

       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.

CMTK 3.3.1p2                                       Feb 26 2025                                      epiunwarp(1)

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

       Report bugs at http://nitrc.org/projects/cmtk/

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

http://www.fsf.org/licensing/licenses/gpl.html

       epiunwarp - Unwarp Echo Planar Images

GlobalToolkitOptions(thesearesharedbyallCMTKtools)--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).

   InputImageParameters--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) [Thisisthedefault]--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.

   OptimizationParameters--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]OutputOptions--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]

epiunwarp InputImage1 InputImage2 OutputImage1 OutputImage2 OutputDField OutputDFieldRev